Atomistry » Zinc » PDB 6mbo-6mlc » 6mbp
Atomistry »
  Zinc »
    PDB 6mbo-6mlc »
      6mbp »

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

Go back to Zinc Binding Sites List in 6mbp
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

Go back to Zinc Binding Sites List in 6mbp
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

Go back to Zinc Binding Sites List in 6mbp
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

Go back to Zinc Binding Sites List in 6mbp
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

Go back to Zinc Binding Sites List in 6mbp
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

Go back to Zinc Binding Sites List in 6mbp
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

Go back to Zinc Binding Sites List in 6mbp
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

Go back to Zinc Binding Sites List in 6mbp
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: Tue Oct 29 03:03:16 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy