Zinc in PDB 2o8j: Human Euchromatic Histone Methyltransferase 2

All present enzymatic activity of Human Euchromatic Histone Methyltransferase 2:
2.1.1.43;

The structure of Human Euchromatic Histone Methyltransferase 2, PDB code: 2o8j was solved by J.Min, H.Wu, T.Antoshenko, P.Loppnau, J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, A.N.Plotnikov, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.31 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	56.586, 70.965, 83.046, 81.11, 75.13, 88.39
R / Rfree (%)	18.2 / 22.1

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Human Euchromatic Histone Methyltransferase 2 (pdb code 2o8j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Human Euchromatic Histone Methyltransferase 2, PDB code: 2o8j:
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 Human Euchromatic Histone Methyltransferase 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Euchromatic Histone Methyltransferase 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1501 b:18.4 occ:1.00 SG A:CYS987 2.3 16.9 1.0 SG A:CYS1021 2.3 14.4 1.0 SG A:CYS1017 2.4 14.9 1.0 SG A:CYS974 2.5 14.9 1.0 CB A:CYS1017 3.2 15.6 1.0 CB A:CYS974 3.3 15.6 1.0 CB A:CYS1021 3.3 15.0 1.0 CB A:CYS987 3.4 18.1 1.0 N A:CYS974 3.6 15.7 1.0 CA A:CYS1017 3.6 14.9 1.0 ZN A:ZN1503 3.8 18.0 1.0 ZN A:ZN1502 3.8 17.6 1.0 CA A:CYS974 4.0 15.5 1.0 SG A:CYS1023 4.2 15.6 1.0 SG A:CYS985 4.3 17.9 1.0 N A:CYS1017 4.5 13.2 1.0 N A:ASN1018 4.6 14.9 1.0 C A:HIS973 4.6 15.9 1.0 CA A:CYS1021 4.6 13.6 1.0 CA A:CYS987 4.7 19.5 1.0 C A:CYS1017 4.7 16.0 1.0 N A:CYS987 4.7 19.1 1.0 SG A:CYS980 4.7 16.1 1.0 CA A:HIS973 4.8 15.6 1.0 C A:CYS974 4.8 15.7 1.0 O A:HOH1520 4.9 17.1 1.0 O A:CYS974 4.9 15.1 1.0 ND2 A:ASN1029 5.0 16.3 1.0

Zinc binding site 2 out of 16 in the Human Euchromatic Histone Methyltransferase 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Euchromatic Histone Methyltransferase 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1502 b:17.6 occ:1.00 SG A:CYS1027 2.3 16.9 1.0 SG A:CYS980 2.3 16.1 1.0 SG A:CYS1023 2.3 15.6 1.0 SG A:CYS1017 2.4 14.9 1.0 CB A:CYS1017 3.1 15.6 1.0 CB A:CYS1027 3.2 17.1 1.0 CB A:CYS1023 3.2 16.2 1.0 CB A:CYS980 3.3 17.2 1.0 ZN A:ZN1503 3.8 18.0 1.0 ZN A:ZN1501 3.8 18.4 1.0 SG A:CYS974 4.1 14.9 1.0 NE A:ARG1030 4.3 18.3 1.0 NH2 A:ARG1030 4.5 19.2 1.0 CB A:ASN1029 4.5 16.6 1.0 CA A:CYS1017 4.6 14.9 1.0 CA A:CYS1023 4.6 14.9 1.0 CA A:CYS1027 4.7 17.4 1.0 CA A:CYS980 4.7 17.4 1.0 O A:TRP1024 4.7 18.1 1.0 CZ A:ARG1030 4.8 20.9 1.0 N A:ASN1029 5.0 15.9 1.0 CB A:CYS1021 5.0 15.0 1.0 N A:CYS980 5.0 16.8 1.0

Zinc binding site 3 out of 16 in the Human Euchromatic Histone Methyltransferase 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Euchromatic Histone Methyltransferase 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1503 b:18.0 occ:1.00 SG A:CYS985 2.3 17.9 1.0 SG A:CYS974 2.3 14.9 1.0 SG A:CYS980 2.4 16.1 1.0 SG A:CYS976 2.4 16.2 1.0 CB A:CYS974 3.1 15.6 1.0 CB A:CYS976 3.2 16.2 1.0 CB A:CYS985 3.3 18.6 1.0 CB A:CYS980 3.4 17.2 1.0 ZN A:ZN1501 3.8 18.4 1.0 ZN A:ZN1502 3.8 17.6 1.0 CA A:CYS985 3.9 19.3 1.0 CA A:CYS980 4.0 17.4 1.0 SG A:CYS1017 4.1 14.9 1.0 N A:CYS976 4.4 16.0 1.0 CA A:CYS976 4.4 15.8 1.0 CA A:CYS974 4.6 15.5 1.0 C A:CYS985 4.7 19.2 1.0 O A:HOH1548 4.7 20.7 1.0 O A:HOH1544 4.7 18.4 1.0 N A:LEU986 4.7 19.3 1.0 SG A:CYS1023 4.8 15.6 1.0 N A:CYS980 4.8 16.8 1.0 CB A:CYS1023 4.9 16.2 1.0 O A:HOH1545 4.9 21.2 1.0

Zinc binding site 4 out of 16 in the Human Euchromatic Histone Methyltransferase 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Euchromatic Histone Methyltransferase 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1504 b:27.3 occ:1.00 SG A:CYS1168 2.2 25.4 1.0 SG A:CYS1170 2.3 27.9 1.0 SG A:CYS1175 2.4 28.6 1.0 SG A:CYS1115 2.5 26.5 1.0 CB A:CYS1175 3.1 30.9 1.0 CB A:CYS1170 3.2 28.7 1.0 CB A:CYS1168 3.3 28.1 1.0 CB A:CYS1115 3.4 23.6 1.0 CA A:CYS1175 3.7 31.7 1.0 N A:CYS1170 4.0 28.2 1.0 N A:CYS1115 4.1 22.9 1.0 O A:HOH1558 4.1 24.1 1.0 CA A:CYS1170 4.2 29.2 1.0 N A:LYS1176 4.3 31.3 1.0 CA A:CYS1115 4.4 23.7 1.0 C A:CYS1175 4.4 31.9 1.0 N A:HIS1177 4.5 29.2 1.0 CA A:CYS1168 4.6 28.3 1.0 CE1 A:HIS1113 4.6 22.1 1.0 ND1 A:HIS1113 4.6 22.0 1.0 C A:CYS1168 4.7 28.7 1.0 N A:GLY1171 4.7 31.8 1.0 C A:CYS1170 4.8 30.1 1.0 CB A:HIS1177 4.8 29.0 1.0 N A:CYS1175 4.8 32.5 1.0 N A:SER1178 4.9 29.4 1.0 N A:GLN1169 5.0 28.5 1.0

Zinc binding site 5 out of 16 in the Human Euchromatic Histone Methyltransferase 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Euchromatic Histone Methyltransferase 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1505 b:26.3 occ:1.00 SG B:CYS1017 2.3 23.1 1.0 SG B:CYS1021 2.4 20.0 1.0 SG B:CYS974 2.4 24.5 1.0 SG B:CYS987 2.4 27.0 1.0 CB B:CYS1017 3.2 20.2 1.0 CB B:CYS974 3.3 26.5 1.0 CB B:CYS1021 3.3 21.1 1.0 CB B:CYS987 3.5 28.1 1.0 CA B:CYS1017 3.6 19.7 1.0 N B:CYS974 3.6 27.2 1.0 ZN B:ZN1507 3.7 27.9 1.0 ZN B:ZN1506 3.8 25.0 1.0 CA B:CYS974 4.1 27.1 1.0 SG B:CYS1023 4.1 21.2 1.0 SG B:CYS985 4.3 26.3 1.0 SG B:CYS980 4.5 24.5 1.0 N B:CYS1017 4.5 19.8 1.0 N B:ASN1018 4.6 17.9 1.0 CA B:CYS1021 4.6 20.9 1.0 C B:HIS973 4.6 28.2 1.0 C B:CYS1017 4.7 19.1 1.0 CA B:CYS987 4.7 28.2 1.0 N B:CYS987 4.7 28.9 1.0 CA B:HIS973 4.8 28.3 1.0 ND2 B:ASN1029 4.9 20.6 1.0 C B:CYS974 4.9 28.0 1.0 O B:HOH1535 4.9 22.9 1.0

Zinc binding site 6 out of 16 in the Human Euchromatic Histone Methyltransferase 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human Euchromatic Histone Methyltransferase 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1506 b:25.0 occ:1.00 SG B:CYS1027 2.2 23.6 1.0 SG B:CYS1017 2.4 23.1 1.0 SG B:CYS1023 2.4 21.2 1.0 SG B:CYS980 2.6 24.5 1.0 CB B:CYS1017 3.1 20.2 1.0 CB B:CYS1027 3.2 24.7 1.0 CB B:CYS980 3.2 29.3 1.0 CB B:CYS1023 3.2 23.2 1.0 ZN B:ZN1507 3.8 27.9 1.0 ZN B:ZN1505 3.8 26.3 1.0 SG B:CYS974 4.2 24.5 1.0 NE B:ARG1030 4.3 24.9 1.0 NH2 B:ARG1030 4.4 22.4 1.0 CB B:ASN1029 4.5 21.9 1.0 CA B:CYS1017 4.6 19.7 1.0 CA B:CYS980 4.7 30.1 1.0 CA B:CYS1027 4.7 24.4 1.0 CA B:CYS1023 4.7 22.4 1.0 CZ B:ARG1030 4.8 23.8 1.0 O B:TRP1024 4.8 23.9 1.0 N B:ASN1029 4.9 23.3 1.0

Zinc binding site 7 out of 16 in the Human Euchromatic Histone Methyltransferase 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human Euchromatic Histone Methyltransferase 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1507 b:27.9 occ:1.00 SG B:CYS980 2.0 24.5 1.0 SG B:CYS974 2.4 24.5 1.0 SG B:CYS985 2.4 26.3 1.0 SG B:CYS976 2.5 27.6 1.0 CB B:CYS976 3.1 31.9 1.0 CB B:CYS974 3.2 26.5 1.0 CB B:CYS980 3.3 29.3 1.0 CB B:CYS985 3.3 30.8 1.0 ZN B:ZN1505 3.7 26.3 1.0 ZN B:ZN1506 3.8 25.0 1.0 CA B:CYS980 3.9 30.1 1.0 CA B:CYS985 4.0 30.9 1.0 SG B:CYS1017 4.0 23.1 1.0 CA B:CYS976 4.4 31.7 1.0 N B:CYS976 4.5 30.7 1.0 O B:HOH1530 4.6 29.5 1.0 CA B:CYS974 4.7 27.1 1.0 C B:CYS985 4.7 30.7 1.0 SG B:CYS1023 4.8 21.2 1.0 N B:CYS980 4.8 30.5 1.0 CB B:CYS1023 4.8 23.2 1.0 N B:LEU986 4.9 30.1 1.0 C B:CYS980 5.0 31.9 1.0

Zinc binding site 8 out of 16 in the Human Euchromatic Histone Methyltransferase 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human Euchromatic Histone Methyltransferase 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1508 b:29.2 occ:1.00 SG B:CYS1170 2.3 30.9 1.0 SG B:CYS1115 2.3 29.8 1.0 SG B:CYS1168 2.4 28.6 1.0 SG B:CYS1175 2.4 32.9 1.0 CB B:CYS1115 3.2 29.3 1.0 CB B:CYS1175 3.2 35.5 1.0 CB B:CYS1170 3.3 33.3 1.0 CB B:CYS1168 3.4 29.5 1.0 CA B:CYS1175 3.7 35.2 1.0 N B:CYS1115 4.0 27.9 1.0 N B:CYS1170 4.0 32.1 1.0 CA B:CYS1170 4.2 33.6 1.0 O B:HOH1582 4.2 33.6 1.0 CA B:CYS1115 4.2 29.2 1.0 N B:LYS1176 4.2 34.2 1.0 C B:CYS1175 4.4 34.7 1.0 CE1 B:HIS1113 4.4 21.8 1.0 N B:HIS1177 4.5 32.0 1.0 ND1 B:HIS1113 4.6 24.5 1.0 CA B:CYS1168 4.6 29.7 1.0 C B:CYS1168 4.7 30.4 1.0 N B:GLY1171 4.8 35.9 1.0 C B:CYS1170 4.9 34.5 1.0 N B:CYS1175 4.9 35.9 1.0 O B:CYS1168 4.9 30.4 1.0 CB B:HIS1177 5.0 31.6 1.0

Zinc binding site 9 out of 16 in the Human Euchromatic Histone Methyltransferase 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Human Euchromatic Histone Methyltransferase 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1509 b:17.4 occ:1.00 SG C:CYS987 2.3 15.4 1.0 SG C:CYS1021 2.3 13.9 1.0 SG C:CYS1017 2.4 12.8 1.0 SG C:CYS974 2.4 13.4 1.0 CB C:CYS1017 3.2 13.7 1.0 CB C:CYS974 3.3 13.7 1.0 CB C:CYS1021 3.3 13.1 1.0 CB C:CYS987 3.4 16.0 1.0 N C:CYS974 3.5 14.8 1.0 CA C:CYS1017 3.6 13.1 1.0 ZN C:ZN1511 3.8 16.9 1.0 ZN C:ZN1510 3.8 16.0 1.0 CA C:CYS974 4.0 14.7 1.0 SG C:CYS1023 4.2 13.6 1.0 SG C:CYS985 4.3 16.5 1.0 N C:CYS1017 4.5 11.8 1.0 N C:ASN1018 4.5 14.1 1.0 C C:HIS973 4.6 16.3 1.0 CA C:CYS987 4.6 17.4 1.0 C C:CYS1017 4.6 13.2 1.0 CA C:CYS1021 4.6 14.1 1.0 N C:CYS987 4.7 16.1 1.0 SG C:CYS980 4.7 14.8 1.0 CA C:HIS973 4.8 16.1 1.0 C C:CYS974 4.9 14.2 1.0 O C:HOH1548 4.9 14.3 1.0 O C:CYS974 5.0 13.0 1.0

Zinc binding site 10 out of 16 in the Human Euchromatic Histone Methyltransferase 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Human Euchromatic Histone Methyltransferase 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1510 b:16.0 occ:1.00 SG C:CYS1023 2.3 13.6 1.0 SG C:CYS1027 2.3 14.8 1.0 SG C:CYS980 2.4 14.8 1.0 SG C:CYS1017 2.4 12.8 1.0 CB C:CYS1017 3.1 13.7 1.0 CB C:CYS1023 3.2 14.9 1.0 CB C:CYS1027 3.2 15.9 1.0 CB C:CYS980 3.3 13.7 1.0 ZN C:ZN1511 3.8 16.9 1.0 ZN C:ZN1509 3.8 17.4 1.0 SG C:CYS974 4.1 13.4 1.0 NE C:ARG1030 4.3 18.4 1.0 NH2 C:ARG1030 4.4 18.6 1.0 CB C:ASN1029 4.6 13.3 1.0 CA C:CYS1017 4.6 13.1 1.0 CA C:CYS1023 4.6 13.7 1.0 CA C:CYS1027 4.7 16.0 1.0 CA C:CYS980 4.7 15.3 1.0 CZ C:ARG1030 4.8 19.4 1.0 O C:TRP1024 4.8 17.4 1.0 N C:ASN1029 5.0 13.2 1.0 CB C:CYS1021 5.0 13.1 1.0 N C:CYS980 5.0 14.3 1.0

H.Wu, J.Min, V.V.Lunin, T.Antoshenko, L.Dombrovski, H.Zeng, A.Allali-Hassani, V.Campagna-Slater, M.Vedadi, C.H.Arrowsmith, A.N.Plotnikov, M.Schapira. Structural Biology of Human H3K9 Methyltransferases Plos One V. 5 E8570 2010.
ISSN: ESSN 1932-6203
PubMed: 20084102
DOI: 10.1371/JOURNAL.PONE.0008570