Atomistry » Zinc » PDB 3q87-3qmb » 3qlc
Atomistry »
  Zinc »
    PDB 3q87-3qmb »
      3qlc »

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

Go back to Zinc Binding Sites List in 3qlc
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

Go back to Zinc Binding Sites List in 3qlc
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

Go back to Zinc Binding Sites List in 3qlc
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

Go back to Zinc Binding Sites List in 3qlc
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

Go back to Zinc Binding Sites List in 3qlc
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

Go back to Zinc Binding Sites List in 3qlc
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: Sat Oct 26 12:08:53 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy