Zinc in PDB 7klr: Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A in Complex with A Histone H3(1-10) Peptide
Enzymatic activity of Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A in Complex with A Histone H3(1-10) Peptide
All present enzymatic activity of Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A in Complex with A Histone H3(1-10) Peptide:
1.14.11.67;
Zinc Binding Sites:
The binding sites of Zinc atom in the Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A in Complex with A Histone H3(1-10) Peptide
(pdb code 7klr). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the
Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A in Complex with A Histone H3(1-10) Peptide, PDB code: 7klr:
Jump to Zinc binding site number:
1;
2;
Zinc binding site 1 out
of 2 in 7klr
Go back to
Zinc Binding Sites List in 7klr
Zinc binding site 1 out
of 2 in the Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A in Complex with A Histone H3(1-10) Peptide
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A in Complex with A Histone H3(1-10) Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:0.0
occ:1.00
|
ND1
|
A:HIS34
|
2.0
|
0.0
|
1.0
|
SG
|
A:CYS37
|
2.3
|
0.0
|
1.0
|
SG
|
A:CYS14
|
2.3
|
0.0
|
1.0
|
SG
|
A:CYS11
|
2.3
|
0.0
|
1.0
|
HB2
|
A:HIS34
|
2.7
|
0.0
|
1.0
|
CE1
|
A:HIS34
|
2.9
|
0.0
|
1.0
|
CG
|
A:HIS34
|
3.0
|
0.0
|
1.0
|
HB3
|
A:CYS14
|
3.1
|
0.0
|
1.0
|
HE1
|
A:HIS34
|
3.2
|
0.0
|
1.0
|
CB
|
A:CYS11
|
3.3
|
0.0
|
1.0
|
HB3
|
A:CYS11
|
3.3
|
0.0
|
1.0
|
CB
|
A:CYS14
|
3.3
|
0.0
|
1.0
|
CB
|
A:HIS34
|
3.4
|
0.0
|
1.0
|
HB2
|
A:CYS11
|
3.4
|
0.0
|
1.0
|
HB2
|
A:CYS37
|
3.4
|
0.0
|
1.0
|
CB
|
A:CYS37
|
3.4
|
0.0
|
1.0
|
HB3
|
A:CYS37
|
3.7
|
0.0
|
1.0
|
H
|
A:HIS34
|
3.8
|
0.0
|
1.0
|
HB3
|
A:HIS34
|
4.0
|
0.0
|
1.0
|
HB2
|
A:CYS14
|
4.0
|
0.0
|
1.0
|
NE2
|
A:HIS34
|
4.1
|
0.0
|
1.0
|
CD2
|
A:HIS34
|
4.1
|
0.0
|
1.0
|
C
|
A:CYS14
|
4.3
|
0.0
|
1.0
|
N
|
A:GLY15
|
4.4
|
0.0
|
1.0
|
CA
|
A:CYS14
|
4.4
|
0.0
|
1.0
|
H
|
A:GLY15
|
4.4
|
0.0
|
1.0
|
CA
|
A:HIS34
|
4.5
|
0.0
|
1.0
|
N
|
A:HIS34
|
4.5
|
0.0
|
1.0
|
HA2
|
A:GLY15
|
4.5
|
0.0
|
1.0
|
HE1
|
A:PHE36
|
4.6
|
0.0
|
1.0
|
HZ
|
A:PHE36
|
4.7
|
0.0
|
1.0
|
CA
|
A:CYS11
|
4.8
|
0.0
|
1.0
|
O
|
A:CYS14
|
4.8
|
0.0
|
1.0
|
CA
|
A:CYS37
|
4.8
|
0.0
|
1.0
|
CE1
|
A:PHE36
|
4.8
|
0.0
|
1.0
|
CZ
|
A:PHE36
|
4.9
|
0.0
|
1.0
|
CA
|
A:GLY15
|
4.9
|
0.0
|
1.0
|
HA3
|
A:GLY15
|
4.9
|
0.0
|
1.0
|
H
|
A:CYS37
|
4.9
|
0.0
|
1.0
|
HE2
|
A:HIS34
|
4.9
|
0.0
|
1.0
|
HB2
|
A:ASN19
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 2 out
of 2 in 7klr
Go back to
Zinc Binding Sites List in 7klr
Zinc binding site 2 out
of 2 in the Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A in Complex with A Histone H3(1-10) Peptide
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A in Complex with A Histone H3(1-10) Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:0.0
occ:1.00
|
SG
|
A:CYS52
|
2.3
|
0.0
|
1.0
|
SG
|
A:CYS55
|
2.3
|
0.0
|
1.0
|
SG
|
A:CYS26
|
2.3
|
0.0
|
1.0
|
SG
|
A:CYS29
|
2.3
|
0.0
|
1.0
|
HB2
|
A:CYS55
|
2.9
|
0.0
|
1.0
|
HB3
|
A:CYS26
|
3.1
|
0.0
|
1.0
|
H
|
A:CYS52
|
3.1
|
0.0
|
1.0
|
HB3
|
A:CYS52
|
3.1
|
0.0
|
1.0
|
CB
|
A:CYS55
|
3.2
|
0.0
|
1.0
|
HB3
|
A:CYS29
|
3.3
|
0.0
|
1.0
|
CB
|
A:CYS26
|
3.3
|
0.0
|
1.0
|
CB
|
A:CYS52
|
3.3
|
0.0
|
1.0
|
CB
|
A:CYS29
|
3.5
|
0.0
|
1.0
|
H
|
A:CYS55
|
3.6
|
0.0
|
1.0
|
H
|
A:CYS29
|
3.8
|
0.0
|
1.0
|
HB2
|
A:CYS26
|
3.8
|
0.0
|
1.0
|
N
|
A:CYS52
|
3.9
|
0.0
|
1.0
|
HB3
|
A:CYS55
|
4.0
|
0.0
|
1.0
|
O
|
A:CYS26
|
4.1
|
0.0
|
1.0
|
N
|
A:CYS55
|
4.1
|
0.0
|
1.0
|
HB2
|
A:CYS52
|
4.2
|
0.0
|
1.0
|
HE1
|
A:TYR33
|
4.2
|
0.0
|
1.0
|
CA
|
A:CYS52
|
4.2
|
0.0
|
1.0
|
HB2
|
A:CYS29
|
4.2
|
0.0
|
1.0
|
CA
|
A:CYS55
|
4.3
|
0.0
|
1.0
|
HB2
|
A:LYS54
|
4.3
|
0.0
|
1.0
|
N
|
A:CYS29
|
4.4
|
0.0
|
1.0
|
CA
|
A:CYS29
|
4.5
|
0.0
|
1.0
|
CA
|
A:CYS26
|
4.6
|
0.0
|
1.0
|
C
|
A:CYS26
|
4.6
|
0.0
|
1.0
|
HA
|
A:ARG51
|
4.7
|
0.0
|
1.0
|
HA
|
A:CYS55
|
4.7
|
0.0
|
1.0
|
O
|
A:CYS52
|
4.7
|
0.0
|
1.0
|
C
|
A:CYS52
|
4.8
|
0.0
|
1.0
|
C
|
A:CYS29
|
4.9
|
0.0
|
1.0
|
HB3
|
A:ARG51
|
4.9
|
0.0
|
1.0
|
|
Reference:
J.E.Longbotham,
M.J.S.Kelly,
D.G.Fujimori.
Recognition of Histone H3 Methylation States By the PHD1 Domain of Histone Demethylase KDM5A. Acs Chem.Biol. 2021.
ISSN: ESSN 1554-8937
PubMed: 33621062
DOI: 10.1021/ACSCHEMBIO.0C00976
Page generated: Sat Apr 3 18:36:56 2021
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