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Bromine in PDB 5hmj: Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution

Enzymatic activity of Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution

All present enzymatic activity of Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution:
3.2.1.17;

Protein crystallography data

The structure of Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution, PDB code: 5hmj was solved by J.R.Helliwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.29 / 1.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.580, 78.580, 37.290, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 21.5

Other elements in 5hmj:

The structure of Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution also contains other interesting chemical elements:

Platinum (Pt) 1 atom
Sodium (Na) 1 atom

Bromine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Bromine atom in the Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution (pdb code 5hmj). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 15 binding sites of Bromine where determined in the Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution, PDB code: 5hmj:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 15 in 5hmj

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Bromine binding site 1 out of 15 in the Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br201

b:25.2
occ:0.73
 PT A:PT210 2.5 23.0 0.8
HB3 A:HIS15 2.8 20.8 1.0
HG23 A:THR89 2.9 22.3 1.0
ND1 A:HIS15 3.1 22.7 1.0
HB A:VAL92 3.2 18.9 1.0
HA A:THR89 3.3 17.6 1.0
HG11 A:VAL92 3.4 21.8 1.0
HG12 A:VAL92 3.5 21.8 1.0
CB A:HIS15 3.6 17.3 1.0
CG A:HIS15 3.7 20.4 1.0
CG1 A:VAL92 3.8 18.2 1.0
HZ2 A:LYS96 3.8 21.2 1.0
CG2 A:THR89 3.8 18.6 1.0
O A:THR89 3.9 14.4 1.0
CB A:VAL92 3.9 15.7 1.0
H A:ASN93 3.9 18.2 1.0
CE1 A:HIS15 4.1 23.3 1.0
O A:HIS15 4.1 19.4 1.0
HG22 A:THR89 4.1 22.3 1.0
HB2 A:ASN93 4.1 27.4 1.0
CA A:THR89 4.1 14.6 1.0
HA A:HIS15 4.2 20.5 1.0
N A:ASN93 4.2 15.1 1.0
HE1 A:HIS15 4.3 27.9 1.0
HB2 A:HIS15 4.3 20.8 1.0
OD1 A:ASN93 4.4 35.4 1.0
CA A:HIS15 4.4 17.1 1.0
C A:THR89 4.4 14.6 1.0
CB A:THR89 4.5 17.2 1.0
HA A:ASN93 4.5 20.2 1.0
HG21 A:THR89 4.5 22.3 1.0
NZ A:LYS96 4.5 17.7 1.0
HZ1 A:LYS96 4.6 21.2 1.0
HG21 A:VAL92 4.6 20.9 1.0
OG1 A:THR89 4.7 18.9 1.0
HG13 A:VAL92 4.7 21.8 1.0
C A:HIS15 4.7 17.5 1.0
CA A:ASN93 4.7 16.8 1.0
CD2 A:HIS15 4.7 20.8 1.0
CB A:ASN93 4.7 22.8 1.0
C A:VAL92 4.8 15.1 1.0
CG2 A:VAL92 4.9 17.4 1.0
HE3 A:LYS96 4.9 19.5 1.0
NE2 A:HIS15 4.9 21.8 1.0
CA A:VAL92 4.9 13.9 1.0
BR A:BR202 4.9 27.7 0.7
CG A:ASN93 4.9 31.7 1.0

Bromine binding site 2 out of 15 in 5hmj

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Bromine binding site 2 out of 15 in the Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br202

b:27.7
occ:0.69
 PT A:PT210 2.4 23.0 0.8
ND1 A:HIS15 3.2 22.7 1.0
HA A:HIS15 3.2 20.5 1.0
HG2 A:ARG14 3.5 31.4 1.0
CE1 A:HIS15 3.6 23.3 1.0
HE1 A:HIS15 3.6 27.9 1.0
O A:HOH367 3.8 33.1 1.0
O A:ARG14 3.9 21.7 1.0
HE A:ARG14 4.0 40.9 1.0
CG A:HIS15 4.0 20.4 1.0
CA A:HIS15 4.1 17.1 1.0
HH21 A:ARG14 4.3 47.1 1.0
NE A:ARG14 4.4 34.1 1.0
C A:ARG14 4.4 18.4 1.0
CG A:ARG14 4.4 26.1 1.0
NE2 A:HIS15 4.5 21.8 1.0
N A:HIS15 4.5 16.1 1.0
CB A:HIS15 4.6 17.3 1.0
HG3 A:ARG14 4.6 31.4 1.0
NH2 A:ARG14 4.7 39.3 1.0
CD2 A:HIS15 4.8 20.8 1.0
HB3 A:HIS15 4.8 20.8 1.0
CZ A:ARG14 4.8 37.7 1.0
BR A:BR201 4.9 25.2 0.7

Bromine binding site 3 out of 15 in 5hmj

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Bromine binding site 3 out of 15 in the Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br203

b:17.5
occ:0.77
 HH A:TYR23 2.5 15.9 1.0
OH A:TYR23 3.2 13.3 1.0
HE2 A:TYR23 3.3 15.1 1.0
HA3 A:GLY104 3.4 14.9 1.0
CE2 A:TYR23 3.8 12.6 1.0
CZ A:TYR23 3.8 12.3 1.0
HA2 A:GLY104 4.1 14.9 1.0
CA A:GLY104 4.1 12.4 1.0
O A:ARG21 4.6 14.9 0.6
O A:ARG21 4.6 14.8 0.5
N A:GLY104 4.7 14.4 1.0
HB3 A:ARG21 4.8 21.4 0.6
H A:MET105 4.9 15.0 1.0
HB3 A:ARG21 4.9 22.2 0.5
H A:GLY104 5.0 17.3 1.0
CD2 A:TYR23 5.0 12.1 1.0

Bromine binding site 4 out of 15 in 5hmj

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Bromine binding site 4 out of 15 in the Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br204

b:20.4
occ:0.72
 H A:GLY26 2.5 16.2 1.0
HG A:SER24 2.9 19.7 1.0
HA A:GLN121 2.9 21.3 1.0
HA3 A:GLY26 3.0 17.6 1.0
HB2 A:SER24 3.0 19.2 1.0
OG A:SER24 3.2 16.4 1.0
HD11 A:ILE124 3.3 27.5 1.0
N A:GLY26 3.3 13.5 1.0
HG2 A:GLN121 3.4 31.2 1.0
HG23 A:VAL120 3.5 22.4 1.0
HD13 A:ILE124 3.5 27.5 1.0
CB A:SER24 3.6 16.0 1.0
CA A:GLY26 3.6 14.7 1.0
CA A:GLN121 3.7 17.8 1.0
HG12 A:ILE124 3.7 24.5 1.0
HB2 A:GLN121 3.7 26.7 1.0
CD1 A:ILE124 3.8 22.9 1.0
CB A:GLN121 4.0 22.2 1.0
N A:GLN121 4.1 16.9 1.0
CG A:GLN121 4.1 26.0 1.0
HA2 A:GLY26 4.2 17.6 1.0
HB3 A:SER24 4.2 19.2 1.0
CG1 A:ILE124 4.3 20.4 1.0
H A:LEU25 4.3 16.3 1.0
N A:LEU25 4.3 13.6 1.0
HB3 A:LEU25 4.4 18.5 1.0
HG3 A:GLN121 4.4 31.2 1.0
H A:GLN121 4.4 20.3 1.0
C A:VAL120 4.4 16.6 1.0
H A:ASN27 4.4 16.2 1.0
CG2 A:VAL120 4.4 18.7 1.0
O A:VAL120 4.4 16.7 1.0
C A:LEU25 4.5 12.4 1.0
C A:SER24 4.5 13.4 1.0
HG21 A:VAL120 4.6 22.4 1.0
HD12 A:ILE124 4.7 27.5 1.0
CA A:SER24 4.7 14.5 1.0
C A:GLY26 4.7 12.9 1.0
HG13 A:ILE124 4.8 24.5 1.0
CA A:LEU25 4.8 13.0 1.0
HB A:VAL120 4.9 21.6 1.0
N A:ASN27 4.9 13.5 1.0
C A:GLN121 4.9 18.3 1.0
HG21 A:ILE124 4.9 21.9 1.0
HG23 A:ILE124 5.0 21.9 1.0
HB3 A:GLN121 5.0 26.7 1.0
O A:SER24 5.0 14.7 1.0
HG22 A:VAL120 5.0 22.4 1.0

Bromine binding site 5 out of 15 in 5hmj

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Bromine binding site 5 out of 15 in the Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br205

b:21.6
occ:0.58
 H A:THR69 2.6 17.0 1.0
HA2 A:GLY67 3.3 18.4 1.0
O A:HOH339 3.3 14.9 1.0
H A:GLY67 3.4 17.4 1.0
N A:THR69 3.4 14.2 1.0
O A:THR69 3.4 15.8 1.0
H A:ARG68 3.5 18.4 0.3
H A:ARG68 3.5 17.5 0.7
OG A:SER72 3.6 17.0 1.0
N A:ARG68 3.6 14.6 0.7
N A:ARG68 3.6 15.4 0.3
C A:GLY67 3.7 15.6 1.0
CA A:GLY67 3.7 15.3 1.0
OD1 A:ASN65 3.7 18.7 1.0
N A:GLY67 3.8 14.5 1.0
HB A:THR69 3.8 18.1 1.0
C A:THR69 3.9 13.2 1.0
O A:HOH353 4.0 16.8 1.0
CA A:THR69 4.1 13.2 1.0
O A:GLY67 4.3 17.6 1.0
H A:ASP66 4.3 14.9 1.0
C A:ARG68 4.4 15.5 0.7
C A:ARG68 4.4 15.5 0.3
CB A:THR69 4.4 15.1 1.0
CA A:ARG68 4.4 14.7 0.7
CA A:ARG68 4.5 15.6 0.3
OD1 A:ASP66 4.5 12.7 1.0
HA A:ARG68 4.5 17.7 0.7
HA A:PRO70 4.5 18.4 1.0
HA A:ARG68 4.6 18.7 0.3
H A:SER72 4.6 21.8 1.0
HG1 A:THR69 4.6 17.9 1.0
HA3 A:GLY67 4.7 18.4 1.0
BR A:BR214 4.7 50.2 0.3
N A:PRO70 4.7 16.0 1.0
NA A:NA207 4.8 14.2 1.0
CB A:SER72 4.8 16.8 1.0
HA A:ASN65 4.9 16.2 1.0
HB3 A:SER72 4.9 20.2 1.0
C A:ASP66 4.9 14.6 1.0
CG A:ASN65 5.0 18.4 1.0

Bromine binding site 6 out of 15 in 5hmj

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Bromine binding site 6 out of 15 in the Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br206

b:26.6
occ:0.60
 HZ3 A:LYS33 2.9 27.1 1.0
HE2 A:PHE38 3.0 17.2 1.0
HZ3 A:TRP123 3.0 21.0 1.0
HD3 A:ARG5 3.2 27.2 1.0
H2 A:ACT216 3.3 36.3 1.0
HB2 A:ARG5 3.5 25.1 1.0
HD3 A:LYS33 3.6 21.6 1.0
NZ A:LYS33 3.8 22.6 1.0
CE2 A:PHE38 3.9 14.3 1.0
CZ3 A:TRP123 3.9 17.5 1.0
HE2 A:LYS33 4.0 23.5 1.0
HZ1 A:LYS33 4.1 27.1 1.0
CD A:ARG5 4.2 22.7 1.0
CE A:LYS33 4.2 19.6 1.0
HE A:ARG5 4.3 27.4 1.0
CH3 A:ACT216 4.3 30.3 1.0
HZ A:PHE38 4.3 16.4 1.0
HZ2 A:LYS33 4.3 27.1 1.0
CD A:LYS33 4.4 18.0 1.0
CB A:ARG5 4.4 20.9 1.0
H1 A:ACT216 4.5 36.3 1.0
CZ A:PHE38 4.5 13.7 1.0
HE3 A:TRP123 4.5 19.8 1.0
HH2 A:TRP123 4.7 22.1 1.0
H3 A:ACT216 4.7 36.3 1.0
NE A:ARG5 4.7 22.9 1.0
CE3 A:TRP123 4.7 16.5 1.0
HD2 A:PHE38 4.7 16.8 1.0
HB3 A:ARG5 4.8 25.1 1.0
CG A:ARG5 4.8 22.4 1.0
HD2 A:ARG5 4.8 27.2 1.0
CD2 A:PHE38 4.8 14.0 1.0
CH2 A:TRP123 4.8 18.4 1.0
HG3 A:ARG5 4.8 26.9 1.0
HD2 A:LYS33 4.9 21.6 1.0

Bromine binding site 7 out of 15 in 5hmj

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Bromine binding site 7 out of 15 in the Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br208

b:37.3
occ:0.54
 H A:ASN74 2.4 20.3 1.0
HE A:ARG73 2.5 32.6 1.0
HB3 A:ARG73 2.9 24.7 1.0
N A:ASN74 3.2 16.9 1.0
NE A:ARG73 3.4 27.2 1.0
HD23 A:LEU75 3.4 26.5 1.0
HB3 A:ASN74 3.6 19.8 1.0
O A:ASN74 3.6 17.9 1.0
HH21 A:ARG73 3.6 37.0 1.0
C A:ASN74 3.7 16.7 1.0
HA A:ARG73 3.7 22.3 1.0
HD2 A:ARG73 3.8 29.5 1.0
CB A:ARG73 3.8 20.6 1.0
CA A:ASN74 3.9 16.3 1.0
HA A:LEU75 4.0 21.3 1.0
CD A:ARG73 4.1 24.6 1.0
CA A:ARG73 4.1 18.6 1.0
C A:ARG73 4.2 16.8 1.0
CB A:ASN74 4.2 16.5 1.0
N A:LEU75 4.2 17.8 1.0
NH2 A:ARG73 4.3 30.9 1.0
CZ A:ARG73 4.3 28.6 1.0
CD2 A:LEU75 4.3 22.1 1.0
HD21 A:LEU75 4.3 26.5 1.0
HB2 A:ARG73 4.5 24.7 1.0
HG A:LEU75 4.5 24.8 1.0
CG A:ARG73 4.6 22.5 1.0
CA A:LEU75 4.6 17.7 1.0
H A:LEU75 4.7 21.3 1.0
O A:HOH369 4.7 34.6 1.0
HB2 A:ASN74 4.7 19.8 1.0
HA A:ASN74 4.8 19.6 1.0
HD3 A:ARG73 4.9 29.5 1.0
CG A:LEU75 4.9 20.6 1.0
HD22 A:LEU75 5.0 26.5 1.0
HG3 A:ARG73 5.0 27.0 1.0

Bromine binding site 8 out of 15 in 5hmj

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Bromine binding site 8 out of 15 in the Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br209

b:29.3
occ:0.53
 HA A:ALA90 2.9 17.8 1.0
O A:HOH341 3.2 21.2 1.0
HD22 A:ASN93 3.3 42.2 1.0
HB2 A:ALA90 3.6 18.9 1.0
HB3 A:ASN93 3.7 27.4 1.0
HG22 A:THR89 3.7 22.3 1.0
CA A:ALA90 3.8 14.8 1.0
HB2 A:ASN93 3.8 27.4 1.0
ND2 A:ASN93 3.8 35.1 1.0
HG21 A:ILE78 3.8 25.2 1.0
HB1 A:ALA90 4.0 18.9 1.0
CB A:ALA90 4.0 15.7 1.0
CB A:ASN93 4.1 22.8 1.0
HD21 A:ASN93 4.3 42.2 1.0
CG A:ASN93 4.3 31.7 1.0
N A:ALA90 4.4 14.6 1.0
CG2 A:ILE78 4.4 21.0 1.0
HG22 A:ILE78 4.5 25.2 1.0
HG23 A:ILE78 4.5 25.2 1.0
O A:HOH350 4.6 23.9 1.0
O A:THR89 4.6 14.4 1.0
CG2 A:THR89 4.6 18.6 1.0
C A:THR89 4.7 14.6 1.0
HG21 A:THR89 4.8 22.3 1.0
O A:ALA90 4.8 14.3 1.0
H A:ALA90 4.8 17.5 1.0
C A:ALA90 4.8 14.9 1.0
HB3 A:ALA90 5.0 18.9 1.0

Bromine binding site 9 out of 15 in 5hmj

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Bromine binding site 9 out of 15 in the Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br211

b:32.2
occ:0.35
 HD3 A:ARG14 3.2 35.4 1.0
O A:HOH331 3.2 24.8 1.0
HA A:ALA11 3.3 18.5 1.0
HH11 A:ARG14 3.6 48.8 1.0
HB1 A:ALA10 3.7 20.8 1.0
HD2 A:ARG14 3.8 35.4 1.0
HB2 A:ARG14 3.9 25.8 1.0
CD A:ARG14 3.9 29.5 1.0
HB3 A:ALA10 3.9 20.8 1.0
O A:ALA10 4.0 16.3 1.0
HB2 A:ALA11 4.0 19.2 1.0
N A:ALA11 4.0 13.8 1.0
CA A:ALA11 4.0 15.4 1.0
C A:ALA10 4.0 14.7 1.0
CB A:ALA10 4.2 17.4 1.0
HB3 A:ARG14 4.3 25.8 1.0
NH1 A:ARG14 4.3 40.6 1.0
H A:ALA11 4.4 16.6 1.0
CB A:ARG14 4.5 21.5 1.0
CB A:ALA11 4.5 16.0 1.0
O A:HOH311 4.7 23.2 1.0
CA A:ALA10 4.8 14.9 1.0
HH12 A:ARG14 4.8 48.8 1.0
CG A:ARG14 4.8 26.1 1.0
HB1 A:ALA11 4.9 19.2 1.0
NE A:ARG14 4.9 34.1 1.0

Bromine binding site 10 out of 15 in 5hmj

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Bromine binding site 10 out of 15 in the Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Re-Refinement of 4XAN: Hen Lysozyme with Carboplatin in Sodium Bromide Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br212

b:29.4
occ:0.39
 H A:CYS6 2.4 20.5 1.0
HB2 A:CYS6 3.0 22.1 1.0
HB3 A:ARG5 3.0 25.1 1.0
N A:CYS6 3.3 17.1 1.0
H A:ARG5 3.5 21.3 1.0
CB A:CYS6 3.6 18.4 1.0
SG A:CYS6 3.7 20.4 1.0
N A:ARG5 3.9 17.8 1.0
CB A:ARG5 3.9 20.9 1.0
CA A:CYS6 4.1 17.5 1.0
CA A:ARG5 4.2 18.0 1.0
C A:ARG5 4.2 17.3 1.0
H A:GLU7 4.3 20.1 1.0
HE A:ARG5 4.3 27.4 1.0
HA3 A:GLY4 4.3 20.1 1.0
HH21 A:ARG5 4.4 27.8 1.0
HB2 A:ARG5 4.4 25.1 1.0
HB3 A:CYS6 4.5 22.1 1.0
C A:GLY4 4.6 16.9 1.0
NE A:ARG5 4.6 22.9 1.0
NH2 A:ARG5 4.7 23.2 1.0
HG2 A:ARG5 4.7 26.9 1.0
HA A:CYS6 4.7 21.0 1.0
CZ A:ARG5 4.8 21.9 1.0
CG A:ARG5 4.9 22.4 1.0
CA A:GLY4 4.9 16.7 1.0
N A:GLU7 4.9 16.7 1.0
HA2 A:GLY4 5.0 20.1 1.0

Reference:

S.W.Tanley, A.M.Schreurs, L.M.Kroon-Batenburg, J.R.Helliwell. Re-Refinement of 4XAN: Hen Egg-White Lysozyme with Carboplatin in Sodium Bromide Solution. Acta Crystallogr F Struct V. 72 251 2016BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 26919531
DOI: 10.1107/S2053230X16000777
Page generated: Wed Jul 10 23:48:31 2024

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