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Zinc in PDB 3rjw: Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor

Enzymatic activity of Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor

All present enzymatic activity of Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor, PDB code: 3rjw was solved by A.Dong, G.A.Wasney, W.Tempel, F.Liu, D.Barsyte, A.Allali-Hassani, X.Chen, I.Chau, T.Hajian, G.Senisterra, N.Chavda, K.Arora, A.Siarheyeva, D.B.Kireev, J.M.Herold, A.Bochkarev, C.Bountra, J.Weigelt, A.M.Edwards, S.V.Frye, C.H.Arrowsmith, P.J.Brown, J.Jin, M.Vedadi, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.25 / 2.56
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.580, 78.083, 70.252, 90.00, 92.16, 90.00
R / Rfree (%) 19.5 / 24.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor (pdb code 3rjw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor, PDB code: 3rjw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3rjw

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Zinc binding site 1 out of 8 in the Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1394

b:56.8
occ:1.00
 SG A:CYS987 2.3 54.8 1.0
SG A:CYS1017 2.3 48.0 1.0
SG A:CYS1021 2.4 45.3 1.0
SG A:CYS974 2.4 57.9 1.0
CB A:CYS974 3.3 56.5 1.0
CB A:CYS1017 3.3 41.9 1.0
CB A:CYS987 3.4 52.3 1.0
CB A:CYS1021 3.4 41.2 1.0
N A:CYS974 3.5 55.7 1.0
CA A:CYS1017 3.6 41.5 1.0
ZN A:ZN1396 3.8 68.3 1.0
ZN A:ZN1395 3.9 52.6 1.0
CA A:CYS974 4.0 56.2 1.0
SG A:CYS985 4.2 64.1 1.0
SG A:CYS1023 4.3 51.5 1.0
C A:HIS973 4.5 59.8 1.0
N A:CYS1017 4.5 41.2 1.0
SG A:CYS980 4.6 57.8 1.0
N A:ASN1018 4.6 42.6 1.0
CA A:CYS987 4.7 55.5 1.0
CA A:CYS1021 4.7 42.6 1.0
CA A:HIS973 4.7 54.6 1.0
C A:CYS1017 4.7 44.4 1.0
N A:CYS987 4.7 58.7 1.0
C A:CYS974 4.9 58.7 1.0
ND2 A:ASN1029 4.9 54.6 1.0
O A:CYS974 5.0 55.5 1.0

Zinc binding site 2 out of 8 in 3rjw

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Zinc binding site 2 out of 8 in the Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1395

b:52.6
occ:1.00
 SG A:CYS1027 2.3 52.6 1.0
SG A:CYS980 2.3 57.8 1.0
SG A:CYS1017 2.3 48.0 1.0
SG A:CYS1023 2.4 51.5 1.0
CB A:CYS1017 3.2 41.9 1.0
CB A:CYS1027 3.2 50.1 1.0
CB A:CYS1023 3.2 49.7 1.0
CB A:CYS980 3.4 56.4 1.0
ZN A:ZN1396 3.9 68.3 1.0
ZN A:ZN1394 3.9 56.8 1.0
SG A:CYS974 4.1 57.9 1.0
NE A:ARG1030 4.2 48.1 1.0
NH2 A:ARG1030 4.5 54.4 1.0
CA A:CYS1017 4.6 41.5 1.0
CA A:CYS1027 4.6 50.6 1.0
CA A:CYS1023 4.7 50.0 1.0
CB A:ASN1029 4.7 46.1 1.0
CA A:CYS980 4.7 59.7 1.0
O A:TRP1024 4.7 56.0 1.0
CZ A:ARG1030 4.8 57.6 1.0
SG A:CYS985 4.9 64.1 1.0
CB A:CYS1021 5.0 41.2 1.0
N A:CYS980 5.0 60.0 1.0
N A:ASN1029 5.0 44.9 1.0

Zinc binding site 3 out of 8 in 3rjw

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Zinc binding site 3 out of 8 in the Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1396

b:68.3
occ:1.00
 SG A:CYS980 2.3 57.8 1.0
SG A:CYS974 2.3 57.9 1.0
SG A:CYS985 2.4 64.1 1.0
SG A:CYS976 2.4 70.1 1.0
CB A:CYS974 3.0 56.5 1.0
CB A:CYS976 3.0 64.7 1.0
CB A:CYS980 3.3 56.4 1.0
CB A:CYS985 3.3 63.7 1.0
ZN A:ZN1394 3.8 56.8 1.0
ZN A:ZN1395 3.9 52.6 1.0
CA A:CYS985 3.9 65.0 1.0
CA A:CYS980 3.9 59.7 1.0
SG A:CYS1017 4.1 48.0 1.0
CA A:CYS976 4.3 64.6 1.0
N A:CYS976 4.3 62.7 1.0
CA A:CYS974 4.5 56.2 1.0
C A:CYS985 4.7 69.4 1.0
N A:CYS980 4.8 60.0 1.0
SG A:CYS1023 4.9 51.5 1.0
CB A:CYS1023 4.9 49.7 1.0
C A:CYS974 4.9 58.7 1.0
N A:LEU986 4.9 64.8 1.0

Zinc binding site 4 out of 8 in 3rjw

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Zinc binding site 4 out of 8 in the Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1397

b:0.9
occ:1.00
 SG A:CYS1115 2.3 92.7 1.0
SG A:CYS1170 2.3 86.5 1.0
SG A:CYS1168 2.3 84.2 1.0
SG A:CYS1175 2.4 95.2 1.0
CB A:CYS1168 3.2 84.0 1.0
CB A:CYS1115 3.3 88.6 1.0
CB A:CYS1170 3.4 78.3 1.0
CB A:CYS1175 3.5 94.4 1.0
CA A:CYS1175 4.0 95.5 1.0
N A:CYS1115 4.1 81.4 1.0
N A:CYS1170 4.2 79.7 1.0
CA A:CYS1115 4.3 84.9 1.0
CA A:CYS1170 4.3 78.4 1.0
N A:HIS1177 4.4 95.5 1.0
CA A:CYS1168 4.5 83.3 1.0
C A:CYS1168 4.5 87.9 1.0
O A:CYS1168 4.5 91.3 1.0
N A:LYS1176 4.5 96.4 1.0
CD2 A:HIS1113 4.6 80.8 1.0
NE2 A:HIS1113 4.6 83.1 1.0
C A:CYS1175 4.7 0.9 1.0
C A:HIS1177 4.7 99.4 1.0
N A:GLY1171 4.8 84.4 1.0
N A:SER1178 4.8 98.4 1.0
CB A:HIS1177 4.9 91.4 1.0
CA A:HIS1177 4.9 94.6 1.0
C A:CYS1170 4.9 84.7 1.0

Zinc binding site 5 out of 8 in 3rjw

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Zinc binding site 5 out of 8 in the Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1394

b:51.8
occ:1.00
 SG B:CYS987 2.2 52.7 1.0
SG B:CYS1017 2.3 44.4 1.0
SG B:CYS1021 2.3 41.0 1.0
SG B:CYS974 2.4 45.8 1.0
CB B:CYS1017 3.2 39.2 1.0
CB B:CYS974 3.3 43.5 1.0
CB B:CYS987 3.4 49.9 1.0
CB B:CYS1021 3.4 37.2 1.0
N B:CYS974 3.6 43.0 1.0
CA B:CYS1017 3.6 38.5 1.0
ZN B:ZN1396 3.8 46.1 1.0
ZN B:ZN1395 3.9 48.4 1.0
CA B:CYS974 4.0 43.5 1.0
SG B:CYS985 4.2 52.9 1.0
SG B:CYS1023 4.3 39.5 1.0
N B:CYS1017 4.5 37.9 1.0
C B:HIS973 4.5 46.5 1.0
N B:ASN1018 4.6 37.5 1.0
SG B:CYS980 4.6 50.0 1.0
CA B:CYS1021 4.6 38.2 1.0
CA B:CYS987 4.7 52.4 1.0
C B:CYS1017 4.7 40.6 1.0
CA B:HIS973 4.7 42.0 1.0
N B:CYS987 4.7 54.2 1.0
C B:CYS974 4.9 47.2 1.0
ND2 B:ASN1029 4.9 51.5 1.0
O B:CYS974 5.0 45.9 1.0

Zinc binding site 6 out of 8 in 3rjw

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Zinc binding site 6 out of 8 in the Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1395

b:48.4
occ:1.00
 SG B:CYS1027 2.3 44.1 1.0
SG B:CYS1017 2.3 44.4 1.0
SG B:CYS980 2.3 50.0 1.0
SG B:CYS1023 2.4 39.5 1.0
CB B:CYS1017 3.1 39.2 1.0
CB B:CYS1027 3.2 40.9 1.0
CB B:CYS1023 3.2 37.2 1.0
CB B:CYS980 3.4 46.3 1.0
ZN B:ZN1396 3.9 46.1 1.0
ZN B:ZN1394 3.9 51.8 1.0
SG B:CYS974 4.1 45.8 1.0
NE B:ARG1030 4.2 47.9 1.0
NH2 B:ARG1030 4.4 31.1 1.0
CA B:CYS1017 4.6 38.5 1.0
CB B:ASN1029 4.6 35.4 1.0
CA B:CYS1027 4.7 41.3 1.0
CA B:CYS1023 4.7 38.6 1.0
CA B:CYS980 4.7 47.4 1.0
CZ B:ARG1030 4.8 51.9 1.0
O B:TRP1024 4.8 46.7 1.0
SG B:CYS985 4.9 52.9 1.0
N B:ASN1029 4.9 38.6 1.0
CB B:CYS1021 4.9 37.2 1.0
N B:CYS980 5.0 47.0 1.0

Zinc binding site 7 out of 8 in 3rjw

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Zinc binding site 7 out of 8 in the Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1396

b:46.1
occ:1.00
 SG B:CYS985 2.3 52.9 1.0
SG B:CYS980 2.3 50.0 1.0
SG B:CYS976 2.4 50.4 1.0
SG B:CYS974 2.4 45.8 1.0
CB B:CYS976 3.0 45.8 1.0
CB B:CYS974 3.1 43.5 1.0
CB B:CYS980 3.3 46.3 1.0
CB B:CYS985 3.3 52.4 1.0
ZN B:ZN1394 3.8 51.8 1.0
CA B:CYS985 3.8 54.9 1.0
ZN B:ZN1395 3.9 48.4 1.0
CA B:CYS980 3.9 47.4 1.0
SG B:CYS1017 4.0 44.4 1.0
CA B:CYS976 4.3 46.9 1.0
N B:CYS976 4.4 45.7 1.0
UNK B:UNX4266 4.5 30.0 1.0
CA B:CYS974 4.5 43.5 1.0
C B:CYS985 4.7 60.6 1.0
N B:CYS980 4.8 47.0 1.0
N B:LEU986 4.9 57.4 1.0
CB B:CYS1023 4.9 37.2 1.0
SG B:CYS1023 4.9 39.5 1.0
C B:CYS974 5.0 47.2 1.0
SG B:CYS987 5.0 52.7 1.0

Zinc binding site 8 out of 8 in 3rjw

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Zinc binding site 8 out of 8 in the Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Histone Lysine Methyltransferase G9A with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1397

b:69.3
occ:1.00
 SG B:CYS1168 2.3 61.6 1.0
SG B:CYS1175 2.4 64.2 1.0
SG B:CYS1115 2.4 58.4 1.0
SG B:CYS1170 2.4 68.2 1.0
CB B:CYS1168 3.3 59.7 1.0
CB B:CYS1115 3.4 55.6 1.0
CB B:CYS1170 3.5 60.9 1.0
CB B:CYS1175 3.5 63.7 1.0
CA B:CYS1175 4.0 65.9 1.0
N B:CYS1115 4.1 52.8 1.0
N B:CYS1170 4.1 60.5 1.0
CA B:CYS1170 4.3 60.2 1.0
CA B:CYS1115 4.3 54.1 1.0
N B:LYS1176 4.5 65.0 1.0
N B:HIS1177 4.5 62.1 1.0
CD2 B:HIS1113 4.5 59.0 1.0
CA B:CYS1168 4.5 59.0 1.0
NE2 B:HIS1113 4.6 60.6 1.0
C B:CYS1168 4.6 64.5 1.0
C B:CYS1175 4.6 71.1 1.0
N B:SER1178 4.8 67.4 1.0
N B:GLY1171 4.8 64.6 1.0
CB B:HIS1177 4.9 59.7 1.0
N B:GLN1169 4.9 59.6 1.0
O B:CYS1168 4.9 66.4 1.0
C B:CYS1170 4.9 65.2 1.0
C B:HIS1177 5.0 67.9 1.0
CA B:HIS1177 5.0 61.4 1.0

Reference:

M.Vedadi, D.Barsyte-Lovejoy, F.Liu, S.Rival-Gervier, A.Allali-Hassani, V.Labrie, T.J.Wigle, P.A.Dimaggio, G.A.Wasney, A.Siarheyeva, A.Dong, W.Tempel, S.C.Wang, X.Chen, I.Chau, T.J.Mangano, X.P.Huang, C.D.Simpson, S.G.Pattenden, J.L.Norris, D.B.Kireev, A.Tripathy, A.Edwards, B.L.Roth, W.P.Janzen, B.A.Garcia, A.Petronis, J.Ellis, P.J.Brown, S.V.Frye, C.H.Arrowsmith, J.Jin. A Chemical Probe Selectively Inhibits G9A and Glp Methyltransferase Activity in Cells. Nat.Chem.Biol. V. 7 566 2011.
ISSN: ISSN 1552-4450
PubMed: 21743462
DOI: 10.1038/NCHEMBIO.599
Page generated: Sat Oct 26 14:57:16 2024

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