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Zinc in PDB 3mo0: Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11

Enzymatic activity of Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11

All present enzymatic activity of Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11:
2.1.1.43;

Protein crystallography data

The structure of Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11, PDB code: 3mo0 was solved by Y.Chang, J.R.Horton, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.55 / 2.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.300, 94.500, 138.200, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 30.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11 (pdb code 3mo0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11, PDB code: 3mo0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 3mo0

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Zinc binding site 1 out of 10 in the Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1236

b:35.7
occ:1.00
 SG A:CYS1031 2.3 39.0 1.0
SG A:CYS1078 2.4 36.4 1.0
SG A:CYS1074 2.4 35.7 1.0
SG A:CYS1044 2.6 28.2 1.0
CB A:CYS1031 3.1 41.6 1.0
CB A:CYS1074 3.2 30.3 1.0
CB A:CYS1078 3.2 36.5 1.0
CA A:CYS1074 3.5 31.6 1.0
N A:CYS1031 3.6 46.7 1.0
CB A:CYS1044 3.6 31.4 1.0
ZN A:ZN3 3.7 36.5 1.0
ZN A:ZN2 3.8 35.2 1.0
SG A:CYS1080 3.9 35.9 1.0
CA A:CYS1031 3.9 43.2 1.0
N A:CYS1074 4.4 30.2 1.0
SG A:CYS1042 4.4 38.0 1.0
C A:TYR1030 4.5 49.7 1.0
CA A:CYS1078 4.6 38.0 1.0
N A:ASN1075 4.6 32.3 1.0
C A:CYS1074 4.6 32.3 1.0
C A:CYS1031 4.7 41.5 1.0
CA A:TYR1030 4.8 53.0 1.0
SG A:CYS1037 4.8 38.6 1.0
N A:CYS1044 4.9 36.0 1.0
CA A:CYS1044 4.9 32.2 1.0
O A:CYS1031 4.9 40.9 1.0

Zinc binding site 2 out of 10 in 3mo0

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Zinc binding site 2 out of 10 in the Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:35.2
occ:1.00
 SG A:CYS1074 2.1 35.7 1.0
SG A:CYS1080 2.2 35.9 1.0
SG A:CYS1037 2.3 38.6 1.0
SG A:CYS1084 2.4 34.0 1.0
CB A:CYS1080 3.0 36.2 1.0
CB A:CYS1074 3.0 30.3 1.0
CB A:CYS1084 3.3 36.7 1.0
CB A:CYS1037 3.5 40.0 1.0
ZN A:ZN3 3.6 36.5 1.0
ZN A:ZN1236 3.8 35.7 1.0
SG A:CYS1031 4.0 39.0 1.0
NH1 A:ARG1087 4.3 31.6 1.0
NE A:ARG1087 4.4 30.1 1.0
CA A:CYS1080 4.4 36.2 1.0
CA A:CYS1074 4.4 31.6 1.0
CB A:ASN1086 4.6 34.2 1.0
CA A:CYS1084 4.7 38.9 1.0
CA A:CYS1037 4.8 42.6 1.0
CZ A:ARG1087 4.8 31.0 1.0
SG A:CYS1042 4.9 38.0 1.0
O A:TRP1081 4.9 36.2 1.0
N A:CYS1080 5.0 38.9 1.0
C A:CYS1080 5.0 35.6 1.0

Zinc binding site 3 out of 10 in 3mo0

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Zinc binding site 3 out of 10 in the Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:36.5
occ:1.00
 SG A:CYS1031 2.4 39.0 1.0
SG A:CYS1037 2.4 38.6 1.0
SG A:CYS1042 2.4 38.0 1.0
SG A:CYS1033 2.6 45.2 1.0
CB A:CYS1031 3.1 41.6 1.0
CB A:CYS1033 3.3 44.4 1.0
CB A:CYS1042 3.4 42.7 1.0
CB A:CYS1037 3.5 40.0 1.0
ZN A:ZN2 3.6 35.2 1.0
ZN A:ZN1236 3.7 35.7 1.0
SG A:CYS1074 3.8 35.7 1.0
CA A:CYS1042 3.9 42.6 1.0
CA A:CYS1037 4.2 42.6 1.0
N A:CYS1033 4.3 43.4 1.0
CA A:CYS1033 4.4 45.9 1.0
SG A:CYS1080 4.5 35.9 1.0
CA A:CYS1031 4.6 43.2 1.0
CB A:CYS1080 4.6 36.2 1.0
C A:CYS1042 4.8 39.3 1.0
N A:MET1043 4.8 36.4 1.0
C A:CYS1031 5.0 41.5 1.0
N A:VAL1032 5.0 39.9 1.0

Zinc binding site 4 out of 10 in 3mo0

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Zinc binding site 4 out of 10 in the Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4

b:70.2
occ:1.00
 SG A:CYS1225 2.6 89.8 1.0
SG A:CYS1172 2.7 57.4 1.0
CB A:CYS1227 2.7 86.3 1.0
SG A:CYS1232 2.8 94.2 1.0
CB A:CYS1172 3.3 54.5 1.0
SG A:CYS1227 3.3 86.8 1.0
CB A:CYS1232 3.4 91.3 1.0
N A:CYS1172 3.6 52.4 1.0
CA A:CYS1232 3.8 90.6 1.0
CA A:CYS1172 4.1 53.5 1.0
CA A:CYS1227 4.1 86.8 1.0
CB A:CYS1225 4.1 90.3 1.0
NE2 A:HIS1170 4.2 48.0 1.0
N A:CYS1227 4.4 87.4 1.0
CD2 A:HIS1170 4.4 47.3 1.0
N A:ARG1233 4.4 90.5 1.0
C A:HIS1171 4.7 51.2 1.0
C A:CYS1232 4.7 90.3 1.0
C A:CYS1227 4.8 87.0 1.0
CB A:SER1229 4.8 87.7 1.0
N A:GLY1228 4.9 87.6 1.0
O A:CYS1225 4.9 90.9 1.0
CA A:HIS1171 4.9 50.9 1.0
N A:CYS1232 4.9 90.1 1.0
N A:SER1229 5.0 88.2 1.0

Zinc binding site 5 out of 10 in 3mo0

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Zinc binding site 5 out of 10 in the Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn10

b:91.7
occ:1.00
 NE2 A:HIS1076 2.2 50.6 1.0
NE2 A:HIS1185 2.4 73.8 1.0
SG B:CYS1014 2.8 90.8 1.0
ND1 A:HIS1027 2.9 90.8 1.0
CE1 A:HIS1185 3.0 75.2 1.0
CE1 A:HIS1076 3.1 51.9 1.0
CD2 A:HIS1076 3.2 50.7 1.0
CE1 A:HIS1027 3.3 90.3 1.0
CB B:CYS1014 3.4 88.0 1.0
CD2 A:HIS1185 3.7 74.0 1.0
CG A:HIS1027 4.1 91.4 1.0
CA B:CYS1014 4.2 87.7 1.0
ND1 A:HIS1185 4.2 75.8 1.0
ND1 A:HIS1076 4.2 51.4 1.0
CG A:HIS1076 4.3 49.4 1.0
CG A:HIS1185 4.6 74.2 1.0
NE2 A:HIS1027 4.6 91.4 1.0
CB A:HIS1027 4.7 91.3 1.0
O B:ASN1013 4.9 80.3 1.0

Zinc binding site 6 out of 10 in 3mo0

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Zinc binding site 6 out of 10 in the Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn5

b:40.1
occ:1.00
 SG B:CYS1078 2.3 32.7 1.0
SG B:CYS1031 2.4 35.1 1.0
SG B:CYS1044 2.5 50.4 1.0
SG B:CYS1074 2.6 37.5 1.0
CB B:CYS1074 3.1 36.7 1.0
CB B:CYS1078 3.3 34.7 1.0
CB B:CYS1031 3.3 36.2 1.0
CA B:CYS1074 3.3 38.1 1.0
N B:CYS1031 3.4 38.3 1.0
CB B:CYS1044 3.5 58.0 1.0
ZN B:ZN7 3.7 35.4 1.0
ZN B:ZN6 3.9 37.3 1.0
CA B:CYS1031 3.9 37.2 1.0
SG B:CYS1080 4.1 36.2 1.0
N B:CYS1074 4.2 38.8 1.0
C B:TYR1030 4.3 42.6 1.0
C B:CYS1074 4.5 38.4 1.0
N B:ASN1075 4.5 38.3 1.0
CA B:CYS1078 4.5 33.9 1.0
CA B:TYR1030 4.5 46.9 1.0
SG B:CYS1042 4.7 47.1 1.0
C B:CYS1031 4.7 36.1 1.0
ND2 B:ASN1086 4.8 35.2 1.0
O B:CYS1031 4.8 36.5 1.0
O B:GLU1073 4.8 40.4 1.0
C B:GLU1073 4.9 39.9 1.0
CA B:CYS1044 4.9 59.2 1.0
SG B:CYS1037 4.9 37.2 1.0

Zinc binding site 7 out of 10 in 3mo0

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Zinc binding site 7 out of 10 in the Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn6

b:37.3
occ:1.00
 SG B:CYS1074 2.3 37.5 1.0
SG B:CYS1080 2.3 36.2 1.0
SG B:CYS1084 2.4 33.7 1.0
SG B:CYS1037 2.6 37.2 1.0
CB B:CYS1080 2.9 35.8 1.0
CB B:CYS1074 3.1 36.7 1.0
CB B:CYS1084 3.2 39.9 1.0
CB B:CYS1037 3.7 42.2 1.0
ZN B:ZN7 3.8 35.4 1.0
ZN B:ZN5 3.9 40.1 1.0
SG B:CYS1031 4.1 35.1 1.0
NE B:ARG1087 4.3 43.5 1.0
CA B:CYS1080 4.4 36.3 1.0
NH1 B:ARG1087 4.4 44.1 1.0
CA B:CYS1074 4.5 38.1 1.0
CB B:ASN1086 4.6 35.1 1.0
CA B:CYS1084 4.7 42.3 1.0
CZ B:ARG1087 4.7 44.0 1.0
O B:TRP1081 4.9 34.0 1.0
N B:CYS1080 4.9 34.2 1.0
CA B:CYS1037 4.9 45.2 1.0
N B:CYS1037 4.9 44.9 1.0
C B:ASP1036 5.0 46.8 1.0
O B:ASP1036 5.0 46.2 1.0
C B:CYS1080 5.0 36.8 1.0

Zinc binding site 8 out of 10 in 3mo0

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Zinc binding site 8 out of 10 in the Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn7

b:35.4
occ:1.00
 SG B:CYS1031 2.2 35.1 1.0
SG B:CYS1042 2.3 47.1 1.0
SG B:CYS1037 2.4 37.2 1.0
SG B:CYS1033 2.5 39.6 1.0
CB B:CYS1031 3.0 36.2 1.0
CB B:CYS1037 3.3 42.2 1.0
CB B:CYS1042 3.5 47.7 1.0
CB B:CYS1033 3.5 34.7 1.0
ZN B:ZN5 3.7 40.1 1.0
ZN B:ZN6 3.8 37.3 1.0
CA B:CYS1042 3.9 49.1 1.0
SG B:CYS1074 3.9 37.5 1.0
CA B:CYS1037 4.1 45.2 1.0
CA B:CYS1031 4.5 37.2 1.0
N B:CYS1033 4.5 32.9 1.0
C B:CYS1042 4.6 51.2 1.0
CA B:CYS1033 4.7 33.9 1.0
CB B:CYS1044 4.8 58.0 1.0
N B:MET1043 4.8 52.6 1.0
SG B:CYS1080 4.8 36.2 1.0
N B:CYS1037 4.9 44.9 1.0
CB B:CYS1080 4.9 35.8 1.0
C B:CYS1031 4.9 36.1 1.0
SG B:CYS1044 4.9 50.4 1.0

Zinc binding site 9 out of 10 in 3mo0

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Zinc binding site 9 out of 10 in the Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8

b:51.1
occ:1.00
 SG B:CYS1225 2.3 50.6 1.0
SG B:CYS1227 2.3 53.2 1.0
SG B:CYS1172 2.6 57.5 1.0
SG B:CYS1232 2.8 51.4 1.0
CB B:CYS1227 3.2 60.2 1.0
CB B:CYS1172 3.4 53.4 1.0
CB B:CYS1232 3.4 50.9 1.0
CA B:CYS1232 3.6 52.5 1.0
CB B:CYS1225 3.8 57.5 1.0
N B:CYS1172 3.9 52.3 1.0
N B:ARG1233 4.1 53.0 1.0
N B:CYS1227 4.2 61.2 1.0
CA B:CYS1227 4.2 61.2 1.0
CA B:CYS1172 4.3 52.3 1.0
CD2 B:HIS1170 4.4 45.8 1.0
C B:CYS1232 4.4 53.2 1.0
N B:GLY1228 4.4 64.7 1.0
NE2 B:HIS1170 4.5 45.9 1.0
C B:HIS1171 4.6 51.2 1.0
C B:CYS1227 4.7 63.2 1.0
N B:SER1229 4.8 64.5 1.0
N B:CYS1232 4.8 53.9 1.0
CA B:HIS1171 4.9 50.1 1.0
C B:CYS1225 4.9 58.7 1.0
O B:CYS1225 4.9 58.5 1.0
N B:HIS1234 4.9 58.3 1.0
CA B:CYS1225 5.0 57.8 1.0
CB B:SER1229 5.0 62.8 1.0

Zinc binding site 10 out of 10 in 3mo0

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Zinc binding site 10 out of 10 in the Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Human G9A-Like (Glp, Also Known As EHMT1) in Complex with Inhibitor E11 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn9

b:53.3
occ:1.00
 NE2 B:HIS1076 2.2 43.7 1.0
SG A:CYS1014 2.2 63.1 1.0
NE2 B:HIS1027 2.3 83.5 1.0
CE1 B:HIS1027 2.7 83.6 1.0
NE2 B:HIS1185 2.8 73.1 1.0
CE1 B:HIS1076 2.8 44.0 1.0
CB A:CYS1014 3.2 62.0 1.0
CE1 B:HIS1185 3.3 74.9 1.0
CD2 B:HIS1076 3.4 43.8 1.0
CD2 B:HIS1027 3.4 83.7 1.0
ND1 B:HIS1027 3.8 84.4 1.0
CD2 B:HIS1185 4.0 73.8 1.0
ND1 B:HIS1076 4.0 45.8 1.0
CA A:CYS1014 4.1 62.4 1.0
CG B:HIS1027 4.2 84.7 1.0
CG B:HIS1076 4.3 44.6 1.0
ND1 B:HIS1185 4.5 74.6 1.0
C A:CYS1014 4.8 64.2 1.0
CG B:HIS1185 4.8 74.4 1.0

Reference:

Y.Chang, T.Ganesh, J.R.Horton, A.Spannhoff, J.Liu, A.Sun, X.Zhang, M.T.Bedford, Y.Shinkai, J.P.Snyder, X.Cheng. Adding A Lysine Mimic in the Design of Potent Inhibitors of Histone Lysine Methyltransferases. J.Mol.Biol. V. 400 1 2010.
ISSN: ISSN 0022-2836
PubMed: 20434463
DOI: 10.1016/J.JMB.2010.04.048
Page generated: Wed Dec 16 04:35:48 2020

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