Zinc in PDB 7x73: Structure of G9A in Complex with Rk-701

The structure of Structure of G9A in Complex with Rk-701, PDB code: 7x73 was solved by H.Niwa, F.Shirai, S.Sato, Y.Nishigaya, M.Shirouzu, T.Umehara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.90 / 1.49
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.215, 56.243, 66.475, 76.05, 72.47, 67.53
R / Rfree (%)	16.7 / 19.3

The binding sites of Zinc atom in the Structure of G9A in Complex with Rk-701 (pdb code 7x73). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of G9A in Complex with Rk-701, PDB code: 7x73:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Structure of G9A in Complex with Rk-701


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of G9A in Complex with Rk-701 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1201 b:21.4 occ:1.00 SG A:CYS987 2.3 24.4 1.0 SG A:CYS1021 2.3 20.6 1.0 SG A:CYS974 2.3 23.5 1.0 SG A:CYS1017 2.4 22.9 1.0 CB A:CYS1017 3.2 22.1 1.0 CB A:CYS974 3.2 24.5 1.0 CB A:CYS1021 3.3 21.1 1.0 CB A:CYS987 3.4 24.1 1.0 N A:CYS974 3.5 25.1 1.0 CA A:CYS1017 3.6 19.6 1.0 ZN A:ZN1203 3.8 23.7 1.0 ZN A:ZN1202 3.8 21.6 1.0 CA A:CYS974 3.9 25.9 1.0 SG A:CYS1023 4.1 23.3 1.0 SG A:CYS985 4.4 27.5 1.0 C A:HIS973 4.5 26.2 1.0 N A:CYS1017 4.5 21.1 1.0 CA A:CYS1021 4.6 22.9 1.0 N A:ASN1018 4.6 21.3 1.0 CA A:CYS987 4.7 26.0 1.0 N A:CYS987 4.7 26.6 1.0 SG A:CYS980 4.7 25.8 1.0 C A:CYS1017 4.7 20.1 1.0 CA A:HIS973 4.7 25.0 1.0 C A:CYS974 4.8 25.4 1.0 O A:HOH1460 4.8 28.4 1.0 O A:CYS974 4.9 24.4 1.0

Zinc binding site 2 out of 8 in the Structure of G9A in Complex with Rk-701


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of G9A in Complex with Rk-701 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1202 b:21.6 occ:1.00 SG A:CYS1023 2.3 23.3 1.0 SG A:CYS1027 2.3 26.0 1.0 SG A:CYS1017 2.3 22.9 1.0 SG A:CYS980 2.4 25.8 1.0 CB A:CYS1017 3.1 22.1 1.0 CB A:CYS1023 3.2 23.7 1.0 CB A:CYS1027 3.2 23.9 1.0 CB A:CYS980 3.4 29.3 1.0 ZN A:ZN1201 3.8 21.4 1.0 ZN A:ZN1203 3.8 23.7 1.0 SG A:CYS974 4.0 23.5 1.0 NE A:ARG1030 4.3 27.0 1.0 NH2 A:ARG1030 4.4 26.2 1.0 CB A:ASN1029 4.6 27.9 1.0 CA A:CYS1017 4.6 19.6 1.0 CA A:CYS1023 4.7 23.0 1.0 CA A:CYS1027 4.7 27.2 1.0 CA A:CYS980 4.8 31.3 1.0 CZ A:ARG1030 4.8 26.8 1.0 O A:TRP1024 4.8 26.6 1.0 CB A:CYS1021 4.9 21.1 1.0 SG A:CYS985 5.0 27.5 1.0 N A:ASN1029 5.0 25.6 1.0

Zinc binding site 3 out of 8 in the Structure of G9A in Complex with Rk-701


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of G9A in Complex with Rk-701 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1203 b:23.7 occ:1.00 SG A:CYS985 2.3 27.5 1.0 SG A:CYS976 2.3 28.3 1.0 SG A:CYS974 2.3 23.5 1.0 SG A:CYS980 2.3 25.8 1.0 CB A:CYS974 3.1 24.5 1.0 CB A:CYS976 3.2 31.6 1.0 CB A:CYS980 3.2 29.3 1.0 CB A:CYS985 3.3 33.1 1.0 ZN A:ZN1201 3.8 21.4 1.0 ZN A:ZN1202 3.8 21.6 1.0 CA A:CYS985 3.8 31.9 1.0 CA A:CYS980 3.9 31.3 1.0 SG A:CYS1017 4.1 22.9 1.0 N A:CYS976 4.4 27.1 1.0 CA A:CYS976 4.4 30.5 1.0 CA A:CYS974 4.5 25.9 1.0 C A:CYS985 4.6 32.5 1.0 O A:HOH1482 4.6 32.7 1.0 N A:LEU986 4.6 29.7 1.0 O A:HOH1322 4.7 32.0 1.0 SG A:CYS1023 4.8 23.3 1.0 N A:CYS980 4.8 29.3 1.0 CB A:CYS1023 4.9 23.7 1.0 O A:HOH1388 5.0 33.9 1.0 N A:CYS987 5.0 26.6 1.0 C A:CYS974 5.0 25.4 1.0

Zinc binding site 4 out of 8 in the Structure of G9A in Complex with Rk-701


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of G9A in Complex with Rk-701 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1204 b:26.2 occ:1.00 SG A:CYS1175 2.3 27.1 1.0 SG A:CYS1170 2.3 29.4 1.0 SG A:CYS1168 2.3 26.3 1.0 SG A:CYS1115 2.4 35.5 1.0 CB A:CYS1175 3.2 30.1 1.0 CB A:CYS1168 3.3 28.1 1.0 CB A:CYS1115 3.3 35.6 1.0 CB A:CYS1170 3.3 30.7 1.0 CA A:CYS1175 3.7 34.8 1.0 N A:CYS1170 4.0 28.3 1.0 N A:CYS1115 4.1 29.9 1.0 O A:HOH1420 4.1 31.5 1.0 N A:LYS1176 4.2 30.3 1.0 CA A:CYS1170 4.2 33.9 1.0 CA A:CYS1115 4.3 32.2 1.0 C A:CYS1175 4.4 32.1 1.0 NE2 A:HIS1113 4.4 29.8 1.0 CD2 A:HIS1113 4.5 27.9 1.0 CA A:CYS1168 4.6 28.1 1.0 N A:HIS1177 4.6 26.4 1.0 C A:CYS1168 4.7 29.2 1.0 N A:GLY1171 4.8 33.9 1.0 C A:CYS1170 4.8 33.9 1.0 N A:CYS1175 4.9 38.1 1.0 O A:CYS1168 4.9 29.3 1.0

Zinc binding site 5 out of 8 in the Structure of G9A in Complex with Rk-701


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of G9A in Complex with Rk-701 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:16.9 occ:1.00 SG B:CYS987 2.3 17.9 1.0 SG B:CYS1021 2.3 15.5 1.0 SG B:CYS974 2.3 16.5 1.0 SG B:CYS1017 2.3 16.3 1.0 CB B:CYS1017 3.2 17.2 1.0 CB B:CYS974 3.3 18.0 1.0 CB B:CYS1021 3.3 17.4 1.0 CB B:CYS987 3.4 17.2 1.0 N B:CYS974 3.5 17.3 1.0 CA B:CYS1017 3.6 13.6 1.0 ZN B:ZN1203 3.8 17.4 1.0 ZN B:ZN1202 3.8 16.6 1.0 CA B:CYS974 4.0 16.7 1.0 SG B:CYS1023 4.2 17.7 1.0 SG B:CYS985 4.3 17.8 1.0 N B:CYS1017 4.5 15.4 1.0 C B:HIS973 4.5 17.9 1.0 N B:ASN1018 4.6 16.0 1.0 CA B:CYS1021 4.6 16.5 1.0 CA B:CYS987 4.6 16.9 1.0 N B:CYS987 4.6 17.3 1.0 C B:CYS1017 4.6 15.9 1.0 SG B:CYS980 4.7 17.3 1.0 CA B:HIS973 4.7 17.1 1.0 C B:CYS974 4.8 17.2 1.0 O B:CYS974 5.0 16.8 1.0

Zinc binding site 6 out of 8 in the Structure of G9A in Complex with Rk-701


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of G9A in Complex with Rk-701 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1202 b:16.6 occ:1.00 SG B:CYS1023 2.3 17.7 1.0 SG B:CYS980 2.3 17.3 1.0 SG B:CYS1027 2.4 16.1 1.0 SG B:CYS1017 2.4 16.3 1.0 CB B:CYS1017 3.2 17.2 1.0 CB B:CYS1023 3.2 18.9 1.0 CB B:CYS1027 3.3 21.2 1.0 CB B:CYS980 3.3 17.7 1.0 ZN B:ZN1203 3.8 17.4 1.0 ZN B:ZN1201 3.8 16.9 1.0 SG B:CYS974 4.0 16.5 1.0 NE B:ARG1030 4.4 19.0 1.0 NH2 B:ARG1030 4.4 20.0 1.0 CB B:ASN1029 4.6 17.1 1.0 CA B:CYS1023 4.6 18.2 1.0 CA B:CYS1017 4.6 13.6 1.0 CA B:CYS980 4.7 18.6 1.0 CA B:CYS1027 4.7 19.4 1.0 O B:TRP1024 4.8 23.9 1.0 CZ B:ARG1030 4.8 20.0 1.0 CB B:CYS1021 4.9 17.4 1.0 N B:ASN1029 5.0 16.9 1.0 SG B:CYS985 5.0 17.8 1.0 N B:CYS980 5.0 20.3 1.0

Zinc binding site 7 out of 8 in the Structure of G9A in Complex with Rk-701


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of G9A in Complex with Rk-701 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1203 b:17.4 occ:1.00 SG B:CYS976 2.3 17.4 1.0 SG B:CYS980 2.3 17.3 1.0 SG B:CYS985 2.3 17.8 1.0 SG B:CYS974 2.4 16.5 1.0 CB B:CYS974 3.1 18.0 1.0 CB B:CYS985 3.2 18.3 1.0 CB B:CYS980 3.3 17.7 1.0 CB B:CYS976 3.3 19.8 1.0 ZN B:ZN1202 3.8 16.6 1.0 ZN B:ZN1201 3.8 16.9 1.0 CA B:CYS985 3.9 18.7 1.0 CA B:CYS980 3.9 18.6 1.0 SG B:CYS1017 4.0 16.3 1.0 N B:CYS976 4.4 17.1 1.0 CA B:CYS976 4.5 18.6 1.0 O B:HOH1372 4.5 20.8 1.0 CA B:CYS974 4.6 16.7 1.0 C B:CYS985 4.6 22.0 1.0 SG B:CYS1023 4.7 17.7 1.0 N B:CYS980 4.8 20.3 1.0 N B:LEU986 4.8 20.2 1.0 CB B:CYS1023 4.8 18.9 1.0 O B:HOH1487 4.9 25.1 1.0 O B:HOH1543 4.9 20.9 1.0

Zinc binding site 8 out of 8 in the Structure of G9A in Complex with Rk-701


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of G9A in Complex with Rk-701 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1204 b:21.0 occ:1.00 SG B:CYS1175 2.3 21.7 1.0 SG B:CYS1168 2.3 20.9 1.0 SG B:CYS1170 2.3 23.4 1.0 SG B:CYS1115 2.4 23.3 1.0 CB B:CYS1175 3.2 23.2 1.0 CB B:CYS1168 3.3 24.2 1.0 CB B:CYS1115 3.4 22.9 1.0 CB B:CYS1170 3.4 23.9 1.0 CA B:CYS1175 3.6 24.0 1.0 N B:CYS1170 4.0 21.2 1.0 N B:CYS1115 4.1 19.1 1.0 N B:LYS1176 4.1 23.1 1.0 O B:HOH1459 4.2 26.4 1.0 CA B:CYS1170 4.2 23.4 1.0 CA B:CYS1115 4.4 21.1 1.0 C B:CYS1175 4.4 24.4 1.0 NE2 B:HIS1113 4.5 20.6 1.0 CD2 B:HIS1113 4.5 19.7 1.0 C B:CYS1168 4.6 24.8 1.0 CA B:CYS1168 4.6 23.1 1.0 N B:HIS1177 4.6 22.8 1.0 O B:CYS1168 4.7 25.0 1.0 N B:CYS1175 4.8 26.8 1.0 N B:GLY1171 4.8 27.1 1.0 C B:CYS1170 4.9 25.0 1.0

S.Takase, T.Hiroyama, F.Shirai, Y.Maemoto, A.Nakata, M.Arata, S.Matsuoka, T.Sonoda, H.Niwa, S.Sato, T.Umehara, M.Shirouzu, Y.Nishigaya, T.Sumiya, N.Hashimoto, R.Namie, M.Usui, T.Ohishi, S.Ohba, M.Kawada, Y.Hayashi, H.Harada, T.Yamaguchi, Y.Shinkai, Y.Nakamura, M.Yoshida, A.Ito. A Specific G9A Inhibitor Unveils BGLT3 Lncrna As A Universal Mediator of Chemically Induced Fetal Globin Gene Expression Nat Commun 2022.
ISSN: ESSN 2041-1723