Zinc in PDB 6mbp: Glp Methyltransferase with Inhibitor EML741- P3121 Crystal Form

Enzymatic activity of Glp Methyltransferase with Inhibitor EML741- P3121 Crystal Form

All present enzymatic activity of Glp Methyltransferase with Inhibitor EML741- P3121 Crystal Form:
2.1.1.43;

Protein crystallography data

The structure of Glp Methyltransferase with Inhibitor EML741- P3121 Crystal Form, PDB code: 6mbp 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) 45.42 / 1.95
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 95.510, 95.510, 147.201, 90.00, 90.00, 120.00
R / Rfree (%) 16.1 / 18.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Glp Methyltransferase with Inhibitor EML741- P3121 Crystal Form (pdb code 6mbp). 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- P3121 Crystal Form, PDB code: 6mbp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6mbp

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Zinc binding site 1 out of 8 in the Glp Methyltransferase with Inhibitor EML741- P3121 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- P3121 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:24.9
occ:1.00
 SG A:CYS1080 2.3 24.0 1.0
SG A:CYS1084 2.3 25.3 1.0
SG A:CYS1074 2.3 25.4 1.0
SG A:CYS1037 2.4 21.9 1.0
CB A:CYS1080 3.2 21.9 1.0
CB A:CYS1074 3.2 22.0 1.0
CB A:CYS1084 3.3 25.3 1.0
CB A:CYS1037 3.3 21.8 1.0
ZN A:ZN2004 3.7 24.4 1.0
ZN A:ZN2003 3.8 26.0 1.0
SG A:CYS1031 4.0 25.1 1.0
NE A:ARG1087 4.3 26.9 1.0
NH1 A:ARG1087 4.3 27.5 1.0
CB A:ASN1086 4.6 25.1 1.0
CA A:CYS1080 4.6 24.8 1.0
CA A:CYS1074 4.7 26.8 1.0
CA A:CYS1037 4.7 23.2 1.0
CZ A:ARG1087 4.7 26.1 1.0
CA A:CYS1084 4.8 26.4 1.0
O A:TRP1081 4.8 21.8 1.0
N A:ASN1086 4.9 25.0 1.0
SG A:CYS1042 4.9 23.4 1.0
CB A:CYS1078 5.0 22.2 1.0

Zinc binding site 2 out of 8 in 6mbp

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Zinc binding site 2 out of 8 in the Glp Methyltransferase with Inhibitor EML741- P3121 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- P3121 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:26.0
occ:1.00
 SG A:CYS1044 2.2 25.1 1.0
SG A:CYS1078 2.4 24.8 1.0
SG A:CYS1074 2.4 25.4 1.0
SG A:CYS1031 2.5 25.1 1.0
CB A:CYS1074 3.2 22.0 1.0
CB A:CYS1031 3.2 23.9 1.0
CB A:CYS1078 3.3 22.2 1.0
CB A:CYS1044 3.5 25.6 1.0
N A:CYS1031 3.6 23.0 1.0
CA A:CYS1074 3.6 26.8 1.0
ZN A:ZN2002 3.8 24.9 1.0
ZN A:ZN2004 3.8 24.4 1.0
CA A:CYS1031 4.0 28.8 1.0
SG A:CYS1080 4.1 24.0 1.0
SG A:CYS1042 4.3 23.4 1.0
N A:CYS1074 4.5 22.7 1.0
C A:TYR1030 4.6 24.5 1.0
N A:ASN1075 4.6 21.4 1.0
CA A:CYS1078 4.6 24.9 1.0
N A:CYS1044 4.7 24.6 1.0
C A:CYS1074 4.7 27.3 1.0
CA A:CYS1044 4.7 25.4 1.0
SG A:CYS1037 4.7 21.9 1.0
C A:CYS1031 4.8 27.2 1.0
CA A:TYR1030 4.8 24.0 1.0
O A:CYS1031 4.8 21.7 1.0
O A:HOH2192 4.9 29.0 1.0

Zinc binding site 3 out of 8 in 6mbp

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Zinc binding site 3 out of 8 in the Glp Methyltransferase with Inhibitor EML741- P3121 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- P3121 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2004

b:24.4
occ:1.00
 SG A:CYS1042 2.2 23.4 1.0
SG A:CYS1037 2.3 21.9 1.0
SG A:CYS1031 2.3 25.1 1.0
SG A:CYS1033 2.4 22.2 1.0
CB A:CYS1031 3.1 23.9 1.0
CB A:CYS1042 3.2 21.1 1.0
CB A:CYS1033 3.2 26.7 1.0
CB A:CYS1037 3.3 21.8 1.0
ZN A:ZN2002 3.7 24.9 1.0
ZN A:ZN2003 3.8 26.0 1.0
CA A:CYS1042 3.9 23.7 1.0
CA A:CYS1037 3.9 23.2 1.0
SG A:CYS1074 4.1 25.4 1.0
N A:CYS1033 4.4 23.2 1.0
CA A:CYS1033 4.4 28.8 1.0
CA A:CYS1031 4.6 28.8 1.0
O A:HOH2108 4.6 24.8 1.0
C A:CYS1042 4.7 23.8 1.0
SG A:CYS1080 4.7 24.0 1.0
N A:MET1043 4.7 27.2 1.0
O A:HOH2166 4.8 38.6 1.0
N A:CYS1037 4.8 24.3 1.0
CB A:CYS1080 4.9 21.9 1.0
SG A:CYS1044 5.0 25.1 1.0
C A:CYS1031 5.0 27.2 1.0
C A:CYS1037 5.0 29.1 1.0

Zinc binding site 4 out of 8 in 6mbp

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Zinc binding site 4 out of 8 in the Glp Methyltransferase with Inhibitor EML741- P3121 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- P3121 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2005

b:34.1
occ:1.00
 SG A:CYS1225 2.3 31.3 1.0
SG A:CYS1172 2.3 39.0 1.0
SG A:CYS1227 2.4 33.1 1.0
SG A:CYS1232 2.4 37.6 1.0
CB A:CYS1232 3.2 38.4 1.0
CB A:CYS1225 3.3 32.2 1.0
CB A:CYS1227 3.3 30.5 1.0
CB A:CYS1172 3.4 35.4 1.0
CA A:CYS1232 3.7 45.0 1.0
O A:HOH2233 4.0 38.7 1.0
N A:CYS1227 4.1 35.0 1.0
N A:CYS1172 4.1 29.9 1.0
CA A:CYS1227 4.3 34.1 1.0
NE2 A:HIS1170 4.3 30.6 1.0
N A:ARG1233 4.3 41.8 1.0
CA A:CYS1172 4.4 36.1 1.0
CD2 A:HIS1170 4.4 28.0 1.0
C A:CYS1232 4.4 46.1 1.0
CA A:CYS1225 4.6 33.4 1.0
N A:HIS1234 4.6 40.2 1.0
C A:CYS1225 4.6 37.0 1.0
O A:CYS1225 4.8 37.5 1.0
N A:GLY1228 4.9 37.8 1.0
C A:CYS1227 4.9 36.0 1.0
N A:CYS1232 5.0 49.5 1.0

Zinc binding site 5 out of 8 in 6mbp

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Zinc binding site 5 out of 8 in the Glp Methyltransferase with Inhibitor EML741- P3121 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- P3121 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1302

b:24.9
occ:1.00
 SG B:CYS1037 2.3 22.9 1.0
SG B:CYS1042 2.3 24.7 1.0
SG B:CYS1031 2.4 24.2 1.0
SG B:CYS1033 2.4 26.8 1.0
CB B:CYS1031 3.1 27.8 1.0
CB B:CYS1042 3.2 24.0 1.0
CB B:CYS1037 3.3 23.1 1.0
CB B:CYS1033 3.3 29.6 1.0
ZN B:ZN1303 3.8 23.7 1.0
ZN B:ZN1304 3.8 24.4 1.0
CA B:CYS1037 3.9 23.2 1.0
CA B:CYS1042 3.9 26.4 1.0
SG B:CYS1074 4.1 22.5 1.0
N B:CYS1033 4.4 24.7 1.0
CA B:CYS1033 4.5 31.3 1.0
O B:HOH1412 4.6 28.2 1.0
CA B:CYS1031 4.6 24.7 1.0
SG B:CYS1080 4.7 24.6 1.0
C B:CYS1042 4.7 27.0 1.0
N B:CYS1037 4.8 25.9 1.0
O B:HOH1436 4.8 28.3 1.0
CB B:CYS1080 4.8 20.8 1.0
N B:MET1043 4.9 26.3 1.0
C B:CYS1037 5.0 25.9 1.0
C B:CYS1031 5.0 27.0 1.0

Zinc binding site 6 out of 8 in 6mbp

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Zinc binding site 6 out of 8 in the Glp Methyltransferase with Inhibitor EML741- P3121 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- P3121 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1303

b:23.7
occ:1.00
 SG B:CYS1080 2.3 24.6 1.0
SG B:CYS1084 2.3 22.5 1.0
SG B:CYS1037 2.3 22.9 1.0
SG B:CYS1074 2.4 22.5 1.0
CB B:CYS1080 3.2 20.8 1.0
CB B:CYS1074 3.2 22.6 1.0
CB B:CYS1084 3.2 23.3 1.0
CB B:CYS1037 3.4 23.1 1.0
ZN B:ZN1302 3.8 24.9 1.0
ZN B:ZN1304 3.8 24.4 1.0
SG B:CYS1031 4.0 24.2 1.0
NE B:ARG1087 4.3 23.6 1.0
NH2 B:ARG1087 4.4 26.0 1.0
CB B:ASN1086 4.6 23.3 1.0
CA B:CYS1080 4.7 25.8 1.0
CA B:CYS1074 4.7 24.5 1.0
CA B:CYS1084 4.7 25.1 1.0
CZ B:ARG1087 4.7 25.7 1.0
CA B:CYS1037 4.8 23.2 1.0
O B:TRP1081 4.8 24.2 1.0
N B:ASN1086 4.9 24.4 1.0

Zinc binding site 7 out of 8 in 6mbp

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Zinc binding site 7 out of 8 in the Glp Methyltransferase with Inhibitor EML741- P3121 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- P3121 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1304

b:24.4
occ:1.00
 SG B:CYS1074 2.3 22.5 1.0
SG B:CYS1044 2.3 23.7 1.0
SG B:CYS1078 2.4 22.9 1.0
SG B:CYS1031 2.5 24.2 1.0
CB B:CYS1074 3.2 22.6 1.0
CB B:CYS1031 3.3 27.8 1.0
CB B:CYS1078 3.3 20.6 1.0
CB B:CYS1044 3.5 20.9 1.0
CA B:CYS1074 3.6 24.5 1.0
N B:CYS1031 3.6 24.3 1.0
ZN B:ZN1303 3.8 23.7 1.0
ZN B:ZN1302 3.8 24.9 1.0
CA B:CYS1031 4.0 24.7 1.0
SG B:CYS1080 4.1 24.6 1.0
SG B:CYS1042 4.3 24.7 1.0
N B:CYS1074 4.6 20.5 1.0
N B:ASN1075 4.6 23.1 1.0
CA B:CYS1078 4.6 22.0 1.0
C B:TYR1030 4.6 25.8 1.0
SG B:CYS1037 4.6 22.9 1.0
C B:CYS1074 4.7 22.6 1.0
N B:CYS1044 4.7 19.1 1.0
CA B:CYS1044 4.7 18.4 1.0
CA B:TYR1030 4.8 23.8 1.0
C B:CYS1031 4.8 27.0 1.0
O B:HOH1501 4.9 32.2 1.0
O B:CYS1031 4.9 23.9 1.0
ND2 B:ASN1086 5.0 24.2 1.0

Zinc binding site 8 out of 8 in 6mbp

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Zinc binding site 8 out of 8 in the Glp Methyltransferase with Inhibitor EML741- P3121 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- P3121 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1305

b:54.9
occ:1.00
 SG B:CYS1227 2.2 52.0 1.0
SG B:CYS1225 2.3 56.0 1.0
SG B:CYS1172 2.4 53.1 1.0
SG B:CYS1232 2.4 60.7 1.0
CB B:CYS1232 3.2 62.8 1.0
CB B:CYS1225 3.3 65.5 1.0
CB B:CYS1227 3.4 47.9 1.0
CB B:CYS1172 3.5 52.0 1.0
CA B:CYS1232 3.7 65.4 1.0
NE2 B:HIS1170 4.1 47.9 1.0
N B:CYS1227 4.1 59.2 1.0
N B:CYS1172 4.1 51.7 1.0
N B:ARG1233 4.2 67.2 1.0
CD2 B:HIS1170 4.3 49.4 1.0
CA B:CYS1227 4.4 55.0 1.0
CA B:CYS1172 4.4 52.5 1.0
C B:CYS1232 4.4 67.7 1.0
CA B:CYS1225 4.6 65.4 1.0
N B:HIS1234 4.6 69.2 1.0
C B:CYS1225 4.7 65.2 1.0
N B:ARG1226 5.0 62.9 1.0
N B:CYS1232 5.0 71.2 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 12:19:10 2020

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