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Zinc in PDB 3qln: Crystal Structure of Atrx Add Domain in Free State

Enzymatic activity of Crystal Structure of Atrx Add Domain in Free State

All present enzymatic activity of Crystal Structure of Atrx Add Domain in Free State:
3.6.4.12;

Protein crystallography data

The structure of Crystal Structure of Atrx Add Domain in Free State, PDB code: 3qln was solved by H.Li, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.12 / 1.90
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 74.167, 74.167, 54.091, 90.00, 90.00, 120.00
R / Rfree (%) 12.7 / 15.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Atrx Add Domain in Free State (pdb code 3qln). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Atrx Add Domain in Free State, PDB code: 3qln:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3qln

Go back to Zinc Binding Sites List in 3qln
Zinc binding site 1 out of 6 in the Crystal Structure of Atrx Add Domain in Free State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Atrx Add Domain in Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:39.6
occ:1.00
 SG A:CYS200 2.4 30.8 1.0
SG A:CYS174 2.4 31.0 1.0
SG A:CYS171 2.5 27.0 1.0
SG A:CYS197 2.5 34.5 1.0
CB A:CYS171 3.1 27.8 1.0
CB A:CYS200 3.2 31.3 1.0
CB A:CYS174 3.4 27.6 1.0
CB A:CYS197 3.6 32.6 1.0
N A:CYS174 3.8 26.2 1.0
N A:CYS197 3.9 31.2 1.0
CA A:CYS174 4.2 26.1 1.0
CA A:CYS197 4.3 31.9 1.0
N A:CYS200 4.3 33.6 1.0
CA A:CYS200 4.3 32.9 1.0
O A:HOH338 4.3 42.2 1.0
C A:ALA173 4.5 27.5 1.0
CA A:CYS171 4.5 27.9 1.0
CB A:ALA173 4.6 23.1 1.0
O A:HOH335 4.6 44.9 1.0
O A:HOH340 4.7 43.2 1.0
N A:ALA173 4.9 25.5 1.0
CA A:ALA173 4.9 23.7 1.0
C A:CYS174 4.9 29.4 1.0
C A:CYS197 4.9 34.9 1.0
CB A:GLN176 5.0 35.0 1.0
O A:CYS197 5.0 31.7 1.0
C A:ILE196 5.0 30.6 1.0
N A:GLY175 5.0 27.9 1.0

Zinc binding site 2 out of 6 in 3qln

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Zinc binding site 2 out of 6 in the Crystal Structure of Atrx Add Domain in Free State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Atrx Add Domain in Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:33.9
occ:1.00
 SG A:CYS243 2.4 24.0 1.0
SG A:CYS223 2.5 25.2 1.0
SG A:CYS220 2.5 21.7 1.0
SG A:CYS240 2.5 24.7 1.0
CB A:CYS220 3.2 22.3 1.0
CB A:CYS243 3.2 25.6 1.0
CB A:CYS223 3.5 25.8 1.0
CB A:CYS240 3.7 25.6 1.0
N A:CYS223 3.8 23.8 1.0
O A:HOH51 4.0 29.2 1.0
N A:CYS240 4.1 26.1 1.0
CB A:TRP222 4.2 24.3 1.0
CA A:CYS223 4.2 25.0 1.0
N A:CYS243 4.2 24.9 1.0
CA A:CYS243 4.3 25.0 1.0
O A:HOH15 4.3 27.3 1.0
CA A:CYS240 4.4 26.9 1.0
CA A:CYS220 4.6 21.8 1.0
C A:TRP222 4.6 22.4 1.0
O A:CYS240 4.8 24.5 1.0
CA A:TRP222 4.8 24.2 1.0
O A:HOH318 4.8 37.0 1.0
N A:TRP222 4.8 22.3 1.0
C A:CYS240 4.9 27.9 1.0

Zinc binding site 3 out of 6 in 3qln

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Zinc binding site 3 out of 6 in the Crystal Structure of Atrx Add Domain in Free State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Atrx Add Domain in Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:33.6
occ:1.00
 SG A:CYS235 2.4 23.2 1.0
SG A:CYS232 2.4 26.0 1.0
SG A:CYS268 2.4 26.9 1.0
SG A:CYS265 2.5 25.1 1.0
CB A:CYS232 3.1 26.8 1.0
CB A:CYS235 3.4 23.8 1.0
CB A:CYS268 3.5 28.8 1.0
CB A:CYS265 3.6 25.8 1.0
N A:CYS265 3.7 28.2 1.0
N A:CYS268 3.9 26.8 1.0
N A:CYS235 4.0 27.6 1.0
CA A:CYS265 4.2 26.2 1.0
CA A:CYS235 4.2 26.2 1.0
CA A:CYS268 4.3 27.8 1.0
O A:HOH63 4.4 29.8 1.0
CA A:CYS232 4.6 28.0 1.0
C A:CYS265 4.7 25.3 1.0
C A:PHE234 4.7 27.2 1.0
CB A:ASN237 4.8 23.5 1.0
C A:CYS235 4.8 24.9 1.0
C A:TYR264 4.8 27.1 1.0
O A:CYS265 4.8 26.2 1.0
CB A:ILE267 4.8 24.6 1.0
ND2 A:ASN237 4.9 25.9 1.0
CB A:PHE234 5.0 25.6 1.0
C A:ILE267 5.0 29.5 1.0

Zinc binding site 4 out of 6 in 3qln

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Zinc binding site 4 out of 6 in the Crystal Structure of Atrx Add Domain in Free State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Atrx Add Domain in Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:45.3
occ:1.00
 SG B:CYS171 2.4 31.3 1.0
SG B:CYS200 2.4 33.8 1.0
SG B:CYS174 2.4 36.0 1.0
SG B:CYS197 2.6 37.4 1.0
CB B:CYS200 3.1 32.6 1.0
CB B:CYS171 3.1 33.5 1.0
CB B:CYS174 3.2 33.4 1.0
CB B:CYS197 3.6 33.8 1.0
N B:CYS174 3.7 30.8 1.0
N B:CYS197 3.9 32.8 1.0
CA B:CYS174 4.0 32.0 1.0
O B:HOH80 4.1 47.7 1.0
N B:CYS200 4.3 30.7 1.0
CA B:CYS200 4.3 32.2 1.0
CA B:CYS197 4.3 34.2 1.0
CB B:ALA173 4.5 25.9 1.0
C B:ALA173 4.5 30.0 1.0
CA B:CYS171 4.6 34.8 1.0
O B:HOH364 4.7 38.6 1.0
C B:CYS174 4.7 34.8 1.0
CA B:ALA173 4.8 29.3 1.0
O B:CYS197 4.9 32.7 1.0
N B:ALA173 4.9 27.6 1.0
N B:GLY175 4.9 31.6 1.0
C B:CYS197 4.9 33.9 1.0
O B:HOH95 4.9 46.7 1.0
C B:ILE196 5.0 33.4 1.0
C B:CYS171 5.0 33.2 1.0

Zinc binding site 5 out of 6 in 3qln

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Zinc binding site 5 out of 6 in the Crystal Structure of Atrx Add Domain in Free State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Atrx Add Domain in Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:35.3
occ:1.00
 SG B:CYS223 2.4 26.0 1.0
SG B:CYS243 2.4 27.1 1.0
SG B:CYS220 2.4 23.3 1.0
SG B:CYS240 2.5 24.8 1.0
CB B:CYS220 3.1 23.2 1.0
CB B:CYS243 3.3 27.2 1.0
CB B:CYS223 3.3 25.9 1.0
CB B:CYS240 3.6 24.7 1.0
N B:CYS223 3.7 24.7 1.0
N B:CYS240 4.1 23.7 1.0
CA B:CYS223 4.1 27.3 1.0
O B:HOH20 4.2 31.1 1.0
O B:HOH302 4.2 38.2 1.0
CB B:TRP222 4.3 26.1 1.0
N B:CYS243 4.3 26.6 1.0
CA B:CYS240 4.4 22.7 1.0
CA B:CYS243 4.4 25.3 1.0
O B:HOH116 4.5 37.8 1.0
CA B:CYS220 4.5 23.6 1.0
C B:TRP222 4.6 25.1 1.0
O B:CYS240 4.8 22.3 1.0
CA B:TRP222 4.8 24.9 1.0
N B:TRP222 4.9 25.4 1.0
C B:CYS240 4.9 21.3 1.0
C B:CYS223 4.9 26.8 1.0
C B:CYS220 5.0 24.2 1.0

Zinc binding site 6 out of 6 in 3qln

Go back to Zinc Binding Sites List in 3qln
Zinc binding site 6 out of 6 in the Crystal Structure of Atrx Add Domain in Free State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Atrx Add Domain in Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3

b:34.3
occ:1.00
 SG B:CYS232 2.3 26.5 1.0
SG B:CYS268 2.3 26.7 1.0
SG B:CYS265 2.4 27.3 1.0
SG B:CYS235 2.5 26.8 1.0
CB B:CYS232 3.2 27.1 1.0
CB B:CYS268 3.4 28.3 1.0
CB B:CYS265 3.4 26.1 1.0
N B:CYS265 3.5 26.8 1.0
CB B:CYS235 3.6 27.3 1.0
N B:CYS235 3.8 28.6 1.0
N B:CYS268 3.9 28.4 1.0
CA B:CYS265 4.0 25.3 1.0
CA B:CYS235 4.2 27.1 1.0
CA B:CYS268 4.2 28.3 1.0
C B:CYS265 4.6 26.7 1.0
C B:TYR264 4.6 28.9 1.0
CA B:CYS232 4.6 27.8 1.0
CB B:ILE267 4.7 28.4 1.0
C B:CYS235 4.7 29.0 1.0
O B:CYS265 4.7 27.1 1.0
CB B:ASN237 4.8 26.4 1.0
C B:PHE234 4.8 31.0 1.0
CA B:TYR264 4.9 29.9 1.0
CB B:PHE234 4.9 31.3 1.0
C B:ILE267 4.9 29.0 1.0
ND2 B:ASN237 4.9 28.8 1.0

Reference:

S.Iwase, B.Xiang, S.Ghosh, T.Ren, P.W.Lewis, J.C.Cochrane, C.D.Allis, D.J.Picketts, D.J.Patel, H.Li, Y.Shi. Atrx Add Domain Links An Atypical Histone Methylation Recognition Mechanism to Human Mental-Retardation Syndrome Nat.Struct.Mol.Biol. V. 18 769 2011.
ISSN: ISSN 1545-9993
PubMed: 21666679
DOI: 10.1038/NSMB.2062
Page generated: Sat Oct 26 12:09:43 2024

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