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Zinc in PDB 3qla: Hexagonal Complex Structure of Atrx Add Bound to H3K9ME3 Peptide

Enzymatic activity of Hexagonal Complex Structure of Atrx Add Bound to H3K9ME3 Peptide

All present enzymatic activity of Hexagonal Complex Structure of Atrx Add Bound to H3K9ME3 Peptide:
3.6.4.12;

Protein crystallography data

The structure of Hexagonal Complex Structure of Atrx Add Bound to H3K9ME3 Peptide, PDB code: 3qla was solved by B.Xiang, H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.60 / 1.60
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 66.709, 66.709, 131.641, 90.00, 90.00, 120.00
R / Rfree (%) 15.7 / 17.9

Other elements in 3qla:

The structure of Hexagonal Complex Structure of Atrx Add Bound to H3K9ME3 Peptide also contains other interesting chemical elements:

Potassium (K) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Hexagonal Complex Structure of Atrx Add Bound to H3K9ME3 Peptide (pdb code 3qla). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Hexagonal Complex Structure of Atrx Add Bound to H3K9ME3 Peptide, PDB code: 3qla:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3qla

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Zinc binding site 1 out of 6 in the Hexagonal Complex Structure of Atrx Add Bound to H3K9ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hexagonal Complex Structure of Atrx Add Bound to H3K9ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:13.3
occ:1.00
 SG A:CYS174 2.3 14.3 1.0
SG A:CYS197 2.3 13.4 1.0
SG A:CYS200 2.3 13.1 1.0
SG A:CYS171 2.3 12.3 1.0
CB A:CYS171 3.1 10.6 1.0
CB A:CYS174 3.2 11.3 1.0
CB A:CYS200 3.2 10.9 1.0
CB A:CYS197 3.4 11.8 1.0
N A:CYS174 3.7 8.6 1.0
N A:CYS197 3.8 12.2 1.0
CA A:CYS174 4.0 10.8 1.0
O A:HOH358 4.0 38.8 1.0
N A:CYS200 4.1 11.2 1.0
O A:HOH73 4.2 24.0 1.0
CA A:CYS197 4.2 12.0 1.0
CA A:CYS200 4.2 12.3 1.0
O A:HOH423 4.3 25.8 1.0
C A:ALA173 4.4 10.0 1.0
CB A:ALA173 4.5 9.5 1.0
CA A:CYS171 4.5 10.3 1.0
C A:CYS174 4.7 12.8 1.0
CA A:ALA173 4.8 9.5 1.0
C A:CYS197 4.8 12.9 1.0
N A:ALA173 4.8 9.4 1.0
O A:CYS197 4.8 12.7 1.0
N A:GLY175 4.9 13.3 1.0
C A:ILE196 4.9 11.2 1.0
C A:CYS171 5.0 11.2 1.0

Zinc binding site 2 out of 6 in 3qla

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Zinc binding site 2 out of 6 in the Hexagonal Complex Structure of Atrx Add Bound to H3K9ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hexagonal Complex Structure of Atrx Add Bound to H3K9ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:10.1
occ:1.00
 SG A:CYS243 2.3 9.4 1.0
SG A:CYS240 2.3 8.7 1.0
SG A:CYS220 2.3 9.0 1.0
SG A:CYS223 2.3 10.4 1.0
CB A:CYS220 3.0 8.8 1.0
CB A:CYS243 3.2 9.1 1.0
CB A:CYS223 3.3 11.3 1.0
CB A:CYS240 3.5 8.6 1.0
N A:CYS223 3.6 7.7 1.0
O A:HOH14 3.7 13.9 1.0
N A:CYS240 3.9 7.4 1.0
CA A:CYS223 4.0 8.8 1.0
N A:CYS243 4.1 8.7 1.0
O A:HOH67 4.2 15.9 1.0
CB A:TRP222 4.2 9.0 1.0
CA A:CYS240 4.2 8.8 1.0
CA A:CYS243 4.2 8.6 1.0
O A:HOH55 4.2 18.9 1.0
CA A:CYS220 4.5 7.8 1.0
O A:CYS240 4.5 7.5 1.0
C A:TRP222 4.6 10.3 1.0
C A:CYS240 4.7 8.3 1.0
CA A:TRP222 4.8 8.2 1.0
N A:TRP222 4.8 8.2 1.0
C A:CYS223 4.9 8.7 1.0
C A:CYS220 5.0 8.5 1.0

Zinc binding site 3 out of 6 in 3qla

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Zinc binding site 3 out of 6 in the Hexagonal Complex Structure of Atrx Add Bound to H3K9ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Hexagonal Complex Structure of Atrx Add Bound to H3K9ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:9.9
occ:1.00
 SG A:CYS235 2.2 10.8 1.0
SG A:CYS232 2.3 9.1 1.0
SG A:CYS268 2.3 11.1 1.0
SG A:CYS265 2.3 9.0 1.0
CB A:CYS232 3.0 9.5 1.0
CB A:CYS268 3.2 10.5 1.0
CB A:CYS235 3.3 10.6 1.0
CB A:CYS265 3.4 8.4 1.0
N A:CYS265 3.6 8.5 1.0
N A:CYS268 3.8 8.6 1.0
N A:CYS235 3.9 8.9 1.0
CA A:CYS265 4.0 7.9 1.0
CA A:CYS268 4.1 9.2 1.0
CA A:CYS235 4.2 9.7 1.0
CA A:CYS232 4.4 8.6 1.0
C A:CYS265 4.5 8.8 1.0
C A:PHE234 4.5 9.4 1.0
O A:CYS265 4.5 8.8 1.0
C A:CYS235 4.7 9.6 1.0
CB A:ASN237 4.7 8.4 1.0
C A:TYR264 4.7 10.7 1.0
ND2 A:ASN237 4.7 10.8 1.0
CB A:ILE267 4.7 9.3 1.0
CB A:PHE234 4.8 8.7 1.0
N A:PHE234 4.8 7.6 1.0
O A:CYS235 4.9 10.2 1.0
C A:ILE267 4.9 10.7 1.0
CA A:TYR264 4.9 9.9 1.0
CA A:PHE234 4.9 7.7 1.0

Zinc binding site 4 out of 6 in 3qla

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Zinc binding site 4 out of 6 in the Hexagonal Complex Structure of Atrx Add Bound to H3K9ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Hexagonal Complex Structure of Atrx Add Bound to H3K9ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1

b:17.2
occ:1.00
 SG D:CYS200 2.2 15.1 1.0
SG D:CYS171 2.3 16.5 1.0
SG D:CYS174 2.3 19.0 1.0
SG D:CYS197 2.3 17.2 1.0
CB D:CYS171 3.1 14.3 1.0
CB D:CYS174 3.1 20.5 1.0
CB D:CYS200 3.2 12.3 1.0
CB D:CYS197 3.4 17.2 1.0
N D:CYS174 3.6 14.8 1.0
N D:CYS197 3.8 18.2 1.0
CA D:CYS174 3.9 14.2 1.0
O D:HOH418 4.0 38.4 1.0
N D:CYS200 4.0 13.9 1.0
CA D:CYS197 4.2 17.6 1.0
CA D:CYS200 4.2 15.9 1.0
O D:HOH448 4.2 27.8 1.0
C D:ALA173 4.4 13.9 1.0
O D:HOH94 4.5 27.8 1.0
CB D:ALA173 4.5 12.5 1.0
CA D:CYS171 4.5 16.3 1.0
C D:CYS197 4.7 18.5 1.0
C D:CYS174 4.7 15.2 1.0
O D:CYS197 4.7 17.5 1.0
CA D:ALA173 4.8 12.7 1.0
N D:ALA173 4.8 12.0 1.0
N D:GLY175 4.9 19.1 1.0
C D:ILE196 4.9 15.9 1.0
C D:CYS171 5.0 12.7 1.0

Zinc binding site 5 out of 6 in 3qla

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Zinc binding site 5 out of 6 in the Hexagonal Complex Structure of Atrx Add Bound to H3K9ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Hexagonal Complex Structure of Atrx Add Bound to H3K9ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2

b:10.4
occ:1.00
 SG D:CYS243 2.3 10.6 1.0
SG D:CYS220 2.3 9.9 1.0
SG D:CYS240 2.3 9.1 1.0
SG D:CYS223 2.3 10.7 1.0
CB D:CYS220 3.0 8.5 1.0
CB D:CYS243 3.2 9.3 1.0
CB D:CYS223 3.3 9.8 1.0
CB D:CYS240 3.4 8.5 1.0
N D:CYS223 3.6 9.9 1.0
O D:HOH40 3.8 18.3 1.0
N D:CYS240 3.9 9.3 1.0
CA D:CYS223 4.0 8.9 1.0
N D:CYS243 4.1 9.3 1.0
CA D:CYS240 4.2 7.4 1.0
CB D:TRP222 4.2 8.8 1.0
CA D:CYS243 4.2 8.7 1.0
O D:HOH64 4.3 20.0 1.0
O D:HOH57 4.3 17.2 1.0
CA D:CYS220 4.4 8.9 1.0
O D:CYS240 4.6 9.8 1.0
C D:TRP222 4.6 10.3 1.0
C D:CYS240 4.7 8.3 1.0
CA D:TRP222 4.8 9.8 1.0
N D:TRP222 4.9 9.5 1.0
C D:CYS223 4.9 12.0 1.0
C D:CYS220 4.9 10.6 1.0

Zinc binding site 6 out of 6 in 3qla

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Zinc binding site 6 out of 6 in the Hexagonal Complex Structure of Atrx Add Bound to H3K9ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Hexagonal Complex Structure of Atrx Add Bound to H3K9ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn3

b:11.7
occ:1.00
 SG D:CYS268 2.3 14.4 1.0
SG D:CYS232 2.3 10.1 1.0
SG D:CYS235 2.3 11.7 1.0
SG D:CYS265 2.3 10.3 1.0
CB D:CYS232 3.0 9.1 1.0
CB D:CYS268 3.3 14.9 1.0
CB D:CYS235 3.4 10.6 1.0
CB D:CYS265 3.4 8.9 1.0
N D:CYS265 3.6 9.5 1.0
N D:CYS268 3.9 10.2 1.0
N D:CYS235 3.9 9.4 1.0
CA D:CYS265 4.0 9.6 1.0
CA D:CYS268 4.2 10.9 1.0
CA D:CYS235 4.2 11.1 1.0
O D:HOH410 4.2 27.5 1.0
CA D:CYS232 4.5 8.4 1.0
C D:PHE234 4.5 9.9 1.0
C D:CYS265 4.5 9.5 1.0
O D:CYS265 4.5 11.9 1.0
C D:CYS235 4.7 11.8 1.0
CB D:ASN237 4.7 9.3 1.0
C D:TYR264 4.7 11.6 1.0
ND2 D:ASN237 4.7 12.2 1.0
CB D:ILE267 4.8 11.0 1.0
N D:PHE234 4.8 10.0 1.0
O D:CYS235 4.8 10.9 1.0
CB D:PHE234 4.9 9.3 1.0
C D:ILE267 4.9 14.7 1.0
CA D:TYR264 4.9 13.1 1.0
CA D:PHE234 5.0 11.2 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 12:08:53 2024

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