Zinc in PDB 5v9i: Crystal Structure of Catalytic Domain of G9A with MS0105

All present enzymatic activity of Crystal Structure of Catalytic Domain of G9A with MS0105:
2.1.1.43;

The structure of Crystal Structure of Catalytic Domain of G9A with MS0105, PDB code: 5v9i was solved by A.Dong, H.Zeng, J.Liu, Y.Xiong, N.Babault, J.Jin, J.R.Walker, C.Bountra, C.H.Arrowsmith, A.M.Edwards, H.Wu, P.J.Brown, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.48 / 1.74
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.607, 77.509, 134.794, 90.00, 91.41, 90.00
R / Rfree (%)	23.4 / 27.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Catalytic Domain of G9A with MS0105 (pdb code 5v9i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of Catalytic Domain of G9A with MS0105, PDB code: 5v9i:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Crystal Structure of Catalytic Domain of G9A with MS0105


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 Catalytic Domain of G9A with MS0105 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1501 b:30.7 occ:1.00 SG A:CYS987 2.2 38.2 1.0 SG A:CYS1021 2.3 29.4 1.0 SG A:CYS1017 2.5 33.9 1.0 SG A:CYS974 2.6 33.1 1.0 CB A:CYS974 3.2 31.2 1.0 CB A:CYS1021 3.2 26.9 1.0 CB A:CYS1017 3.4 28.7 1.0 CB A:CYS987 3.4 34.6 1.0 N A:CYS974 3.4 30.8 1.0 CA A:CYS1017 3.6 27.2 1.0 CA A:CYS974 3.9 31.5 1.0 ZN A:ZN1503 4.0 36.0 1.0 ZN A:ZN1502 4.1 32.2 1.0 SG A:CYS1023 4.4 30.6 1.0 C A:HIS973 4.4 35.4 1.0 SG A:CYS985 4.4 37.5 1.0 CA A:HIS973 4.5 32.9 1.0 CA A:CYS1021 4.5 27.9 1.0 N A:ASN1018 4.5 25.6 1.0 N A:CYS1017 4.6 27.2 1.0 CA A:CYS987 4.6 34.6 1.0 C A:CYS1017 4.7 28.3 1.0 N A:CYS987 4.7 35.4 1.0 C A:CYS974 4.8 39.0 1.0 O A:CYS974 4.8 38.1 1.0 O A:HOH1678 4.9 29.0 1.0 SG A:CYS980 4.9 33.7 1.0 CB A:HIS973 5.0 32.3 1.0

Zinc binding site 2 out of 16 in the Crystal Structure of Catalytic Domain of G9A with MS0105


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 Catalytic Domain of G9A with MS0105 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1502 b:32.2 occ:1.00 SG A:CYS1027 2.2 34.0 1.0 SG A:CYS1023 2.2 30.6 1.0 SG A:CYS1017 2.3 33.9 1.0 SG A:CYS980 2.5 33.7 1.0 CB A:CYS1017 3.1 28.7 1.0 CB A:CYS1027 3.2 31.7 1.0 CB A:CYS1023 3.2 29.1 1.0 CB A:CYS980 3.4 31.9 1.0 ZN A:ZN1503 3.8 36.0 1.0 SG A:CYS974 4.1 33.1 1.0 ZN A:ZN1501 4.1 30.7 1.0 NE A:ARG1030 4.4 27.9 1.0 NH2 A:ARG1030 4.4 26.3 1.0 CA A:CYS1017 4.6 27.2 1.0 CA A:CYS1027 4.6 32.1 1.0 CB A:ASN1029 4.6 27.0 1.0 CA A:CYS1023 4.6 28.9 1.0 O A:TRP1024 4.7 26.9 1.0 CZ A:ARG1030 4.7 30.9 1.0 CA A:CYS980 4.8 34.0 1.0 CB A:CYS1021 5.0 26.9 1.0

Zinc binding site 3 out of 16 in the Crystal Structure of Catalytic Domain of G9A with MS0105


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 Catalytic Domain of G9A with MS0105 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1503 b:36.0 occ:1.00 SG A:CYS980 2.2 33.7 1.0 SG A:CYS985 2.2 37.5 1.0 SG A:CYS974 2.4 33.1 1.0 SG A:CYS976 2.5 40.4 1.0 CB A:CYS980 3.1 31.9 1.0 CB A:CYS976 3.2 36.3 1.0 CB A:CYS974 3.2 31.2 1.0 CB A:CYS985 3.2 36.3 1.0 ZN A:ZN1502 3.8 32.2 1.0 CA A:CYS985 3.9 37.8 1.0 CA A:CYS980 3.9 34.0 1.0 SG A:CYS1017 4.0 33.9 1.0 ZN A:ZN1501 4.0 30.7 1.0 O A:HOH1625 4.3 36.7 1.0 CA A:CYS976 4.5 37.4 1.0 N A:CYS976 4.6 37.6 1.0 CA A:CYS974 4.7 31.5 1.0 C A:CYS985 4.7 41.6 1.0 SG A:CYS1023 4.7 30.6 1.0 O A:HOH1728 4.8 34.8 1.0 N A:CYS980 4.8 34.7 1.0 CB A:CYS1023 4.8 29.1 1.0 N A:LEU986 5.0 39.1 1.0

Zinc binding site 4 out of 16 in the Crystal Structure of Catalytic Domain of G9A with MS0105


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 Catalytic Domain of G9A with MS0105 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1504 b:40.9 occ:1.00 SG A:CYS1168 2.2 35.1 1.0 SG A:CYS1175 2.2 39.5 1.0 SG A:CYS1115 2.3 40.2 1.0 SG A:CYS1170 2.4 45.2 1.0 CB A:CYS1168 3.2 32.3 1.0 CB A:CYS1175 3.4 38.9 1.0 CB A:CYS1170 3.5 40.4 1.0 CB A:CYS1115 3.5 37.9 1.0 CA A:CYS1175 3.7 41.2 1.0 N A:CYS1170 4.1 41.0 1.0 N A:CYS1115 4.2 35.9 1.0 N A:LYS1176 4.3 44.0 1.0 CA A:CYS1170 4.3 40.8 1.0 CA A:CYS1168 4.4 32.3 1.0 CA A:CYS1115 4.4 37.4 1.0 C A:CYS1175 4.4 46.1 1.0 N A:HIS1177 4.5 37.5 1.0 C A:CYS1168 4.5 40.2 1.0 CD2 A:HIS1113 4.6 33.6 1.0 NE2 A:HIS1113 4.7 34.5 1.0 O A:CYS1168 4.8 39.6 1.0 N A:SER1178 4.9 40.5 1.0 CB A:HIS1177 4.9 31.6 1.0 N A:CYS1175 4.9 45.6 1.0 N A:GLN1169 5.0 39.4 1.0 C A:CYS1170 5.0 47.5 1.0

Zinc binding site 5 out of 16 in the Crystal Structure of Catalytic Domain of G9A with MS0105


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 Catalytic Domain of G9A with MS0105 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1501 b:18.8 occ:1.00 SG B:CYS1021 2.2 22.1 1.0 SG B:CYS987 2.4 20.1 1.0 SG B:CYS1017 2.4 19.3 1.0 SG B:CYS974 2.5 19.9 1.0 CB B:CYS1017 3.1 15.2 1.0 CB B:CYS1021 3.2 19.0 1.0 CB B:CYS974 3.3 17.2 1.0 CB B:CYS987 3.5 17.8 1.0 N B:CYS974 3.6 18.9 1.0 CA B:CYS1017 3.6 14.3 1.0 ZN B:ZN1503 3.8 19.3 1.0 ZN B:ZN1502 3.9 19.8 1.0 CA B:CYS974 4.0 16.9 1.0 SG B:CYS1023 4.1 20.0 1.0 SG B:CYS985 4.4 21.3 1.0 CA B:CYS1021 4.4 18.2 1.0 C B:HIS973 4.5 18.5 1.0 N B:CYS1017 4.5 13.4 1.0 N B:ASN1018 4.6 13.0 1.0 CA B:HIS973 4.7 17.2 1.0 C B:CYS1017 4.7 18.6 1.0 N B:CYS987 4.7 20.6 1.0 CA B:CYS987 4.7 18.7 1.0 SG B:CYS980 4.8 21.0 1.0 C B:CYS974 4.8 19.7 1.0 O B:HOH1732 4.9 19.9 1.0 O B:CYS974 4.9 21.1 1.0

Zinc binding site 6 out of 16 in the Crystal Structure of Catalytic Domain of G9A with MS0105


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 Catalytic Domain of G9A with MS0105 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1502 b:19.8 occ:1.00 SG B:CYS1023 2.3 20.0 1.0 SG B:CYS1027 2.3 19.2 1.0 SG B:CYS1017 2.4 19.3 1.0 SG B:CYS980 2.4 21.0 1.0 CB B:CYS1023 3.2 17.8 1.0 CB B:CYS1017 3.2 15.2 1.0 CB B:CYS1027 3.2 17.1 1.0 CB B:CYS980 3.3 19.0 1.0 ZN B:ZN1503 3.8 19.3 1.0 ZN B:ZN1501 3.9 18.8 1.0 SG B:CYS974 4.1 19.9 1.0 NE B:ARG1030 4.3 17.0 1.0 NH2 B:ARG1030 4.5 23.7 1.0 CB B:ASN1029 4.5 17.1 1.0 CA B:CYS1023 4.6 18.2 1.0 CA B:CYS1017 4.6 14.3 1.0 CA B:CYS1027 4.7 18.7 1.0 CA B:CYS980 4.7 20.0 1.0 O B:TRP1024 4.8 22.9 1.0 CZ B:ARG1030 4.8 27.9 1.0 CB B:CYS1021 4.9 19.0 1.0

Zinc binding site 7 out of 16 in the Crystal Structure of Catalytic Domain of G9A with MS0105


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 Catalytic Domain of G9A with MS0105 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1503 b:19.3 occ:1.00 SG B:CYS980 2.3 21.0 1.0 SG B:CYS985 2.3 21.3 1.0 SG B:CYS974 2.4 19.9 1.0 SG B:CYS976 2.4 23.0 1.0 CB B:CYS974 3.2 17.2 1.0 CB B:CYS980 3.2 19.0 1.0 CB B:CYS976 3.3 19.8 1.0 CB B:CYS985 3.3 19.9 1.0 ZN B:ZN1502 3.8 19.8 1.0 ZN B:ZN1501 3.8 18.8 1.0 CA B:CYS980 3.9 20.0 1.0 CA B:CYS985 3.9 21.2 1.0 SG B:CYS1017 4.1 19.3 1.0 N B:CYS976 4.4 18.2 1.0 CA B:CYS976 4.5 19.1 1.0 O B:HOH1641 4.6 21.5 1.0 CA B:CYS974 4.6 16.9 1.0 C B:CYS985 4.7 23.7 1.0 SG B:CYS1023 4.7 20.0 1.0 N B:LEU986 4.8 20.5 1.0 O B:HOH1709 4.8 26.0 1.0 N B:CYS980 4.8 19.2 1.0 CB B:CYS1023 4.9 17.8 1.0 O B:HOH1763 5.0 21.8 1.0 C B:CYS974 5.0 19.7 1.0

Zinc binding site 8 out of 16 in the Crystal Structure of Catalytic Domain of G9A with MS0105


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 Catalytic Domain of G9A with MS0105 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1504 b:24.9 occ:1.00 SG B:CYS1168 2.3 26.9 1.0 SG B:CYS1175 2.3 27.4 1.0 SG B:CYS1170 2.4 26.5 1.0 SG B:CYS1115 2.4 27.5 1.0 CB B:CYS1175 3.2 26.2 1.0 CB B:CYS1170 3.4 22.8 1.0 CB B:CYS1168 3.4 23.1 1.0 CB B:CYS1115 3.4 24.0 1.0 CA B:CYS1175 3.7 27.2 1.0 O B:HOH1747 4.0 28.1 1.0 N B:CYS1170 4.1 24.6 1.0 N B:CYS1115 4.1 22.6 1.0 CA B:CYS1170 4.2 24.3 1.0 N B:LYS1176 4.3 30.8 1.0 CA B:CYS1115 4.4 23.9 1.0 C B:CYS1175 4.4 32.8 1.0 NE2 B:HIS1113 4.5 24.0 1.0 CD2 B:HIS1113 4.5 23.7 1.0 N B:HIS1177 4.6 24.1 1.0 CA B:CYS1168 4.6 21.9 1.0 C B:CYS1168 4.7 25.9 1.0 N B:GLY1171 4.9 27.5 1.0 N B:CYS1175 4.9 29.6 1.0 O B:CYS1168 4.9 25.2 1.0 C B:CYS1170 4.9 29.7 1.0 CB B:HIS1177 4.9 19.3 1.0

Zinc binding site 9 out of 16 in the Crystal Structure of Catalytic Domain of G9A with MS0105


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Catalytic Domain of G9A with MS0105 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1501 b:22.1 occ:1.00 SG C:CYS1021 2.2 21.2 1.0 SG C:CYS987 2.3 24.6 1.0 SG C:CYS1017 2.4 23.5 1.0 SG C:CYS974 2.6 23.3 1.0 CB C:CYS1017 3.2 19.3 1.0 CB C:CYS1021 3.2 19.2 1.0 CB C:CYS974 3.3 21.2 1.0 CB C:CYS987 3.4 21.9 1.0 N C:CYS974 3.5 19.3 1.0 CA C:CYS1017 3.6 18.9 1.0 ZN C:ZN1503 3.9 24.9 1.0 CA C:CYS974 4.0 21.4 1.0 ZN C:ZN1502 4.0 22.1 1.0 SG C:CYS1023 4.2 19.9 1.0 SG C:CYS985 4.4 26.0 1.0 N C:CYS1017 4.5 18.6 1.0 C C:HIS973 4.5 24.0 1.0 CA C:CYS1021 4.5 20.1 1.0 N C:ASN1018 4.5 19.6 1.0 CA C:CYS987 4.6 22.1 1.0 C C:CYS1017 4.6 22.2 1.0 CA C:HIS973 4.7 22.2 1.0 N C:CYS987 4.7 23.5 1.0 SG C:CYS980 4.7 25.2 1.0 O C:HOH1729 4.8 22.9 1.0 C C:CYS974 4.9 26.8 1.0 ND2 C:ASN1029 5.0 19.1 1.0

Zinc binding site 10 out of 16 in the Crystal Structure of Catalytic Domain of G9A with MS0105


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Catalytic Domain of G9A with MS0105 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1502 b:22.1 occ:1.00 SG C:CYS1027 2.2 23.4 1.0 SG C:CYS1023 2.2 19.9 1.0 SG C:CYS980 2.3 25.2 1.0 SG C:CYS1017 2.4 23.5 1.0 CB C:CYS1027 3.1 21.7 1.0 CB C:CYS1023 3.1 18.9 1.0 CB C:CYS1017 3.2 19.3 1.0 CB C:CYS980 3.3 21.6 1.0 ZN C:ZN1503 3.8 24.9 1.0 ZN C:ZN1501 4.0 22.1 1.0 SG C:CYS974 4.2 23.3 1.0 NE C:ARG1030 4.4 17.7 1.0 NH2 C:ARG1030 4.4 20.9 1.0 CA C:CYS1027 4.5 22.2 1.0 CA C:CYS1023 4.6 20.8 1.0 CB C:ASN1029 4.6 17.6 1.0 CA C:CYS980 4.7 21.6 1.0 O C:TRP1024 4.7 23.4 1.0 CA C:CYS1017 4.7 18.9 1.0 CZ C:ARG1030 4.8 25.0 1.0 N C:CYS980 4.9 19.6 1.0 CB C:CYS1021 5.0 19.2 1.0

H.Zeng, A.Dong, J.Liu, Y.Xiong, N.Babault, J.Jin, J.R.Walker, C.Bountra, C.H.Arrowsmith, A.M.Edwards, H.Wu, P.J.Brown. Crystal Structure of Catalytic Domain of G9A with MS0105 To Be Published.