Zinc in PDB 3qlc: Complex Structure of Atrx Add Domain Bound to Unmodified H3 1-15 Peptide

Enzymatic activity of Complex Structure of Atrx Add Domain Bound to Unmodified H3 1-15 Peptide

All present enzymatic activity of Complex Structure of Atrx Add Domain Bound to Unmodified H3 1-15 Peptide:
3.6.4.12;

Protein crystallography data

The structure of Complex Structure of Atrx Add Domain Bound to Unmodified H3 1-15 Peptide, PDB code: 3qlc 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) 38.05 / 2.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.607, 80.607, 136.173, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 24.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Complex Structure of Atrx Add Domain Bound to Unmodified H3 1-15 Peptide (pdb code 3qlc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Complex Structure of Atrx Add Domain Bound to Unmodified H3 1-15 Peptide, PDB code: 3qlc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3qlc

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Zinc binding site 1 out of 6 in the Complex Structure of Atrx Add Domain Bound to Unmodified H3 1-15 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex Structure of Atrx Add Domain Bound to Unmodified H3 1-15 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn661

b:42.3
occ:1.00
 SG A:CYS200 2.2 44.5 1.0
SG A:CYS174 2.3 42.0 1.0
SG A:CYS197 2.4 42.7 1.0
SG A:CYS171 2.4 40.9 1.0
CB A:CYS174 3.1 31.7 1.0
CB A:CYS200 3.2 46.5 1.0
CB A:CYS171 3.2 37.4 1.0
N A:CYS174 3.6 39.5 1.0
CB A:CYS197 3.6 40.0 1.0
CA A:CYS174 3.9 41.5 1.0
N A:CYS197 4.0 43.0 1.0
N A:CYS200 4.3 48.9 1.0
CA A:CYS200 4.3 48.9 1.0
CA A:CYS197 4.4 47.9 1.0
C A:ALA173 4.6 38.9 1.0
CB A:ALA173 4.6 37.4 1.0
CA A:CYS171 4.7 35.5 1.0
C A:CYS174 4.8 39.1 1.0
N A:GLY175 4.9 37.2 1.0
O A:CYS197 4.9 49.8 1.0
CA A:ALA173 5.0 37.5 1.0
C A:CYS197 5.0 50.6 1.0

Zinc binding site 2 out of 6 in 3qlc

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Zinc binding site 2 out of 6 in the Complex Structure of Atrx Add Domain Bound to Unmodified H3 1-15 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex Structure of Atrx Add Domain Bound to Unmodified H3 1-15 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn662

b:37.4
occ:1.00
 SG A:CYS240 2.3 36.4 1.0
SG A:CYS243 2.3 36.9 1.0
SG A:CYS220 2.4 36.8 1.0
SG A:CYS223 2.5 39.8 1.0
CB A:CYS220 3.1 42.2 1.0
CB A:CYS243 3.2 35.1 1.0
CB A:CYS223 3.4 32.2 1.0
CB A:CYS240 3.6 35.2 1.0
N A:CYS223 3.7 37.2 1.0
O A:HOH320 3.8 41.2 1.0
N A:CYS240 3.9 34.2 1.0
CA A:CYS223 4.1 39.7 1.0
N A:CYS243 4.2 35.0 1.0
CA A:CYS243 4.3 34.9 1.0
CA A:CYS240 4.3 37.5 1.0
O A:HOH309 4.3 48.3 1.0
CB A:TRP222 4.4 39.5 1.0
CA A:CYS220 4.6 38.1 1.0
O A:CYS240 4.7 34.4 1.0
C A:TRP222 4.7 40.1 1.0
C A:CYS240 4.8 37.7 1.0
CA A:TRP222 4.9 38.0 1.0
N A:TRP222 5.0 39.8 1.0

Zinc binding site 3 out of 6 in 3qlc

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Zinc binding site 3 out of 6 in the Complex Structure of Atrx Add Domain Bound to Unmodified H3 1-15 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complex Structure of Atrx Add Domain Bound to Unmodified H3 1-15 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn663

b:39.4
occ:1.00
 SG A:CYS232 2.2 35.7 1.0
SG A:CYS268 2.3 42.0 1.0
SG A:CYS235 2.5 39.7 1.0
SG A:CYS265 2.5 38.2 1.0
CB A:CYS232 3.1 39.3 1.0
CB A:CYS268 3.4 41.5 1.0
CB A:CYS265 3.5 38.4 1.0
CB A:CYS235 3.5 38.5 1.0
N A:CYS265 3.7 39.1 1.0
N A:CYS235 3.9 42.6 1.0
N A:CYS268 4.0 40.3 1.0
CA A:CYS265 4.1 39.2 1.0
CA A:CYS235 4.2 38.2 1.0
CA A:CYS268 4.3 43.5 1.0
C A:PHE234 4.5 41.2 1.0
CA A:CYS232 4.5 35.9 1.0
O A:CYS265 4.5 36.5 1.0
C A:CYS265 4.6 38.3 1.0
N A:PHE234 4.7 39.0 1.0
C A:TYR264 4.7 41.8 1.0
CB A:PHE234 4.8 40.3 1.0
C A:CYS235 4.8 40.0 1.0
CB A:ASN237 4.9 34.3 1.0
CA A:PHE234 4.9 39.3 1.0
CB A:ILE267 4.9 39.9 1.0
ND2 A:ASN237 5.0 44.5 1.0
CA A:TYR264 5.0 37.8 1.0

Zinc binding site 4 out of 6 in 3qlc

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Zinc binding site 4 out of 6 in the Complex Structure of Atrx Add Domain Bound to Unmodified H3 1-15 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Complex Structure of Atrx Add Domain Bound to Unmodified H3 1-15 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn661

b:50.5
occ:1.00
 SG B:CYS197 2.2 44.6 1.0
SG B:CYS200 2.3 46.8 1.0
SG B:CYS171 2.4 44.2 1.0
SG B:CYS174 2.4 48.6 1.0
CB B:CYS171 3.2 43.9 1.0
CB B:CYS200 3.2 48.2 1.0
CB B:CYS174 3.3 43.7 1.0
CB B:CYS197 3.4 42.9 1.0
N B:CYS197 3.9 44.5 1.0
N B:CYS174 3.9 49.1 1.0
N B:CYS200 4.1 55.2 1.0
CA B:CYS174 4.2 48.9 1.0
CA B:CYS197 4.2 50.1 1.0
CA B:CYS200 4.3 52.4 1.0
CB B:ALA173 4.5 39.5 1.0
CA B:CYS171 4.6 44.5 1.0
O B:CYS197 4.7 49.4 1.0
C B:ALA173 4.8 47.4 1.0
C B:CYS197 4.8 52.8 1.0
C B:CYS174 4.9 51.4 1.0
C B:ILE196 5.0 47.0 1.0
N B:ALA173 5.0 40.0 1.0

Zinc binding site 5 out of 6 in 3qlc

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Zinc binding site 5 out of 6 in the Complex Structure of Atrx Add Domain Bound to Unmodified H3 1-15 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Complex Structure of Atrx Add Domain Bound to Unmodified H3 1-15 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn662

b:44.9
occ:1.00
 SG B:CYS243 2.3 43.0 1.0
SG B:CYS223 2.3 42.5 1.0
SG B:CYS240 2.4 43.1 1.0
SG B:CYS220 2.5 42.5 1.0
CB B:CYS220 3.2 44.7 1.0
CB B:CYS243 3.2 35.3 1.0
CB B:CYS223 3.3 41.6 1.0
CB B:CYS240 3.6 39.7 1.0
N B:CYS223 3.7 41.7 1.0
O B:HOH304 3.8 45.3 1.0
CA B:CYS223 4.1 46.6 1.0
N B:CYS240 4.1 38.9 1.0
N B:CYS243 4.2 46.1 1.0
CA B:CYS243 4.3 41.1 1.0
CB B:TRP222 4.3 32.3 1.0
CA B:CYS240 4.4 43.6 1.0
O B:HOH314 4.4 53.6 1.0
CA B:CYS220 4.6 42.1 1.0
C B:TRP222 4.7 41.0 1.0
O B:CYS240 4.7 46.0 1.0
C B:CYS240 4.9 45.4 1.0
C B:CYS223 4.9 47.6 1.0
CA B:TRP222 4.9 37.7 1.0

Zinc binding site 6 out of 6 in 3qlc

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Zinc binding site 6 out of 6 in the Complex Structure of Atrx Add Domain Bound to Unmodified H3 1-15 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Complex Structure of Atrx Add Domain Bound to Unmodified H3 1-15 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn663

b:37.1
occ:1.00
 SG B:CYS235 2.2 38.3 1.0
SG B:CYS268 2.4 40.5 1.0
SG B:CYS232 2.4 39.1 1.0
SG B:CYS265 2.4 36.4 1.0
CB B:CYS232 3.2 38.0 1.0
CB B:CYS235 3.2 35.2 1.0
CB B:CYS268 3.4 34.5 1.0
CB B:CYS265 3.6 37.4 1.0
N B:CYS265 3.8 33.5 1.0
N B:CYS235 3.9 33.4 1.0
N B:CYS268 4.0 34.1 1.0
CA B:CYS235 4.1 36.4 1.0
CA B:CYS265 4.2 34.9 1.0
CA B:CYS268 4.3 35.2 1.0
C B:PHE234 4.4 38.5 1.0
CA B:CYS232 4.6 34.4 1.0
ND2 B:ASN237 4.7 40.8 1.0
C B:CYS265 4.7 35.1 1.0
O B:CYS265 4.7 34.8 1.0
C B:CYS235 4.7 37.5 1.0
N B:PHE234 4.8 34.7 1.0
CB B:PHE234 4.8 35.1 1.0
C B:TYR264 4.8 37.0 1.0
CB B:ASN237 4.9 40.6 1.0
CA B:PHE234 4.9 37.7 1.0
O B:PHE234 4.9 37.2 1.0
CB B:ILE267 4.9 35.4 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: Wed Dec 16 04:45:25 2020

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