Atomistry » Zinc » PDB 5vmx-5vuo » 5vsd
Atomistry »
  Zinc »
    PDB 5vmx-5vuo »
      5vsd »

Zinc in PDB 5vsd: Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13

Enzymatic activity of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13

All present enzymatic activity of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13:
2.1.1.43;

Protein crystallography data

The structure of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13, PDB code: 5vsd was solved by N.Babault, Y.Xiong, J.Liu, J.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.91 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.864, 96.594, 102.478, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 23.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13 (pdb code 5vsd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13, PDB code: 5vsd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5vsd

Go back to Zinc Binding Sites List in 5vsd
Zinc binding site 1 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3002

b:22.3
occ:1.00
 SG A:CYS1109 2.3 19.2 1.0
SG A:CYS1075 2.4 23.4 1.0
SG A:CYS1105 2.4 19.8 1.0
SG A:CYS1062 2.4 19.0 1.0
CB A:CYS1105 3.2 13.4 1.0
CB A:CYS1109 3.2 15.1 1.0
CB A:CYS1062 3.2 19.6 1.0
CB A:CYS1075 3.4 18.9 1.0
N A:CYS1062 3.6 26.0 1.0
CA A:CYS1105 3.6 26.5 1.0
ZN A:ZN3003 3.8 22.1 1.0
ZN A:ZN3004 3.8 21.6 1.0
CA A:CYS1062 4.0 26.8 1.0
SG A:CYS1111 4.0 19.3 1.0
SG A:CYS1073 4.4 20.9 1.0
C A:TYR1061 4.5 19.6 1.0
N A:CYS1105 4.6 22.8 1.0
CA A:CYS1109 4.6 15.8 1.0
N A:ASN1106 4.6 21.4 1.0
CA A:CYS1075 4.6 20.4 1.0
SG A:CYS1068 4.6 22.2 1.0
N A:CYS1075 4.7 20.0 1.0
C A:CYS1105 4.7 24.7 1.0
CA A:TYR1061 4.8 21.7 1.0
C A:CYS1062 4.8 26.3 1.0
O A:CYS1062 4.9 19.7 1.0
O A:HOH3262 4.9 24.3 1.0
ND2 A:ASN1117 4.9 17.2 1.0

Zinc binding site 2 out of 8 in 5vsd

Go back to Zinc Binding Sites List in 5vsd
Zinc binding site 2 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3003

b:22.1
occ:1.00
 SG A:CYS1111 2.3 19.3 1.0
SG A:CYS1115 2.3 19.5 1.0
SG A:CYS1105 2.3 19.8 1.0
SG A:CYS1068 2.4 22.2 1.0
CB A:CYS1111 3.1 19.1 1.0
CB A:CYS1105 3.2 13.4 1.0
CB A:CYS1115 3.2 24.1 1.0
CB A:CYS1068 3.4 22.7 1.0
ZN A:ZN3004 3.7 21.6 1.0
ZN A:ZN3002 3.8 22.3 1.0
SG A:CYS1062 3.9 19.0 1.0
NH2 A:ARG1118 4.2 21.5 1.0
NE A:ARG1118 4.3 25.7 1.0
CA A:CYS1111 4.5 24.8 1.0
CB A:ASN1117 4.6 19.6 1.0
CZ A:ARG1118 4.7 26.4 1.0
CA A:CYS1105 4.7 26.5 1.0
CA A:CYS1115 4.7 23.1 1.0
O A:TRP1112 4.8 23.1 1.0
CA A:CYS1068 4.8 20.2 1.0
CB A:CYS1109 4.9 15.1 1.0
N A:ASN1117 5.0 23.3 1.0

Zinc binding site 3 out of 8 in 5vsd

Go back to Zinc Binding Sites List in 5vsd
Zinc binding site 3 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3004

b:21.6
occ:1.00
 SG A:CYS1068 2.2 22.2 1.0
SG A:CYS1062 2.4 19.0 1.0
SG A:CYS1064 2.4 21.9 1.0
SG A:CYS1073 2.4 20.9 1.0
CB A:CYS1062 3.1 19.6 1.0
CB A:CYS1064 3.2 20.4 1.0
CB A:CYS1073 3.2 21.3 1.0
CB A:CYS1068 3.2 22.7 1.0
ZN A:ZN3003 3.7 22.1 1.0
ZN A:ZN3002 3.8 22.3 1.0
CA A:CYS1073 3.9 21.2 1.0
CA A:CYS1068 3.9 20.2 1.0
SG A:CYS1105 4.0 19.8 1.0
N A:CYS1064 4.4 20.6 1.0
CA A:CYS1064 4.4 20.8 1.0
O A:HOH3216 4.4 24.2 1.0
O A:HOH3213 4.5 17.6 1.0
N A:MET1074 4.5 25.7 1.0
C A:CYS1073 4.6 27.2 1.0
CA A:CYS1062 4.6 26.8 1.0
SG A:CYS1111 4.7 19.3 1.0
N A:CYS1068 4.8 20.4 1.0
CB A:CYS1111 4.8 19.1 1.0
O A:HOH3289 4.8 32.1 1.0
C A:CYS1062 5.0 26.3 1.0

Zinc binding site 4 out of 8 in 5vsd

Go back to Zinc Binding Sites List in 5vsd
Zinc binding site 4 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3005

b:22.8
occ:1.00
 SG A:CYS1203 2.3 23.2 1.0
SG A:CYS1258 2.3 24.1 1.0
SG A:CYS1263 2.4 22.0 1.0
SG A:CYS1256 2.4 25.5 1.0
CB A:CYS1263 3.2 24.7 1.0
CB A:CYS1256 3.4 22.2 1.0
CB A:CYS1203 3.4 29.9 1.0
CB A:CYS1258 3.4 19.7 1.0
CA A:CYS1263 3.8 31.6 1.0
O A:HOH3236 4.1 20.8 1.0
N A:CYS1203 4.1 22.1 1.0
N A:ARG1264 4.1 24.3 1.0
N A:CYS1258 4.2 21.3 1.0
NE2 A:HIS1201 4.3 19.2 1.0
CA A:CYS1258 4.4 20.5 1.0
CA A:CYS1203 4.4 22.0 1.0
C A:CYS1263 4.4 22.1 1.0
CD2 A:HIS1201 4.5 21.6 1.0
N A:HIS1265 4.5 27.3 1.0
CA A:CYS1256 4.7 26.8 1.0
N A:GLY1259 4.8 28.9 1.0
C A:CYS1256 4.8 33.0 1.0
CB A:SER1260 4.9 20.2 1.0
C A:CYS1258 4.9 30.8 1.0
N A:SER1260 5.0 25.0 1.0

Zinc binding site 5 out of 8 in 5vsd

Go back to Zinc Binding Sites List in 5vsd
Zinc binding site 5 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3002

b:23.2
occ:1.00
 SG B:CYS1075 2.4 24.5 1.0
SG B:CYS1062 2.4 18.9 1.0
SG B:CYS1109 2.4 23.0 1.0
SG B:CYS1105 2.4 22.3 1.0
CB B:CYS1105 3.1 18.5 1.0
CB B:CYS1062 3.2 23.7 1.0
CB B:CYS1109 3.2 24.8 1.0
CB B:CYS1075 3.4 29.6 1.0
CA B:CYS1105 3.6 24.2 1.0
N B:CYS1062 3.6 19.8 1.0
ZN B:ZN3003 3.7 21.5 1.0
ZN B:ZN3004 3.8 23.3 1.0
CA B:CYS1062 4.0 22.2 1.0
SG B:CYS1111 4.2 20.8 1.0
SG B:CYS1073 4.2 24.4 1.0
N B:ASN1106 4.5 21.1 1.0
N B:CYS1105 4.5 16.4 1.0
CA B:CYS1109 4.6 20.8 1.0
C B:TYR1061 4.6 29.6 1.0
C B:CYS1105 4.6 22.2 1.0
CA B:CYS1075 4.6 20.8 1.0
N B:CYS1075 4.7 24.6 1.0
SG B:CYS1068 4.7 23.3 1.0
C B:CYS1062 4.8 24.2 1.0
CA B:TYR1061 4.8 23.2 1.0
O B:HOH3260 4.8 29.5 1.0
O B:CYS1062 4.9 26.0 1.0

Zinc binding site 6 out of 8 in 5vsd

Go back to Zinc Binding Sites List in 5vsd
Zinc binding site 6 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3003

b:21.5
occ:1.00
 SG B:CYS1105 2.3 22.3 1.0
SG B:CYS1111 2.3 20.8 1.0
SG B:CYS1068 2.3 23.3 1.0
SG B:CYS1115 2.4 21.5 1.0
CB B:CYS1105 3.1 18.5 1.0
CB B:CYS1111 3.2 23.0 1.0
CB B:CYS1068 3.3 18.3 1.0
CB B:CYS1115 3.3 20.1 1.0
ZN B:ZN3004 3.7 23.3 1.0
ZN B:ZN3002 3.7 23.2 1.0
SG B:CYS1062 3.9 18.9 1.0
NH2 B:ARG1118 4.3 25.7 1.0
NE B:ARG1118 4.4 25.2 1.0
CB B:ASN1117 4.5 21.4 1.0
CA B:CYS1105 4.6 24.2 1.0
CA B:CYS1111 4.6 21.3 1.0
CA B:CYS1068 4.7 25.8 1.0
CZ B:ARG1118 4.7 17.7 1.0
CA B:CYS1115 4.8 21.4 1.0
O B:TRP1112 4.9 21.9 1.0
SG B:CYS1073 4.9 24.4 1.0
CB B:CYS1109 4.9 24.8 1.0
N B:ASN1117 4.9 19.5 1.0

Zinc binding site 7 out of 8 in 5vsd

Go back to Zinc Binding Sites List in 5vsd
Zinc binding site 7 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3004

b:23.3
occ:1.00
 SG B:CYS1073 2.3 24.4 1.0
SG B:CYS1068 2.3 23.3 1.0
SG B:CYS1064 2.4 24.7 1.0
SG B:CYS1062 2.4 18.9 1.0
CB B:CYS1062 3.1 23.7 1.0
CB B:CYS1073 3.1 24.4 1.0
CB B:CYS1068 3.2 18.3 1.0
CB B:CYS1064 3.2 27.8 1.0
ZN B:ZN3003 3.7 21.5 1.0
ZN B:ZN3002 3.8 23.2 1.0
CA B:CYS1068 3.8 25.8 1.0
CA B:CYS1073 3.9 24.3 1.0
SG B:CYS1105 4.0 22.3 1.0
N B:CYS1064 4.4 30.2 1.0
CA B:CYS1064 4.4 31.1 1.0
O B:HOH3157 4.5 31.2 1.0
CA B:CYS1062 4.6 22.2 1.0
SG B:CYS1111 4.7 20.8 1.0
N B:CYS1068 4.7 27.5 1.0
C B:CYS1073 4.7 29.6 1.0
O B:HOH3133 4.7 23.1 1.0
N B:MET1074 4.9 22.5 1.0
C B:CYS1068 4.9 30.2 1.0
CB B:CYS1111 4.9 23.0 1.0
O B:CYS1068 5.0 33.4 1.0
C B:CYS1062 5.0 24.2 1.0

Zinc binding site 8 out of 8 in 5vsd

Go back to Zinc Binding Sites List in 5vsd
Zinc binding site 8 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3005

b:30.3
occ:1.00
 SG B:CYS1256 2.3 27.3 1.0
SG B:CYS1258 2.3 28.4 1.0
SG B:CYS1263 2.4 32.6 1.0
SG B:CYS1203 2.5 29.7 1.0
CB B:CYS1263 3.2 36.0 1.0
CB B:CYS1258 3.3 26.0 1.0
CB B:CYS1256 3.3 30.4 1.0
CB B:CYS1203 3.5 30.9 1.0
CA B:CYS1263 3.8 32.2 1.0
O B:HOH3190 4.0 32.7 1.0
N B:CYS1258 4.0 29.9 1.0
N B:CYS1203 4.1 26.9 1.0
CA B:CYS1258 4.2 30.4 1.0
N B:ARG1264 4.2 39.0 1.0
NE2 B:HIS1201 4.3 23.7 1.0
CA B:CYS1203 4.4 23.7 1.0
C B:CYS1263 4.4 36.9 1.0
CD2 B:HIS1201 4.5 23.7 1.0
N B:HIS1265 4.6 38.3 1.0
CA B:CYS1256 4.6 37.9 1.0
C B:CYS1256 4.7 33.2 1.0
N B:GLY1259 4.7 30.3 1.0
C B:CYS1258 4.8 36.2 1.0
O B:CYS1256 5.0 34.8 1.0

Reference:

Y.Xiong, F.Li, N.Babault, H.Wu, A.Dong, H.Zeng, X.Chen, C.H.Arrowsmith, P.J.Brown, J.Liu, M.Vedadi, J.Jin. Structure-Activity Relationship Studies of G9A-Like Protein (Glp) Inhibitors. Bioorg. Med. Chem. V. 25 4414 2017.
ISSN: ESSN 1464-3391
PubMed: 28662962
DOI: 10.1016/J.BMC.2017.06.021
Page generated: Mon Oct 28 13:21:03 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy