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Zinc in PDB 3fpd: G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294

Enzymatic activity of G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294

All present enzymatic activity of G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294:
2.1.1.43;

Protein crystallography data

The structure of G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294, PDB code: 3fpd was solved by Y.Chang, X.Zhang, J.R.Horton, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.26 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.300, 95.200, 101.700, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 26.2

Zinc Binding Sites:

The binding sites of Zinc atom in the G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294 (pdb code 3fpd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294, PDB code: 3fpd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3fpd

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Zinc binding site 1 out of 8 in the G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1236

b:30.4
occ:1.00
 SG A:CYS1074 2.4 26.8 1.0
SG A:CYS1031 2.4 31.6 1.0
SG A:CYS1044 2.5 30.6 1.0
SG A:CYS1078 2.5 29.6 1.0
CB A:CYS1074 3.2 22.7 1.0
CB A:CYS1031 3.2 29.1 1.0
CB A:CYS1078 3.3 24.8 1.0
CB A:CYS1044 3.4 30.5 1.0
CA A:CYS1074 3.5 24.8 1.0
ZN A:ZN3 3.7 30.2 1.0
ZN A:ZN2 3.7 29.1 1.0
N A:CYS1031 3.7 29.0 1.0
SG A:CYS1080 4.0 31.6 1.0
CA A:CYS1031 4.0 29.7 1.0
SG A:CYS1042 4.3 27.2 1.0
N A:CYS1074 4.5 22.9 1.0
N A:ASN1075 4.5 26.1 1.0
C A:CYS1074 4.6 25.8 1.0
CA A:CYS1078 4.6 25.9 1.0
CA A:CYS1044 4.7 30.7 1.0
N A:CYS1044 4.7 31.0 1.0
SG A:CYS1037 4.8 36.1 1.0
O A:CYS1031 4.8 31.6 1.0
C A:CYS1031 4.8 31.7 1.0
C A:TYR1030 4.8 29.5 1.0
ND2 A:ASN1086 4.9 31.0 1.0

Zinc binding site 2 out of 8 in 3fpd

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Zinc binding site 2 out of 8 in the G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:29.1
occ:1.00
 SG A:CYS1074 2.3 26.8 1.0
SG A:CYS1037 2.3 36.1 1.0
SG A:CYS1084 2.3 22.1 1.0
SG A:CYS1080 2.4 31.6 1.0
CB A:CYS1080 3.0 25.9 1.0
CB A:CYS1084 3.2 24.5 1.0
CB A:CYS1074 3.2 22.7 1.0
CB A:CYS1037 3.5 36.9 1.0
ZN A:ZN3 3.6 30.2 1.0
ZN A:ZN1236 3.7 30.4 1.0
SG A:CYS1031 4.0 31.6 1.0
NH1 A:ARG1087 4.4 18.2 1.0
NE A:ARG1087 4.5 25.4 1.0
CA A:CYS1080 4.5 24.8 1.0
CB A:ASN1086 4.6 30.3 1.0
CA A:CYS1084 4.6 25.5 1.0
CA A:CYS1074 4.7 24.8 1.0
CZ A:ARG1087 4.7 23.8 1.0
CA A:CYS1037 4.9 37.5 1.0
O A:TRP1081 4.9 24.4 1.0
N A:ASN1086 4.9 31.2 1.0
CB A:CYS1078 4.9 24.8 1.0

Zinc binding site 3 out of 8 in 3fpd

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Zinc binding site 3 out of 8 in the G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:30.2
occ:1.00
 SG A:CYS1037 2.4 36.1 1.0
SG A:CYS1031 2.4 31.6 1.0
SG A:CYS1033 2.5 30.6 1.0
SG A:CYS1042 2.5 27.2 1.0
CB A:CYS1031 3.1 29.1 1.0
CB A:CYS1042 3.3 28.1 1.0
CB A:CYS1037 3.3 36.9 1.0
CB A:CYS1033 3.3 33.0 1.0
ZN A:ZN2 3.6 29.1 1.0
ZN A:ZN1236 3.7 30.4 1.0
SG A:CYS1074 3.9 26.8 1.0
CA A:CYS1042 4.0 29.3 1.0
CA A:CYS1037 4.0 37.5 1.0
N A:CYS1033 4.5 32.9 1.0
CA A:CYS1033 4.5 34.4 1.0
CA A:CYS1031 4.6 29.7 1.0
O A:HOH77 4.6 26.5 1.0
CB A:CYS1080 4.8 25.9 1.0
SG A:CYS1080 4.8 31.6 1.0
C A:CYS1042 4.8 29.3 1.0
N A:CYS1037 4.8 35.8 1.0
O A:HOH15 4.9 34.4 1.0
N A:MET1043 5.0 29.3 1.0
C A:CYS1031 5.0 31.7 1.0

Zinc binding site 4 out of 8 in 3fpd

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Zinc binding site 4 out of 8 in the G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4

b:48.6
occ:1.00
 SG A:CYS1225 2.4 49.9 1.0
SG A:CYS1172 2.7 47.4 1.0
SG A:CYS1227 2.7 57.8 1.0
SG A:CYS1232 2.7 60.6 1.0
CB A:CYS1227 2.7 56.8 1.0
CB A:CYS1232 3.5 58.9 1.0
CB A:CYS1225 3.7 55.6 1.0
CB A:CYS1172 3.8 42.6 1.0
CA A:CYS1232 3.9 59.0 1.0
CA A:CYS1227 4.0 57.8 1.0
N A:CYS1172 4.0 43.5 1.0
CE1 A:HIS1170 4.1 42.4 1.0
N A:CYS1227 4.2 59.0 1.0
N A:ARG1233 4.3 58.4 1.0
ND1 A:HIS1170 4.4 42.8 1.0
CA A:CYS1172 4.5 42.5 1.0
C A:CYS1227 4.6 57.7 1.0
N A:GLY1228 4.6 58.9 1.0
O A:CYS1225 4.6 55.6 1.0
C A:CYS1232 4.7 59.0 1.0
CB A:SER1229 4.7 58.8 1.0
N A:HIS1234 4.7 60.0 1.0
N A:SER1229 4.8 59.6 1.0
C A:CYS1225 4.8 56.8 1.0
CA A:CYS1225 4.9 56.2 1.0
C A:HIS1171 5.0 44.2 1.0

Zinc binding site 5 out of 8 in 3fpd

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Zinc binding site 5 out of 8 in the G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn5

b:28.6
occ:1.00
 SG B:CYS1074 2.4 27.7 1.0
SG B:CYS1031 2.4 23.4 1.0
SG B:CYS1078 2.4 23.4 1.0
SG B:CYS1044 2.5 28.7 1.0
CB B:CYS1074 3.0 24.5 1.0
CB B:CYS1078 3.2 24.4 1.0
CB B:CYS1031 3.3 26.0 1.0
CB B:CYS1044 3.4 30.7 1.0
CA B:CYS1074 3.5 24.4 1.0
ZN B:ZN7 3.6 27.0 1.0
N B:CYS1031 3.6 28.7 1.0
ZN B:ZN6 3.6 24.1 1.0
SG B:CYS1080 3.9 20.7 1.0
CA B:CYS1031 4.0 27.3 1.0
SG B:CYS1042 4.2 22.7 1.0
N B:CYS1074 4.5 22.9 1.0
N B:ASN1075 4.5 25.4 1.0
CA B:CYS1078 4.6 27.4 1.0
C B:CYS1074 4.6 24.3 1.0
C B:TYR1030 4.6 30.2 1.0
SG B:CYS1037 4.6 25.3 1.0
CA B:CYS1044 4.6 32.9 1.0
N B:CYS1044 4.7 33.7 1.0
CA B:TYR1030 4.8 31.2 1.0
C B:CYS1031 4.8 28.3 1.0
ND2 B:ASN1086 4.9 30.2 1.0
O B:CYS1031 4.9 27.2 1.0

Zinc binding site 6 out of 8 in 3fpd

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Zinc binding site 6 out of 8 in the G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn6

b:24.1
occ:1.00
 SG B:CYS1080 2.3 20.7 1.0
SG B:CYS1084 2.4 22.7 1.0
SG B:CYS1074 2.4 27.7 1.0
SG B:CYS1037 2.4 25.3 1.0
CB B:CYS1074 3.1 24.5 1.0
CB B:CYS1080 3.2 23.3 1.0
CB B:CYS1084 3.3 25.5 1.0
CB B:CYS1037 3.4 25.6 1.0
ZN B:ZN5 3.6 28.6 1.0
ZN B:ZN7 3.8 27.0 1.0
SG B:CYS1031 4.0 23.4 1.0
NH2 B:ARG1087 4.1 38.1 1.0
NE B:ARG1087 4.1 36.1 1.0
CZ B:ARG1087 4.5 37.4 1.0
CB B:ASN1086 4.5 27.1 1.0
CA B:CYS1074 4.5 24.4 1.0
CA B:CYS1080 4.6 26.0 1.0
CA B:CYS1084 4.7 25.7 1.0
O B:TRP1081 4.8 31.9 1.0
CA B:CYS1037 4.8 29.2 1.0
CB B:CYS1078 4.9 24.4 1.0
N B:ASN1086 4.9 28.1 1.0

Zinc binding site 7 out of 8 in 3fpd

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Zinc binding site 7 out of 8 in the G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn7

b:27.0
occ:1.00
 SG B:CYS1031 2.4 23.4 1.0
SG B:CYS1042 2.4 22.7 1.0
SG B:CYS1037 2.5 25.3 1.0
SG B:CYS1033 2.5 28.4 1.0
CB B:CYS1031 2.9 26.0 1.0
CB B:CYS1042 3.2 24.1 1.0
CB B:CYS1037 3.3 25.6 1.0
CB B:CYS1033 3.3 29.4 1.0
ZN B:ZN5 3.6 28.6 1.0
CA B:CYS1042 3.8 26.7 1.0
ZN B:ZN6 3.8 24.1 1.0
SG B:CYS1074 4.0 27.7 1.0
CA B:CYS1037 4.0 29.2 1.0
CA B:CYS1031 4.4 27.3 1.0
N B:CYS1033 4.4 28.1 1.0
CA B:CYS1033 4.5 28.9 1.0
C B:CYS1042 4.5 28.6 1.0
O B:HOH59 4.5 22.5 1.0
N B:MET1043 4.7 30.5 1.0
SG B:CYS1080 4.7 20.7 1.0
CB B:CYS1080 4.8 23.3 1.0
N B:CYS1037 4.8 30.4 1.0
C B:CYS1031 4.9 28.3 1.0
CB B:CYS1044 4.9 30.7 1.0
N B:CYS1042 5.0 26.6 1.0

Zinc binding site 8 out of 8 in 3fpd

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Zinc binding site 8 out of 8 in the G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of G9A-Like Protein Lysine Methyltransferase Inhibition By Bix- 01294 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8

b:36.7
occ:1.00
 SG B:CYS1172 2.3 32.3 1.0
SG B:CYS1227 2.4 38.0 1.0
SG B:CYS1225 2.4 46.2 1.0
SG B:CYS1232 2.6 50.9 1.0
CB B:CYS1232 3.3 44.4 1.0
CB B:CYS1225 3.4 46.2 1.0
CB B:CYS1227 3.5 41.1 1.0
CB B:CYS1172 3.5 34.1 1.0
CA B:CYS1232 3.7 44.0 1.0
N B:CYS1172 4.0 35.9 1.0
N B:CYS1227 4.2 42.6 1.0
N B:ARG1233 4.2 43.3 1.0
CE1 B:HIS1170 4.3 36.1 1.0
CA B:CYS1227 4.4 42.2 1.0
CA B:CYS1172 4.4 36.0 1.0
C B:CYS1232 4.4 44.1 1.0
ND1 B:HIS1170 4.5 37.0 1.0
N B:HIS1234 4.5 44.9 1.0
CA B:CYS1225 4.7 46.5 1.0
N B:GLY1228 4.9 42.9 1.0
C B:CYS1225 4.9 45.1 1.0
N B:ARG1226 4.9 43.5 1.0
N B:CYS1232 5.0 43.4 1.0

Reference:

Y.Chang, X.Zhang, J.R.Horton, A.K.Upadhyay, A.Spannhoff, J.Liu, J.P.Snyder, M.T.Bedford, X.Cheng. Structural Basis For G9A-Like Protein Lysine Methyltransferase Inhibition By Bix-01294. Nat.Struct.Mol.Biol. V. 16 312 2009.
ISSN: ISSN 1545-9993
PubMed: 19219047
DOI: 10.1038/NSMB.1560
Page generated: Thu Oct 24 13:21:18 2024

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