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: Wed Dec 16 11:12:12 2020

Last articles

Zn in 2YRC
Zn in 2YQP
Zn in 2YR2
Zn in 2YQL
Zn in 2YPT
Zn in 2YPA
Zn in 2YPU
Zn in 2YNW
Zn in 2YNT
Zn in 2YNV
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy