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Bromine in PDB 5d5f: In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K

Enzymatic activity of In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K

All present enzymatic activity of In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K:
3.2.1.17;

Protein crystallography data

The structure of In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K, PDB code: 5d5f was solved by C.-Y.Huang, V.Olieric, K.Diederichs, M.Wang, M.Caffrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.06 / 1.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.390, 78.390, 37.880, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.2

Other elements in 5d5f:

The structure of In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K also contains other interesting chemical elements:

Sodium (Na) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K (pdb code 5d5f). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 7 binding sites of Bromine where determined in the In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K, PDB code: 5d5f:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7;

Bromine binding site 1 out of 7 in 5d5f

Go back to Bromine Binding Sites List in 5d5f
Bromine binding site 1 out of 7 in the In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br201

b:19.6
occ:0.69
 OH A:TYR23 3.1 14.6 1.0
O A:HOH348 3.3 18.9 1.0
CE2 A:TYR23 3.8 15.2 1.0
CZ A:TYR23 3.8 15.4 1.0
CA A:GLY104 4.1 18.0 1.0
O A:HOH432 4.5 29.5 0.6
O A:ARG21 4.6 18.5 1.0
N A:GLY104 4.7 20.3 1.0
O A:HOH331 4.9 22.6 0.9

Bromine binding site 2 out of 7 in 5d5f

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Bromine binding site 2 out of 7 in the In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br202

b:21.6
occ:0.68
 N A:ILE88 3.5 18.0 1.0
O A:HOH336 3.5 22.8 1.0
NH1 A:ARG14 3.8 28.6 0.9
NH2 A:ARG14 3.8 27.8 0.1
CG1 A:ILE88 3.8 17.0 1.0
CE1 A:HIS15 3.8 22.1 1.0
CA A:ASP87 4.0 18.2 1.0
CB A:ALA11 4.1 17.4 1.0
C A:ASP87 4.2 19.0 1.0
CZ A:PHE3 4.3 19.5 1.0
O A:HOH344 4.3 27.2 0.7
O A:SER86 4.3 18.3 1.0
CG A:ASP87 4.3 26.2 1.0
OD1 A:ASP87 4.4 20.0 1.0
CB A:ILE88 4.4 17.0 1.0
CG2 A:ILE88 4.5 17.8 1.0
OD2 A:ASP87 4.5 29.9 1.0
CA A:ILE88 4.5 16.8 1.0
NE2 A:HIS15 4.6 23.8 1.0
CD1 A:ILE88 4.6 18.1 1.0
ND1 A:HIS15 4.7 23.0 1.0
CB A:ASP87 4.7 18.2 1.0
CE2 A:PHE3 4.7 17.5 1.0
CZ A:ARG14 4.8 26.6 0.1
NH1 A:ARG14 4.9 25.5 0.1
N A:ASP87 5.0 18.3 1.0
CZ A:ARG14 5.0 27.8 0.9

Bromine binding site 3 out of 7 in 5d5f

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Bromine binding site 3 out of 7 in the In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br203

b:21.7
occ:0.68
 OG A:SER24 3.1 19.2 1.0
N A:GLY26 3.3 16.4 1.0
CB A:SER24 3.5 19.1 1.0
CA A:GLY26 3.6 17.2 1.0
CA A:GLN121 3.6 22.2 1.0
CD1 A:ILE124 3.9 27.8 1.0
CB A:GLN121 4.0 23.4 1.0
N A:GLN121 4.0 19.2 1.0
CG A:GLN121 4.1 26.1 1.0
CG1 A:ILE124 4.3 22.4 1.0
N A:LEU25 4.4 17.0 1.0
C A:VAL120 4.4 18.1 1.0
O A:VAL120 4.4 20.9 1.0
CG2 A:VAL120 4.5 19.9 1.0
C A:SER24 4.5 16.1 1.0
C A:LEU25 4.5 13.8 1.0
CA A:SER24 4.7 16.6 1.0
C A:GLY26 4.7 16.8 1.0
N A:ASN27 4.8 15.4 1.0
C A:GLN121 4.8 19.3 1.0
CA A:LEU25 4.9 17.3 1.0
O A:SER24 5.0 16.9 1.0

Bromine binding site 4 out of 7 in 5d5f

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Bromine binding site 4 out of 7 in the In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br204

b:36.5
occ:0.69
 NZ A:LYS33 3.7 29.6 1.0
CE2 A:PHE38 3.8 17.7 1.0
O A:HOH369 3.9 34.0 1.0
CZ3 A:TRP123 4.0 21.6 1.0
CE A:LYS33 4.2 25.6 1.0
CD A:ARG5 4.3 21.7 1.0
CD A:LYS33 4.3 19.1 1.0
CB A:ARG5 4.4 23.0 1.0
CZ A:PHE38 4.5 19.0 1.0
O A:HOH393 4.6 41.8 1.0
CD2 A:PHE38 4.7 18.2 1.0
CE3 A:TRP123 4.8 20.9 1.0
C6 A:PE5210 4.8 37.3 1.0
NE A:ARG5 4.8 23.0 1.0
CG A:ARG5 4.8 24.2 1.0
CH2 A:TRP123 4.9 21.6 1.0

Bromine binding site 5 out of 7 in 5d5f

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Bromine binding site 5 out of 7 in the In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br205

b:28.5
occ:0.57
 O A:HOH390 3.2 20.0 1.0
O A:HOH355 3.4 33.4 0.7
N A:THR69 3.4 19.8 1.0
O A:THR69 3.4 20.4 1.0
OD1 A:ASN65 3.5 25.5 1.0
N A:ARG68 3.6 18.9 1.0
C A:THR69 3.7 23.8 1.0
CA A:GLY67 3.7 20.7 1.0
C A:GLY67 3.7 24.3 1.0
N A:GLY67 3.8 18.3 1.0
OG A:SER72 3.8 24.4 1.0
O A:HOH375 3.9 21.4 0.9
CA A:THR69 4.0 20.4 1.0
N A:PRO70 4.4 26.7 1.0
C A:ARG68 4.4 20.6 1.0
CB A:THR69 4.4 18.1 1.0
O A:GLY67 4.4 24.2 1.0
CA A:ARG68 4.4 18.0 1.0
OD1 A:ASP66 4.5 15.8 1.0
CG A:ASN65 4.6 22.7 1.0
CA A:PRO70 4.8 30.6 1.0
NA A:NA208 4.8 20.3 1.0
O A:HOH345 4.9 30.0 0.9
N A:ASP66 4.9 18.0 1.0
C A:ASP66 4.9 17.6 1.0

Bromine binding site 6 out of 7 in 5d5f

Go back to Bromine Binding Sites List in 5d5f
Bromine binding site 6 out of 7 in the In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br206

b:61.7
occ:0.72
 NH1 A:ARG68 3.1 22.7 1.0
O A:HOH416 3.5 17.1 1.0
CD A:ARG68 3.7 20.6 1.0
CZ A:ARG68 4.1 22.9 1.0
NE A:ARG68 4.4 24.4 1.0
NH1 A:ARG45 4.9 27.6 1.0

Bromine binding site 7 out of 7 in 5d5f

Go back to Bromine Binding Sites List in 5d5f
Bromine binding site 7 out of 7 in the In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme By Bromine-Sad at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br207

b:47.9
occ:0.72
 N A:ASN74 3.2 22.1 1.0
CB A:ARG73 3.7 25.5 1.0
C A:ASN74 3.8 20.2 1.0
NE A:ARG73 3.8 49.8 1.0
O A:ASN74 3.9 19.3 1.0
CD2 A:LEU75 4.0 27.2 1.0
CA A:ASN74 4.0 19.3 1.0
CA A:ARG73 4.0 24.2 1.0
N A:LEU75 4.1 20.8 1.0
NH2 A:ARG73 4.1 59.2 1.0
C A:ARG73 4.1 23.9 1.0
O A:HOH384 4.3 30.9 0.7
O A:HOH435 4.3 33.1 0.8
CZ A:ARG73 4.4 52.8 1.0
CA A:LEU75 4.4 21.4 1.0
CB A:ASN74 4.5 17.9 1.0
CG A:LEU75 4.5 24.4 1.0
CG A:ARG73 4.7 26.1 1.0
CD A:ARG73 4.7 36.3 1.0

Reference:

C.Y.Huang, V.Olieric, P.Ma, N.Howe, L.Vogeley, X.Liu, R.Warshamanage, T.Weinert, E.Panepucci, B.Kobilka, K.Diederichs, M.Wang, M.Caffrey. In Meso in Situ Serial X-Ray Crystallography of Soluble and Membrane Proteins at Cryogenic Temperatures. Acta Crystallogr D Struct V. 72 93 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 26894538
DOI: 10.1107/S2059798315021683
Page generated: Wed Jul 10 23:23:07 2024

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