Zinc in PDB 6mbo: Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form

Enzymatic activity of Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form

All present enzymatic activity of Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form:
2.1.1.43;

Protein crystallography data

The structure of Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form, PDB code: 6mbo was solved by J.R.Horton, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.05 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.732, 88.306, 95.124, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 19.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form (pdb code 6mbo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form, PDB code: 6mbo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6mbo

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Zinc binding site 1 out of 8 in the Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1303

b:16.1
occ:1.00
SG A:CYS1080 2.3 14.7 1.0
SG A:CYS1037 2.3 14.5 1.0
SG A:CYS1074 2.3 14.1 1.0
SG A:CYS1084 2.3 16.3 1.0
CB A:CYS1074 3.2 17.4 1.0
CB A:CYS1080 3.2 18.5 1.0
CB A:CYS1084 3.2 17.7 1.0
CB A:CYS1037 3.3 17.9 1.0
ZN A:ZN1305 3.8 19.0 1.0
ZN A:ZN1304 3.8 21.6 1.0
SG A:CYS1031 4.0 14.3 1.0
NE A:ARG1087 4.3 14.5 1.0
NH1 A:ARG1087 4.3 18.4 1.0
CB A:ASN1086 4.5 16.3 1.0
CA A:CYS1080 4.6 21.1 1.0
CA A:CYS1074 4.6 10.0 1.0
CA A:CYS1037 4.7 15.9 1.0
CA A:CYS1084 4.7 15.9 1.0
CZ A:ARG1087 4.7 14.5 1.0
O A:TRP1081 4.8 15.0 1.0
N A:ASN1086 4.9 17.0 1.0
CB A:CYS1078 5.0 14.2 1.0

Zinc binding site 2 out of 8 in 6mbo

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Zinc binding site 2 out of 8 in the Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1304

b:21.6
occ:1.00
SG A:CYS1044 2.3 16.4 1.0
SG A:CYS1078 2.3 14.1 1.0
SG A:CYS1074 2.4 14.1 1.0
SG A:CYS1031 2.4 14.3 1.0
CB A:CYS1074 3.2 17.4 1.0
CB A:CYS1031 3.3 12.7 1.0
CB A:CYS1078 3.3 14.2 1.0
CB A:CYS1044 3.5 17.3 1.0
CA A:CYS1074 3.6 10.0 1.0
N A:CYS1031 3.6 14.9 1.0
ZN A:ZN1303 3.8 16.1 1.0
ZN A:ZN1305 3.8 19.0 1.0
CA A:CYS1031 4.0 14.9 1.0
SG A:CYS1080 4.1 14.7 1.0
SG A:CYS1042 4.3 16.7 1.0
N A:CYS1074 4.5 11.7 1.0
N A:ASN1075 4.6 12.0 1.0
C A:TYR1030 4.6 16.0 1.0
CA A:CYS1078 4.6 13.4 1.0
SG A:CYS1037 4.6 14.5 1.0
C A:CYS1074 4.6 11.4 1.0
N A:CYS1044 4.7 15.3 1.0
CA A:CYS1044 4.7 15.8 1.0
C A:CYS1031 4.8 19.1 1.0
O A:CYS1031 4.8 15.2 1.0
CA A:TYR1030 4.8 16.5 1.0
O A:HOH1601 4.9 19.5 1.0

Zinc binding site 3 out of 8 in 6mbo

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Zinc binding site 3 out of 8 in the Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1305

b:19.0
occ:1.00
SG A:CYS1037 2.3 14.5 1.0
SG A:CYS1033 2.3 15.2 1.0
SG A:CYS1042 2.3 16.7 1.0
SG A:CYS1031 2.4 14.3 1.0
CB A:CYS1031 3.1 12.7 1.0
CB A:CYS1037 3.2 17.9 1.0
CB A:CYS1033 3.2 18.2 1.0
CB A:CYS1042 3.3 18.7 1.0
ZN A:ZN1303 3.8 16.1 1.0
ZN A:ZN1304 3.8 21.6 1.0
CA A:CYS1037 3.9 15.9 1.0
CA A:CYS1042 4.0 15.9 1.0
SG A:CYS1074 4.1 14.1 1.0
N A:CYS1033 4.4 17.7 1.0
CA A:CYS1033 4.4 17.6 1.0
O A:HOH1464 4.5 20.2 1.0
CA A:CYS1031 4.5 14.9 1.0
O A:HOH1514 4.7 24.3 1.0
SG A:CYS1080 4.7 14.7 1.0
N A:CYS1037 4.7 18.7 1.0
C A:CYS1042 4.8 17.0 1.0
N A:MET1043 4.8 20.2 1.0
CB A:CYS1080 4.8 18.5 1.0
C A:CYS1031 4.9 19.1 1.0
C A:CYS1037 5.0 23.2 1.0

Zinc binding site 4 out of 8 in 6mbo

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Zinc binding site 4 out of 8 in the Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1306

b:16.4
occ:1.00
SG A:CYS1225 2.3 15.5 1.0
SG A:CYS1227 2.3 19.8 1.0
SG A:CYS1232 2.3 17.2 1.0
SG A:CYS1172 2.3 18.0 1.0
CB A:CYS1232 3.3 20.3 1.0
CB A:CYS1225 3.3 15.4 1.0
CB A:CYS1227 3.4 16.9 1.0
CB A:CYS1172 3.4 16.6 1.0
CA A:CYS1232 3.8 21.9 1.0
N A:CYS1172 4.1 15.4 1.0
O A:HOH1580 4.1 19.6 1.0
N A:CYS1227 4.1 17.5 1.0
N A:ARG1233 4.2 20.3 1.0
NE2 A:HIS1170 4.3 14.6 1.0
CA A:CYS1227 4.3 17.6 1.0
CA A:CYS1172 4.4 14.6 1.0
CD2 A:HIS1170 4.4 13.1 1.0
C A:CYS1232 4.5 20.9 1.0
CA A:CYS1225 4.6 14.1 1.0
N A:HIS1234 4.6 18.7 1.0
C A:CYS1225 4.6 14.5 1.0
O A:CYS1225 4.9 16.4 1.0
N A:GLY1228 4.9 18.1 1.0
C A:CYS1227 5.0 18.7 1.0
N A:CYS1232 5.0 21.3 1.0
CB A:HIS1234 5.0 16.0 1.0

Zinc binding site 5 out of 8 in 6mbo

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Zinc binding site 5 out of 8 in the Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1303

b:19.2
occ:1.00
SG B:CYS1037 2.3 18.1 1.0
SG B:CYS1033 2.3 21.1 1.0
SG B:CYS1042 2.3 19.2 1.0
SG B:CYS1031 2.4 17.1 1.0
CB B:CYS1031 3.0 21.9 1.0
CB B:CYS1037 3.2 19.7 1.0
CB B:CYS1033 3.2 23.0 1.0
CB B:CYS1042 3.3 21.0 1.0
ZN B:ZN1304 3.8 16.9 1.0
ZN B:ZN1305 3.8 16.8 1.0
CA B:CYS1037 3.8 20.2 1.0
CA B:CYS1042 3.9 21.9 1.0
SG B:CYS1074 4.1 15.2 1.0
N B:CYS1033 4.4 26.1 1.0
CA B:CYS1033 4.4 27.7 1.0
CA B:CYS1031 4.5 19.7 1.0
O B:HOH1460 4.6 25.1 1.0
N B:CYS1037 4.7 24.1 1.0
C B:CYS1042 4.7 22.1 1.0
SG B:CYS1080 4.8 16.3 1.0
N B:MET1043 4.8 19.5 1.0
O B:HOH1507 4.8 21.4 1.0
C B:CYS1031 4.9 22.2 1.0
C B:CYS1037 4.9 21.2 1.0
CB B:CYS1080 4.9 18.4 1.0

Zinc binding site 6 out of 8 in 6mbo

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Zinc binding site 6 out of 8 in the Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1304

b:16.9
occ:1.00
SG B:CYS1080 2.3 16.3 1.0
SG B:CYS1074 2.3 15.2 1.0
SG B:CYS1037 2.3 18.1 1.0
SG B:CYS1084 2.3 16.7 1.0
CB B:CYS1074 3.2 13.0 1.0
CB B:CYS1080 3.2 18.4 1.0
CB B:CYS1084 3.2 18.1 1.0
CB B:CYS1037 3.3 19.7 1.0
ZN B:ZN1303 3.8 19.2 1.0
ZN B:ZN1305 3.8 16.8 1.0
SG B:CYS1031 4.0 17.1 1.0
NE B:ARG1087 4.4 17.0 1.0
NH2 B:ARG1087 4.4 19.3 1.0
CB B:ASN1086 4.6 14.9 1.0
CA B:CYS1074 4.6 13.1 1.0
CA B:CYS1080 4.6 17.2 1.0
CA B:CYS1084 4.7 16.8 1.0
CA B:CYS1037 4.7 20.2 1.0
CZ B:ARG1087 4.8 19.2 1.0
O B:TRP1081 4.9 18.0 1.0
N B:ASN1086 4.9 16.0 1.0
CB B:CYS1078 5.0 13.9 1.0

Zinc binding site 7 out of 8 in 6mbo

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Zinc binding site 7 out of 8 in the Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1305

b:16.8
occ:1.00
SG B:CYS1044 2.3 19.8 1.0
SG B:CYS1078 2.3 14.6 1.0
SG B:CYS1031 2.3 17.1 1.0
SG B:CYS1074 2.4 15.2 1.0
CB B:CYS1074 3.2 13.0 1.0
CB B:CYS1031 3.2 21.9 1.0
CB B:CYS1078 3.3 13.9 1.0
CB B:CYS1044 3.5 16.4 1.0
CA B:CYS1074 3.6 13.1 1.0
N B:CYS1031 3.6 17.6 1.0
ZN B:ZN1303 3.8 19.2 1.0
ZN B:ZN1304 3.8 16.9 1.0
CA B:CYS1031 4.0 19.7 1.0
SG B:CYS1080 4.2 16.3 1.0
SG B:CYS1042 4.3 19.2 1.0
N B:CYS1074 4.5 14.7 1.0
N B:ASN1075 4.6 14.4 1.0
C B:TYR1030 4.6 19.2 1.0
CA B:CYS1078 4.6 15.7 1.0
N B:CYS1044 4.6 16.3 1.0
SG B:CYS1037 4.6 18.1 1.0
C B:CYS1074 4.7 13.6 1.0
CA B:CYS1044 4.7 14.8 1.0
CA B:TYR1030 4.8 19.1 1.0
C B:CYS1031 4.8 22.2 1.0
O B:CYS1031 4.8 19.0 1.0
O B:HOH1590 4.9 18.3 1.0

Zinc binding site 8 out of 8 in 6mbo

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Zinc binding site 8 out of 8 in the Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Glp Methyltransferase with Inhibitor EML741-P212121 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1306

b:21.2
occ:1.00
SG B:CYS1232 2.3 21.7 1.0
SG B:CYS1225 2.3 20.1 1.0
SG B:CYS1227 2.3 19.2 1.0
SG B:CYS1172 2.3 21.2 1.0
CB B:CYS1232 3.3 24.2 1.0
CB B:CYS1225 3.3 21.4 1.0
CB B:CYS1227 3.4 22.9 1.0
CB B:CYS1172 3.5 24.3 1.0
CA B:CYS1232 3.7 23.4 1.0
O B:HOH1517 4.0 22.1 1.0
N B:CYS1172 4.0 16.0 1.0
N B:CYS1227 4.1 21.7 1.0
CA B:CYS1227 4.3 23.0 1.0
N B:ARG1233 4.3 24.6 1.0
NE2 B:HIS1170 4.3 20.1 1.0
CA B:CYS1172 4.4 19.5 1.0
CD2 B:HIS1170 4.4 16.7 1.0
C B:CYS1232 4.5 25.1 1.0
CA B:CYS1225 4.6 22.1 1.0
C B:CYS1225 4.6 23.3 1.0
N B:HIS1234 4.7 23.4 1.0
O B:CYS1225 4.8 29.4 1.0
N B:GLY1228 4.9 20.7 1.0
C B:CYS1227 4.9 21.6 1.0
N B:CYS1232 4.9 25.3 1.0

Reference:

C.Milite, A.Feoli, J.R.Horton, D.Rescigno, A.Cipriano, V.Pisapia, M.Viviano, G.Pepe, G.Amendola, E.Novellino, S.Cosconati, X.Cheng, S.Castellano, G.Sbardella. Discovery of A Novel Chemotype of Histone Lysine Methyltransferase EHMT1/2 (Glp/G9A) Inhibitors: Rational Design, Synthesis, Biological Evaluation, and Co-Crystal Structure. J. Med. Chem. V. 62 2666 2019.
ISSN: ISSN 1520-4804
PubMed: 30753076
DOI: 10.1021/ACS.JMEDCHEM.8B02008
Page generated: Wed Dec 16 12:19:08 2020

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