Zinc in PDB 3wok: Crystal Structure of the Dap Bii (Space)

The structure of Crystal Structure of the Dap Bii (Space), PDB code: 3wok was solved by Y.Sakamoto, Y.Suzuki, I.Iizuka, C.Tateoka, S.Roppongi, M.Fujimoto, T.Nonaka, W.Ogasawara, N.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.56 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.740, 130.440, 171.460, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22.5

The binding sites of Zinc atom in the Crystal Structure of the Dap Bii (Space) (pdb code 3wok). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Dap Bii (Space), PDB code: 3wok:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Dap Bii (Space)


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 the Dap Bii (Space) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn809 b:14.5 occ:1.00 C2 A:GOL805 3.5 27.1 1.0 NH1 A:ARG175 3.6 41.6 1.0 O2 A:GOL805 3.7 27.1 1.0 CG A:PHE125 3.8 12.7 1.0 OD1 A:ASN190 3.8 20.5 1.0 O A:HOH1485 3.9 32.0 1.0 CD1 A:PHE125 3.9 13.3 1.0 CD2 A:PHE125 3.9 14.0 1.0 CG A:ARG173 3.9 29.8 1.0 CG A:ARG175 4.1 21.5 1.0 NH1 A:ARG173 4.1 49.0 1.0 C3 A:GOL805 4.1 25.1 1.0 CD A:ARG175 4.1 26.1 1.0 CE1 A:PHE125 4.2 13.6 1.0 CE2 A:PHE125 4.2 13.8 1.0 CB A:PHE125 4.2 12.6 1.0 CZ A:PHE125 4.4 14.0 1.0 O A:HOH1108 4.4 25.1 1.0 CG A:ASN190 4.6 14.8 1.0 CD A:ARG173 4.6 32.8 1.0 CZ A:ARG175 4.7 36.2 1.0 C1 A:GOL805 4.7 23.8 1.0 CB A:ASN190 4.8 13.6 1.0 O3 A:GOL805 4.9 26.6 1.0 NE A:ARG175 4.9 31.5 1.0 CZ A:ARG173 4.9 48.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Dap Bii (Space)


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 the Dap Bii (Space) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn810 b:15.8 occ:1.00 O3 A:GOL803 2.1 17.6 1.0 NE2 A:HIS252 2.1 11.8 1.0 C3 A:GOL803 2.7 19.7 1.0 C2 A:GOL803 2.9 23.4 1.0 CD2 A:HIS252 3.0 11.0 1.0 CE1 A:HIS252 3.1 12.3 1.0 O2 A:GOL803 3.3 23.6 1.0 O A:HOH1296 4.2 20.3 1.0 CG A:HIS252 4.2 11.2 1.0 ND1 A:HIS252 4.2 11.4 1.0 O A:HOH1446 4.3 29.7 1.0 C1 A:GOL803 4.4 24.1 1.0 CB A:ASP59 4.5 18.9 1.0 N A:ASP59 4.7 14.5 1.0 O1 A:GOL803 4.8 27.0 1.0 O A:HOH1273 4.9 27.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Dap Bii (Space)


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 the Dap Bii (Space) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn811 b:20.2 occ:1.00 NE2 A:GLN32 3.3 21.1 1.0 O A:HOH1272 3.3 20.6 1.0 O A:HOH1058 3.5 27.4 1.0 NE A:ARG186 4.0 12.9 1.0 CG1 A:ILE130 4.0 20.0 1.0 N A:ASP132 4.1 14.6 1.0 CD A:ARG186 4.1 12.5 1.0 CB A:ASP132 4.2 14.8 1.0 CD1 A:ILE130 4.2 21.7 1.0 CD A:GLN32 4.3 20.5 1.0 O A:HOH965 4.5 19.4 1.0 CG A:GLN32 4.5 19.1 1.0 C A:THR131 4.5 14.0 1.0 CA A:ASP132 4.6 14.6 1.0 CG2 A:ILE130 4.6 20.1 1.0 CG A:ARG186 4.7 11.6 1.0 O A:ILE130 4.8 15.0 1.0 C A:ILE130 4.9 14.7 1.0 CB A:ILE130 4.9 17.9 1.0 CA A:THR131 4.9 15.2 1.0 N A:THR131 5.0 14.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Dap Bii (Space)


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 the Dap Bii (Space) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn804 b:12.8 occ:1.00 C B:GLY640 3.7 11.4 1.0 CG B:GLU635 3.9 16.4 1.0 CA B:GLY640 3.9 10.3 1.0 O B:GLY640 3.9 13.1 1.0 N B:SER641 4.1 10.2 1.0 CA B:LYS637 4.2 17.3 1.0 CB B:GLU635 4.2 14.6 1.0 CE2 B:TYR631 4.4 12.4 1.0 CB B:LYS637 4.6 21.7 1.0 CD2 B:TYR631 4.7 11.7 1.0 N B:LYS637 4.8 14.7 1.0 N B:GLY640 4.8 10.4 1.0 CA B:SER641 4.8 11.2 1.0 O B:ASP636 4.9 11.3 1.0 O B:HOH1149 5.0 36.8 1.0

Y.Sakamoto, Y.Suzuki, I.Iizuka, C.Tateoka, S.Roppongi, M.Fujimoto, K.Inaka, H.Tanaka, M.Masaki, K.Ohta, H.Okada, T.Nonaka, Y.Morikawa, K.T.Nakamura, W.Ogasawara, N.Tanaka. S46 Peptidases Are the First Exopeptidases to Be Members of Clan Pa Sci Rep V. 4 4977 2014.
ISSN: ESSN 2045-2322
PubMed: 24827749
DOI: 10.1038/SREP04977