Atomistry » Zinc » PDB 5vmz-5vuq » 5vsf
Atomistry »
  Zinc »
    PDB 5vmz-5vuq »
      5vsf »

Zinc in PDB 5vsf: Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 17

Enzymatic activity of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 17

All present enzymatic activity of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 17:
2.1.1.43;

Protein crystallography data

The structure of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 17, PDB code: 5vsf 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) 19.96 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.851, 96.088, 102.101, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 18.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 17 (pdb code 5vsf). 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 17, PDB code: 5vsf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5vsf

Go back to Zinc Binding Sites List in 5vsf
Zinc binding site 1 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 17


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 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3002

b:17.1
occ:1.00
 SG A:CYS1109 2.3 15.5 1.0
SG A:CYS1075 2.3 16.9 1.0
SG A:CYS1062 2.4 15.0 1.0
SG A:CYS1105 2.4 16.1 1.0
CB A:CYS1062 3.3 15.3 1.0
CB A:CYS1105 3.3 16.6 1.0
CB A:CYS1109 3.3 14.4 1.0
CB A:CYS1075 3.4 15.7 1.0
N A:CYS1062 3.6 15.1 1.0
CA A:CYS1105 3.6 14.5 1.0
ZN A:ZN3003 3.8 16.5 1.0
ZN A:ZN3004 3.9 16.9 1.0
CA A:CYS1062 4.0 15.6 1.0
SG A:CYS1111 4.2 16.6 1.0
SG A:CYS1073 4.4 15.8 1.0
C A:TYR1061 4.5 18.2 1.0
N A:CYS1105 4.5 13.8 1.0
CA A:CYS1109 4.6 15.9 1.0
N A:ASN1106 4.6 14.9 1.0
CA A:CYS1075 4.6 15.1 1.0
N A:CYS1075 4.7 15.5 1.0
C A:CYS1105 4.7 17.1 1.0
SG A:CYS1068 4.7 15.8 1.0
CA A:TYR1061 4.8 16.0 1.0
C A:CYS1062 4.8 16.0 1.0
O A:CYS1062 4.9 17.2 1.0
O A:HOH3264 4.9 20.8 1.0
OD1 A:ASN1117 5.0 17.7 1.0

Zinc binding site 2 out of 8 in 5vsf

Go back to Zinc Binding Sites List in 5vsf
Zinc binding site 2 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 17


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 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3003

b:16.5
occ:1.00
 SG A:CYS1111 2.3 16.6 1.0
SG A:CYS1115 2.3 16.3 1.0
SG A:CYS1068 2.3 15.8 1.0
SG A:CYS1105 2.4 16.1 1.0
CB A:CYS1111 3.2 16.8 1.0
CB A:CYS1105 3.2 16.6 1.0
CB A:CYS1115 3.2 17.8 1.0
CB A:CYS1068 3.4 15.0 1.0
ZN A:ZN3004 3.8 16.9 1.0
ZN A:ZN3002 3.8 17.1 1.0
SG A:CYS1062 4.0 15.0 1.0
NH2 A:ARG1118 4.3 19.8 1.0
NE A:ARG1118 4.4 17.5 1.0
CB A:ASN1117 4.5 18.9 1.0
CA A:CYS1111 4.6 18.1 1.0
CA A:CYS1105 4.7 14.5 1.0
CA A:CYS1115 4.7 21.2 1.0
CA A:CYS1068 4.7 17.8 1.0
CZ A:ARG1118 4.8 18.9 1.0
O A:TRP1112 4.8 19.0 1.0
CB A:CYS1109 4.9 14.4 1.0
N A:ASN1117 5.0 15.9 1.0

Zinc binding site 3 out of 8 in 5vsf

Go back to Zinc Binding Sites List in 5vsf
Zinc binding site 3 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 17


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 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3004

b:16.9
occ:1.00
 SG A:CYS1064 2.3 16.2 1.0
SG A:CYS1068 2.3 15.8 1.0
SG A:CYS1073 2.3 15.8 1.0
SG A:CYS1062 2.4 15.0 1.0
CB A:CYS1062 3.2 15.3 1.0
CB A:CYS1064 3.2 18.0 1.0
CB A:CYS1068 3.3 15.0 1.0
CB A:CYS1073 3.3 17.8 1.0
ZN A:ZN3003 3.8 16.5 1.0
ZN A:ZN3002 3.9 17.1 1.0
CA A:CYS1073 3.9 16.8 1.0
CA A:CYS1068 3.9 17.8 1.0
SG A:CYS1105 4.1 16.1 1.0
N A:CYS1064 4.4 16.8 1.0
CA A:CYS1064 4.4 19.5 1.0
O A:HOH3148 4.5 18.3 1.0
O A:HOH3280 4.5 19.1 1.0
C A:CYS1073 4.6 16.8 1.0
N A:MET1074 4.6 18.3 1.0
CA A:CYS1062 4.6 15.6 1.0
N A:CYS1068 4.8 15.9 1.0
SG A:CYS1111 4.8 16.6 1.0
CB A:CYS1111 4.8 16.8 1.0
N A:CYS1075 4.9 15.5 1.0

Zinc binding site 4 out of 8 in 5vsf

Go back to Zinc Binding Sites List in 5vsf
Zinc binding site 4 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 17


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 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3005

b:20.1
occ:1.00
 SG A:CYS1263 2.3 19.1 1.0
SG A:CYS1258 2.3 19.9 1.0
SG A:CYS1256 2.3 19.4 1.0
SG A:CYS1203 2.4 19.2 1.0
CB A:CYS1263 3.3 21.0 1.0
CB A:CYS1256 3.4 21.2 1.0
CB A:CYS1203 3.4 19.0 1.0
CB A:CYS1258 3.4 19.7 1.0
CA A:CYS1263 3.8 18.5 1.0
O A:HOH3247 4.0 23.1 1.0
N A:CYS1203 4.1 15.4 1.0
N A:CYS1258 4.1 23.7 1.0
CE1 A:HIS1201 4.2 17.2 1.0
N A:ARG1264 4.3 19.6 1.0
CA A:CYS1258 4.3 22.7 1.0
CA A:CYS1203 4.3 19.9 1.0
ND1 A:HIS1201 4.4 20.2 1.0
C A:CYS1263 4.5 19.9 1.0
N A:HIS1265 4.6 23.4 1.0
CA A:CYS1256 4.7 21.0 1.0
C A:CYS1256 4.8 26.9 1.0
N A:GLY1259 4.8 20.2 1.0
CB A:HIS1265 4.9 21.6 1.0
C A:CYS1258 4.9 20.7 1.0
CB A:SER1260 5.0 17.6 1.0
O A:CYS1256 5.0 26.7 1.0

Zinc binding site 5 out of 8 in 5vsf

Go back to Zinc Binding Sites List in 5vsf
Zinc binding site 5 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 17


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 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3002

b:17.9
occ:1.00
 SG B:CYS1109 2.3 16.8 1.0
SG B:CYS1075 2.4 18.2 1.0
SG B:CYS1062 2.4 17.9 1.0
SG B:CYS1105 2.4 16.6 1.0
CB B:CYS1105 3.2 15.9 1.0
CB B:CYS1062 3.2 21.8 1.0
CB B:CYS1109 3.3 19.1 1.0
CB B:CYS1075 3.4 17.4 1.0
CA B:CYS1105 3.6 15.7 1.0
N B:CYS1062 3.6 18.4 1.0
ZN B:ZN3004 3.8 18.4 1.0
ZN B:ZN3003 3.8 16.9 1.0
CA B:CYS1062 4.0 18.0 1.0
SG B:CYS1111 4.2 17.7 1.0
SG B:CYS1073 4.3 17.6 1.0
N B:ASN1106 4.5 13.0 1.0
N B:CYS1105 4.5 14.0 1.0
CA B:CYS1109 4.6 19.1 1.0
C B:TYR1061 4.6 21.8 1.0
C B:CYS1105 4.6 17.5 1.0
N B:CYS1075 4.6 15.9 1.0
CA B:CYS1075 4.7 15.2 1.0
SG B:CYS1068 4.7 17.7 1.0
C B:CYS1062 4.8 19.8 1.0
CA B:TYR1061 4.9 18.8 1.0
O B:CYS1062 4.9 21.7 1.0

Zinc binding site 6 out of 8 in 5vsf

Go back to Zinc Binding Sites List in 5vsf
Zinc binding site 6 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 17


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 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3003

b:16.9
occ:1.00
 SG B:CYS1115 2.3 17.1 1.0
SG B:CYS1111 2.3 17.7 1.0
SG B:CYS1105 2.3 16.6 1.0
SG B:CYS1068 2.3 17.7 1.0
CB B:CYS1105 3.2 15.9 1.0
CB B:CYS1111 3.2 18.5 1.0
CB B:CYS1115 3.2 18.4 1.0
CB B:CYS1068 3.3 16.9 1.0
ZN B:ZN3004 3.8 18.4 1.0
ZN B:ZN3002 3.8 17.9 1.0
SG B:CYS1062 4.0 17.9 1.0
NE B:ARG1118 4.3 19.2 1.0
NH2 B:ARG1118 4.4 18.0 1.0
CB B:ASN1117 4.6 15.5 1.0
CA B:CYS1111 4.6 19.4 1.0
CA B:CYS1105 4.6 15.7 1.0
CA B:CYS1115 4.7 18.2 1.0
CA B:CYS1068 4.7 17.2 1.0
CZ B:ARG1118 4.8 15.9 1.0
O B:TRP1112 4.8 19.1 1.0
N B:ASN1117 4.9 15.1 1.0
CB B:CYS1109 5.0 19.1 1.0

Zinc binding site 7 out of 8 in 5vsf

Go back to Zinc Binding Sites List in 5vsf
Zinc binding site 7 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 17


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 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3004

b:18.4
occ:1.00
 SG B:CYS1073 2.3 17.6 1.0
SG B:CYS1064 2.3 19.4 1.0
SG B:CYS1062 2.4 17.9 1.0
SG B:CYS1068 2.4 17.7 1.0
CB B:CYS1062 3.1 21.8 1.0
CB B:CYS1073 3.2 18.9 1.0
CB B:CYS1064 3.2 21.6 1.0
CB B:CYS1068 3.3 16.9 1.0
ZN B:ZN3003 3.8 16.9 1.0
ZN B:ZN3002 3.8 17.9 1.0
CA B:CYS1068 3.9 17.2 1.0
CA B:CYS1073 3.9 19.4 1.0
SG B:CYS1105 4.1 16.6 1.0
N B:CYS1064 4.4 21.0 1.0
CA B:CYS1064 4.4 23.6 1.0
O B:HOH3166 4.6 24.6 1.0
CA B:CYS1062 4.6 18.0 1.0
C B:CYS1073 4.7 19.4 1.0
O B:HOH3142 4.7 20.7 1.0
N B:CYS1068 4.8 21.3 1.0
SG B:CYS1111 4.8 17.7 1.0
N B:MET1074 4.8 19.0 1.0
CB B:CYS1111 4.8 18.5 1.0
C B:CYS1068 5.0 24.1 1.0
C B:CYS1062 5.0 19.8 1.0

Zinc binding site 8 out of 8 in 5vsf

Go back to Zinc Binding Sites List in 5vsf
Zinc binding site 8 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor 17


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 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3005

b:24.0
occ:1.00
 SG B:CYS1263 2.3 24.6 1.0
SG B:CYS1256 2.3 23.9 1.0
SG B:CYS1258 2.3 23.3 1.0
SG B:CYS1203 2.4 25.3 1.0
CB B:CYS1263 3.2 32.4 1.0
CB B:CYS1256 3.4 21.6 1.0
CB B:CYS1258 3.4 21.3 1.0
CB B:CYS1203 3.4 22.7 1.0
CA B:CYS1263 3.7 28.5 1.0
O B:HOH3241 4.0 26.3 1.0
N B:CYS1203 4.1 21.3 1.0
N B:CYS1258 4.1 24.7 1.0
NE2 B:HIS1201 4.3 18.2 1.0
CA B:CYS1258 4.3 24.2 1.0
N B:ARG1264 4.3 28.1 1.0
CA B:CYS1203 4.4 20.1 1.0
CD2 B:HIS1201 4.4 17.4 1.0
C B:CYS1263 4.5 27.5 1.0
N B:HIS1265 4.6 28.3 1.0
CA B:CYS1256 4.6 27.2 1.0
C B:CYS1256 4.7 24.7 1.0
N B:GLY1259 4.8 23.7 1.0
C B:CYS1258 4.9 24.0 1.0
N B:CYS1263 4.9 29.9 1.0
CB B:HIS1265 5.0 32.0 1.0
O B:CYS1256 5.0 25.6 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 13:22:08 2024

Last articles

Mg in 4PQ9
Mg in 4PMW
Mg in 4PPM
Mg in 4PJO
Mg in 4PM0
Mg in 4PL5
Mg in 4PLM
Mg in 4PKO
Mg in 4PKN
Mg in 4PL4
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy