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Bromine in PDB 5d5c: In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme at 100 K

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

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

Protein crystallography data

The structure of In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme at 100 K, PDB code: 5d5c 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) 39.55 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.090, 79.090, 38.290, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.2

Other elements in 5d5c:

The structure of In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme 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 at 100 K (pdb code 5d5c). 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 at 100 K, PDB code: 5d5c:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7;

Bromine binding site 1 out of 7 in 5d5c

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Bromine binding site 1 out of 7 in the In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme 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 at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br201

b:26.8
occ:0.45
 OH A:TYR23 3.0 18.4 1.0
O A:HOH374 3.1 27.5 0.7
CZ A:TYR23 3.7 18.8 1.0
CE2 A:TYR23 3.7 19.0 1.0
CA A:GLY104 4.2 17.2 1.0
O A:ARG21 4.6 22.4 1.0
N A:GLY104 4.7 20.3 1.0
CE1 A:TYR23 4.9 15.1 1.0
O A:HOH314 4.9 24.9 1.0
CD2 A:TYR23 4.9 17.0 1.0

Bromine binding site 2 out of 7 in 5d5c

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Bromine binding site 2 out of 7 in the In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme 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 at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br202

b:54.8
occ:0.43
 NH1 A:ARG68 3.0 28.5 1.0
CD A:ARG68 3.5 24.1 1.0
CZ A:ARG68 4.0 29.3 1.0
NE A:ARG68 4.2 28.8 1.0
CB A:ARG68 4.7 25.5 1.0
CG A:ARG68 4.7 24.6 1.0
NH1 A:ARG45 5.0 33.2 1.0

Bromine binding site 3 out of 7 in 5d5c

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Bromine binding site 3 out of 7 in the In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme 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 at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br203

b:42.9
occ:0.39
 OH A:TYR53 2.9 18.8 1.0
CZ A:ARG68 3.3 29.3 1.0
NH2 A:ARG68 3.4 21.9 1.0
NE A:ARG68 3.5 28.8 1.0
NH1 A:ARG68 3.8 28.5 1.0
CZ A:TYR53 3.9 16.2 1.0
CE2 A:TYR53 4.0 16.4 1.0
CD A:ARG68 4.3 24.1 1.0
OD2 A:ASP66 4.5 20.0 1.0
OG1 A:THR51 4.5 17.6 1.0
CG2 A:THR51 4.6 17.0 1.0
CB A:THR51 4.8 17.2 1.0
CB A:ASP66 4.9 16.6 1.0
CG A:ARG68 4.9 24.6 1.0

Bromine binding site 4 out of 7 in 5d5c

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Bromine binding site 4 out of 7 in the In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme 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 at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br204

b:29.3
occ:0.46
 OG A:SER24 3.0 20.7 1.0
N A:GLY26 3.1 15.4 1.0
O A:HOH395 3.3 24.6 0.7
CB A:SER24 3.4 20.9 1.0
CA A:GLY26 3.5 19.4 1.0
CA A:GLN121 3.6 24.1 1.0
CD1 A:ILE124 3.8 27.8 1.0
CB A:GLN121 4.0 25.9 1.0
CG A:GLN121 4.1 33.3 1.0
N A:GLN121 4.1 25.2 1.0
N A:LEU25 4.2 19.6 1.0
CG1 A:ILE124 4.2 23.4 1.0
C A:SER24 4.3 20.1 1.0
C A:LEU25 4.3 16.9 1.0
O A:VAL120 4.4 21.1 1.0
C A:VAL120 4.5 22.1 1.0
CG2 A:VAL120 4.5 24.9 1.0
CA A:SER24 4.5 19.7 1.0
C A:GLY26 4.6 19.9 1.0
N A:ASN27 4.7 17.0 1.0
CA A:LEU25 4.7 17.9 1.0
C A:GLN121 4.8 25.1 1.0
O A:SER24 4.8 19.6 1.0
O A:GLN121 4.9 25.3 1.0
O A:HOH331 4.9 23.1 1.0

Bromine binding site 5 out of 7 in 5d5c

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Bromine binding site 5 out of 7 in the In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme 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 at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br205

b:33.7
occ:0.45
 O A:HOH341 3.0 19.5 1.0
N A:THR69 3.2 22.0 1.0
O A:THR69 3.4 21.7 1.0
N A:ARG68 3.5 20.3 1.0
N A:GLY67 3.5 19.9 1.0
OD1 A:ASN65 3.6 24.9 1.0
CA A:GLY67 3.6 21.9 1.0
C A:THR69 3.6 24.3 1.0
C A:GLY67 3.7 22.3 1.0
CA A:THR69 3.8 21.9 1.0
OG A:SER72 3.8 24.0 1.0
OD1 A:ASP66 4.0 18.3 1.0
O A:HOH380 4.1 20.8 1.0
CB A:THR69 4.2 19.7 1.0
C A:ARG68 4.2 20.6 1.0
N A:PRO70 4.3 24.3 1.0
CA A:ARG68 4.3 20.2 1.0
O A:GLY67 4.4 22.9 1.0
C A:ASP66 4.6 19.0 1.0
N A:ASP66 4.7 19.5 1.0
NA A:NA208 4.7 18.3 0.8
OG1 A:THR69 4.7 20.8 1.0
CG A:ASN65 4.7 25.3 1.0
CA A:PRO70 4.8 27.0 1.0

Bromine binding site 6 out of 7 in 5d5c

Go back to Bromine Binding Sites List in 5d5c
Bromine binding site 6 out of 7 in the In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme 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 at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br206

b:47.0
occ:0.44
 NH2 A:ARG114 3.0 24.5 1.0
NH1 A:ARG114 3.5 19.1 1.0
CZ A:ARG114 3.7 21.4 1.0
O A:HOH365 4.0 25.5 0.8
CD1 A:PHE34 4.6 19.3 1.0
CE1 A:PHE34 4.8 20.1 1.0
NE A:ARG114 5.0 19.0 1.0

Bromine binding site 7 out of 7 in 5d5c

Go back to Bromine Binding Sites List in 5d5c
Bromine binding site 7 out of 7 in the In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme 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 at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br207

b:37.7
occ:0.43
 OD1 A:ASP87 3.4 34.8 1.0
N A:ILE88 3.4 19.8 1.0
O A:HOH326 3.7 25.4 0.8
CG1 A:ILE88 3.7 21.4 1.0
NH2 A:ARG14 3.8 25.4 0.1
NH1 A:ARG14 3.9 26.6 0.9
CA A:ASP87 3.9 22.2 1.0
CE1 A:HIS15 3.9 22.4 1.0
C A:ASP87 4.1 23.6 1.0
CG A:ASP87 4.3 30.8 1.0
CB A:ALA11 4.3 19.9 1.0
CA A:ILE88 4.4 18.2 1.0
CB A:ILE88 4.4 18.6 1.0
O A:SER86 4.4 25.1 1.0
CZ A:PHE3 4.4 21.1 1.0
CG2 A:ILE88 4.5 19.6 1.0
CB A:ASP87 4.6 23.1 1.0
ND1 A:HIS15 4.6 25.5 1.0
CD1 A:ILE88 4.7 23.4 1.0
CE2 A:PHE3 4.9 22.8 1.0
N A:THR89 4.9 20.7 1.0
CZ A:ARG14 4.9 24.7 0.1
NE2 A:HIS15 4.9 28.0 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 23:22:43 2024

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