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Zinc in PDB 5ttg: Crystal Structure of Catalytic Domain of Glp with MS012

Enzymatic activity of Crystal Structure of Catalytic Domain of Glp with MS012

All present enzymatic activity of Crystal Structure of Catalytic Domain of Glp with MS012:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of Catalytic Domain of Glp with MS012, PDB code: 5ttg was solved by A.Dong, H.Zeng, J.Liu, Y.Xiong, N.Babault, J.Jin, W.Tempel, C.Bountra, C.H.Arrowsmith, A.M.Edwards, H.Wu, P.J.Brown, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.429, 95.900, 102.113, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 19.2

Other elements in 5ttg:

The structure of Crystal Structure of Catalytic Domain of Glp with MS012 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Catalytic Domain of Glp with MS012 (pdb code 5ttg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Catalytic Domain of Glp with MS012, PDB code: 5ttg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5ttg

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Zinc binding site 1 out of 8 in the Crystal Structure of Catalytic Domain of Glp with MS012


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Catalytic Domain of Glp with MS012 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1303

b:15.4
occ:1.00
 SG A:CYS1109 2.3 13.8 1.0
SG A:CYS1075 2.3 15.2 1.0
SG A:CYS1105 2.4 13.5 1.0
SG A:CYS1062 2.4 14.4 1.0
CB A:CYS1062 3.3 15.1 1.0
CB A:CYS1105 3.3 13.7 1.0
CB A:CYS1109 3.3 14.8 1.0
CB A:CYS1075 3.5 14.8 1.0
CA A:CYS1105 3.6 13.1 1.0
N A:CYS1062 3.6 15.2 1.0
ZN A:ZN1304 3.8 14.0 1.0
ZN A:ZN1305 3.8 15.2 1.0
CA A:CYS1062 4.0 15.8 1.0
SG A:CYS1111 4.1 14.3 1.0
SG A:CYS1073 4.3 15.4 1.0
N A:ASN1106 4.5 13.2 1.0
N A:CYS1105 4.5 12.1 1.0
CA A:CYS1109 4.6 15.2 1.0
C A:TYR1061 4.6 16.0 1.0
N A:CYS1075 4.7 15.4 1.0
C A:CYS1105 4.7 13.8 1.0
CA A:CYS1075 4.7 14.8 1.0
SG A:CYS1068 4.7 15.7 1.0
C A:CYS1062 4.8 16.9 1.0
CA A:TYR1061 4.8 16.7 1.0
O A:CYS1062 4.9 17.1 1.0
O A:HOH1594 4.9 19.6 1.0

Zinc binding site 2 out of 8 in 5ttg

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Zinc binding site 2 out of 8 in the Crystal Structure of Catalytic Domain of Glp with MS012


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Catalytic Domain of Glp with MS012 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1304

b:14.0
occ:1.00
 SG A:CYS1111 2.3 14.3 1.0
SG A:CYS1105 2.3 13.5 1.0
SG A:CYS1068 2.3 15.7 1.0
SG A:CYS1115 2.3 14.1 1.0
CB A:CYS1105 3.2 13.7 1.0
CB A:CYS1111 3.2 15.2 1.0
CB A:CYS1115 3.2 13.7 1.0
CB A:CYS1068 3.3 15.7 1.0
ZN A:ZN1305 3.7 15.2 1.0
ZN A:ZN1303 3.8 15.4 1.0
SG A:CYS1062 4.0 14.4 1.0
NE A:ARG1118 4.4 16.0 1.0
NH2 A:ARG1118 4.4 17.1 1.0
CA A:CYS1105 4.6 13.1 1.0
CB A:ASN1117 4.6 13.0 1.0
CA A:CYS1111 4.7 15.8 1.0
CA A:CYS1115 4.7 14.4 1.0
CA A:CYS1068 4.7 17.2 1.0
O A:TRP1112 4.8 15.7 1.0
CZ A:ARG1118 4.8 16.3 1.0
N A:ASN1117 4.9 13.7 1.0
SG A:CYS1073 5.0 15.4 1.0
CB A:CYS1109 5.0 14.8 1.0

Zinc binding site 3 out of 8 in 5ttg

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Zinc binding site 3 out of 8 in the Crystal Structure of Catalytic Domain of Glp with MS012


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Catalytic Domain of Glp with MS012 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1305

b:15.2
occ:1.00
 SG A:CYS1073 2.3 15.4 1.0
SG A:CYS1064 2.3 15.9 1.0
SG A:CYS1068 2.3 15.7 1.0
SG A:CYS1062 2.3 14.4 1.0
CB A:CYS1062 3.1 15.1 1.0
CB A:CYS1068 3.2 15.7 1.0
CB A:CYS1073 3.2 16.8 1.0
CB A:CYS1064 3.3 18.4 1.0
ZN A:ZN1304 3.7 14.0 1.0
ZN A:ZN1303 3.8 15.4 1.0
CA A:CYS1068 3.9 17.2 1.0
CA A:CYS1073 3.9 17.3 1.0
SG A:CYS1105 4.1 13.5 1.0
N A:CYS1064 4.4 18.7 1.0
CA A:CYS1064 4.5 19.4 1.0
CA A:CYS1062 4.6 15.8 1.0
O A:HOH1481 4.6 21.8 1.0
SG A:CYS1111 4.7 14.3 1.0
C A:CYS1073 4.7 16.8 1.0
N A:CYS1068 4.8 17.2 1.0
O A:HOH1519 4.8 18.8 1.0
N A:MET1074 4.8 16.5 1.0
CB A:CYS1111 4.8 15.2 1.0
C A:CYS1062 5.0 16.9 1.0

Zinc binding site 4 out of 8 in 5ttg

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Zinc binding site 4 out of 8 in the Crystal Structure of Catalytic Domain of Glp with MS012


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Catalytic Domain of Glp with MS012 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1306

b:20.1
occ:1.00
 SG A:CYS1256 2.3 22.8 1.0
SG A:CYS1263 2.3 20.6 1.0
SG A:CYS1258 2.3 19.7 1.0
SG A:CYS1203 2.4 19.9 1.0
CB A:CYS1263 3.3 22.6 1.0
CB A:CYS1258 3.3 20.2 1.0
CB A:CYS1256 3.4 21.6 1.0
CB A:CYS1203 3.4 18.6 1.0
CA A:CYS1263 3.7 23.4 1.0
O A:HOH1589 4.0 22.7 1.0
N A:CYS1203 4.1 16.3 1.0
N A:CYS1258 4.1 21.6 1.0
NE2 A:HIS1201 4.2 15.8 1.0
CA A:CYS1258 4.2 20.6 1.0
N A:ARG1264 4.3 23.7 1.0
CD2 A:HIS1201 4.3 15.3 1.0
CA A:CYS1203 4.4 17.6 1.0
C A:CYS1263 4.4 24.3 1.0
CA A:CYS1256 4.6 22.3 1.0
N A:HIS1265 4.6 25.0 1.0
C A:CYS1256 4.7 23.3 1.0
N A:GLY1259 4.8 21.2 1.0
O A:CYS1256 4.8 25.1 1.0
C A:CYS1258 4.9 21.0 1.0
N A:CYS1263 5.0 24.3 1.0

Zinc binding site 5 out of 8 in 5ttg

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Zinc binding site 5 out of 8 in the Crystal Structure of Catalytic Domain of Glp with MS012


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Catalytic Domain of Glp with MS012 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1303

b:15.1
occ:1.00
 SG B:CYS1105 2.3 13.8 1.0
SG B:CYS1075 2.3 15.1 1.0
SG B:CYS1109 2.4 13.3 1.0
SG B:CYS1062 2.4 13.8 1.0
CB B:CYS1062 3.2 14.7 1.0
CB B:CYS1105 3.3 14.2 1.0
CB B:CYS1109 3.4 13.5 1.0
CB B:CYS1075 3.4 15.7 1.0
N B:CYS1062 3.6 15.2 1.0
CA B:CYS1105 3.6 14.3 1.0
ZN B:ZN1304 3.8 14.4 1.0
ZN B:ZN1305 3.8 14.5 1.0
CA B:CYS1062 4.0 14.9 1.0
SG B:CYS1111 4.1 14.2 1.0
SG B:CYS1073 4.4 13.8 1.0
N B:ASN1106 4.5 14.9 1.0
C B:TYR1061 4.5 17.2 1.0
N B:CYS1105 4.6 13.7 1.0
CA B:CYS1109 4.6 14.1 1.0
CA B:CYS1075 4.6 16.6 1.0
C B:CYS1105 4.7 14.6 1.0
SG B:CYS1068 4.7 14.0 1.0
N B:CYS1075 4.7 16.4 1.0
C B:CYS1062 4.8 15.7 1.0
CA B:TYR1061 4.8 17.5 1.0
O B:HOH1592 4.9 18.8 1.0
O B:CYS1062 4.9 15.5 1.0
ND2 B:ASN1117 5.0 14.0 1.0

Zinc binding site 6 out of 8 in 5ttg

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Zinc binding site 6 out of 8 in the Crystal Structure of Catalytic Domain of Glp with MS012


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Catalytic Domain of Glp with MS012 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1304

b:14.4
occ:1.00
 SG B:CYS1111 2.3 14.2 1.0
SG B:CYS1115 2.3 14.6 1.0
SG B:CYS1068 2.3 14.0 1.0
SG B:CYS1105 2.4 13.8 1.0
CB B:CYS1105 3.2 14.2 1.0
CB B:CYS1111 3.2 14.6 1.0
CB B:CYS1115 3.2 15.0 1.0
CB B:CYS1068 3.3 15.0 1.0
ZN B:ZN1305 3.8 14.5 1.0
ZN B:ZN1303 3.8 15.1 1.0
SG B:CYS1062 4.0 13.8 1.0
NH2 B:ARG1118 4.3 17.2 1.0
NE B:ARG1118 4.4 16.0 1.0
CB B:ASN1117 4.6 15.0 1.0
CA B:CYS1111 4.6 15.2 1.0
CA B:CYS1105 4.6 14.3 1.0
CA B:CYS1068 4.7 15.4 1.0
CA B:CYS1115 4.7 15.6 1.0
O B:TRP1112 4.7 15.7 1.0
CZ B:ARG1118 4.8 16.7 1.0
CB B:CYS1109 4.9 13.5 1.0
N B:ASN1117 5.0 15.4 1.0
N B:CYS1068 5.0 15.3 1.0

Zinc binding site 7 out of 8 in 5ttg

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Zinc binding site 7 out of 8 in the Crystal Structure of Catalytic Domain of Glp with MS012


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Catalytic Domain of Glp with MS012 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1305

b:14.5
occ:1.00
 SG B:CYS1064 2.3 13.8 1.0
SG B:CYS1073 2.3 13.8 1.0
SG B:CYS1068 2.3 14.0 1.0
SG B:CYS1062 2.4 13.8 1.0
CB B:CYS1064 3.2 14.9 1.0
CB B:CYS1062 3.2 14.7 1.0
CB B:CYS1073 3.3 15.2 1.0
CB B:CYS1068 3.3 15.0 1.0
ZN B:ZN1304 3.8 14.4 1.0
ZN B:ZN1303 3.8 15.1 1.0
CA B:CYS1068 3.9 15.4 1.0
CA B:CYS1073 3.9 16.4 1.0
SG B:CYS1105 4.1 13.8 1.0
N B:CYS1064 4.4 16.1 1.0
CA B:CYS1064 4.4 16.3 1.0
O B:HOH1615 4.6 19.5 1.0
O B:HOH1465 4.6 18.3 1.0
C B:CYS1073 4.6 16.9 1.0
CA B:CYS1062 4.6 14.9 1.0
N B:MET1074 4.7 17.6 1.0
N B:CYS1068 4.7 15.3 1.0
SG B:CYS1111 4.8 14.2 1.0
CB B:CYS1111 4.9 14.6 1.0
O B:HOH1503 4.9 26.3 1.0

Zinc binding site 8 out of 8 in 5ttg

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Zinc binding site 8 out of 8 in the Crystal Structure of Catalytic Domain of Glp with MS012


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Catalytic Domain of Glp with MS012 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1306

b:16.1
occ:1.00
 SG B:CYS1263 2.3 15.7 1.0
SG B:CYS1256 2.3 15.8 1.0
SG B:CYS1258 2.3 16.7 1.0
SG B:CYS1203 2.4 15.5 1.0
CB B:CYS1263 3.3 15.6 1.0
CB B:CYS1256 3.3 17.9 1.0
CB B:CYS1258 3.4 17.0 1.0
CB B:CYS1203 3.4 15.5 1.0
CA B:CYS1263 3.8 15.3 1.0
O B:HOH1579 4.0 18.9 1.0
N B:CYS1203 4.1 14.4 1.0
N B:CYS1258 4.1 18.4 1.0
NE2 B:HIS1201 4.2 14.6 1.0
CA B:CYS1258 4.3 17.8 1.0
N B:ARG1264 4.3 16.1 1.0
CD2 B:HIS1201 4.3 14.3 1.0
CA B:CYS1203 4.4 15.4 1.0
C B:CYS1263 4.5 15.5 1.0
N B:HIS1265 4.6 18.4 1.0
CA B:CYS1256 4.6 19.1 1.0
C B:CYS1256 4.7 19.5 1.0
N B:GLY1259 4.8 16.8 1.0
CB B:HIS1265 4.9 18.8 1.0
C B:CYS1258 4.9 16.9 1.0
O B:CYS1256 4.9 19.9 1.0

Reference:

Y.Xiong, F.Li, N.Babault, A.Dong, H.Zeng, H.Wu, X.Chen, C.H.Arrowsmith, P.J.Brown, J.Liu, M.Vedadi, J.Jin. Discovery of Potent and Selective Inhibitors For G9A-Like Protein (Glp) Lysine Methyltransferase. J. Med. Chem. V. 60 1876 2017.
ISSN: ISSN 1520-4804
PubMed: 28135087
DOI: 10.1021/ACS.JMEDCHEM.6B01645
Page generated: Mon Oct 28 08:48:18 2024

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