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

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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

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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

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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

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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

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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

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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

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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

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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: Wed Dec 16 11:12:14 2020

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