Zinc in PDB 4lmy: Structure of Gas Perr-Zn-Zn

The structure of Structure of Gas Perr-Zn-Zn, PDB code: 4lmy was solved by C.S.Lin, S.Y.Chao, J.C.Nix, H.L.Tseng, C.C.Tsou, C.H.Fei, H.S.Ciou, U.S.Jeng, Y.S.Lin, W.J.Chuang, J.J.Wu, S.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.17 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.109, 87.496, 59.389, 90.00, 94.78, 90.00
R / Rfree (%)	22 / 23.9

The binding sites of Zinc atom in the Structure of Gas Perr-Zn-Zn (pdb code 4lmy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Gas Perr-Zn-Zn, PDB code: 4lmy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Gas Perr-Zn-Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Gas Perr-Zn-Zn within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:25.5 occ:1.00 NE2 A:HIS99 2.2 25.5 1.0 NE2 A:HIS19 2.2 23.3 1.0 NE2 A:HIS4 2.2 23.0 1.0 ND2 A:ASN15 2.2 19.3 1.0 NE2 A:HIS6 2.2 24.9 1.0 NE2 A:HIS97 2.2 24.8 1.0 CD2 A:HIS6 3.1 28.1 1.0 CE1 A:HIS99 3.1 23.9 1.0 CE1 A:HIS4 3.1 27.8 1.0 CD2 A:HIS19 3.1 24.9 1.0 CD2 A:HIS99 3.1 20.8 1.0 CE1 A:HIS97 3.2 24.2 1.0 CE1 A:HIS19 3.2 26.4 1.0 CD2 A:HIS4 3.2 27.4 1.0 CD2 A:HIS97 3.2 21.1 1.0 CG A:ASN15 3.3 24.2 1.0 CE1 A:HIS6 3.3 26.5 1.0 OD1 A:ASN15 3.6 27.7 1.0 ND1 A:HIS99 4.2 26.1 1.0 ND1 A:HIS4 4.3 28.4 1.0 CG A:HIS99 4.3 23.9 1.0 CG A:HIS6 4.3 30.5 1.0 ND1 A:HIS19 4.3 27.6 1.0 CG A:HIS19 4.3 23.0 1.0 ND1 A:HIS97 4.3 23.1 1.0 CG A:HIS4 4.3 28.9 1.0 ND1 A:HIS6 4.4 29.5 1.0 CG A:HIS97 4.4 21.1 1.0 CB A:ASN15 4.6 20.3 1.0 CE A:MET114 4.8 35.0 1.0

Zinc binding site 2 out of 4 in the Structure of Gas Perr-Zn-Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Gas Perr-Zn-Zn within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:21.4 occ:1.00 SG A:CYS107 2.3 21.9 1.0 SG A:CYS144 2.3 20.3 1.0 SG A:CYS104 2.4 20.3 1.0 SG A:CYS147 2.4 23.0 1.0 CB A:CYS104 3.2 20.2 1.0 CB A:CYS147 3.3 20.6 1.0 CB A:CYS107 3.3 18.9 1.0 CB A:CYS144 3.4 16.0 1.0 N A:CYS107 3.7 18.7 1.0 NZ A:LYS109 3.8 41.8 1.0 N A:CYS144 4.0 16.1 1.0 CA A:CYS107 4.1 18.6 1.0 N A:CYS147 4.2 23.7 1.0 CA A:CYS144 4.2 18.9 1.0 CA A:CYS147 4.3 22.0 1.0 CB A:ILE106 4.7 22.7 1.0 CA A:CYS104 4.7 17.6 1.0 O A:CYS144 4.7 19.0 1.0 C A:CYS144 4.8 17.1 1.0 N A:GLY108 4.8 20.3 1.0 C A:CYS107 4.8 20.8 1.0 C A:ILE106 4.8 26.1 1.0 CE A:LYS109 4.9 30.2 1.0

Zinc binding site 3 out of 4 in the Structure of Gas Perr-Zn-Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Gas Perr-Zn-Zn within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:27.3 occ:1.00 NE2 B:HIS99 2.1 22.1 1.0 NE2 B:HIS6 2.2 29.4 1.0 NE2 B:HIS19 2.2 22.2 1.0 NE2 B:HIS4 2.2 23.4 1.0 NE2 B:HIS97 2.2 26.8 1.0 ND2 B:ASN15 2.2 19.7 1.0 CE1 B:HIS4 3.1 23.8 1.0 CD2 B:HIS6 3.1 27.3 1.0 CE1 B:HIS99 3.1 29.4 1.0 CD2 B:HIS19 3.1 25.2 1.0 CD2 B:HIS99 3.1 25.2 1.0 CD2 B:HIS97 3.1 22.6 1.0 CE1 B:HIS19 3.2 31.2 1.0 CE1 B:HIS6 3.2 31.5 1.0 CE1 B:HIS97 3.2 21.3 1.0 CG B:ASN15 3.2 24.4 1.0 CD2 B:HIS4 3.3 31.4 1.0 OD1 B:ASN15 3.5 28.1 1.0 ND1 B:HIS99 4.2 25.2 1.0 ND1 B:HIS4 4.2 28.9 1.0 CG B:HIS99 4.3 22.8 1.0 CG B:HIS6 4.3 30.0 1.0 ND1 B:HIS19 4.3 31.1 1.0 ND1 B:HIS6 4.3 30.1 1.0 CG B:HIS19 4.3 26.1 1.0 ND1 B:HIS97 4.3 25.0 1.0 CG B:HIS97 4.3 25.0 1.0 CG B:HIS4 4.3 32.5 1.0 CB B:ASN15 4.6 21.5 1.0

Zinc binding site 4 out of 4 in the Structure of Gas Perr-Zn-Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Gas Perr-Zn-Zn within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:23.7 occ:1.00 SG B:CYS144 2.3 23.4 1.0 SG B:CYS104 2.3 22.5 1.0 SG B:CYS107 2.3 26.0 1.0 SG B:CYS147 2.4 25.5 1.0 CB B:CYS147 3.2 22.7 1.0 CB B:CYS104 3.2 22.3 1.0 CB B:CYS107 3.3 25.6 1.0 CB B:CYS144 3.4 19.6 1.0 N B:CYS107 3.7 23.5 1.0 N B:CYS144 4.0 22.2 1.0 O B:HOH358 4.0 30.8 1.0 CA B:CYS107 4.1 23.0 1.0 O B:HOH353 4.1 29.8 1.0 N B:CYS147 4.3 23.5 1.0 CA B:CYS144 4.3 21.6 1.0 CA B:CYS147 4.3 26.3 1.0 CB B:ILE106 4.6 25.7 1.0 CA B:CYS104 4.7 19.2 1.0 O B:CYS144 4.7 21.8 1.0 C B:ILE106 4.8 28.8 1.0 C B:CYS107 4.8 26.4 1.0 CB B:LYS109 4.8 26.1 1.0 C B:CYS144 4.9 23.4 1.0 N B:GLY108 4.9 21.6 1.0

C.S.Lin, S.Y.Chao, M.Hammel, J.C.Nix, H.L.Tseng, C.C.Tsou, C.H.Fei, H.S.Chiou, U.S.Jeng, Y.S.Lin, W.J.Chuang, J.J.Wu, S.Wang. Distinct Structural Features of the Peroxide Response Regulator From Group A Streptococcus Drive Dna Binding Plos One V. 9 89027 2014.
ISSN: ESSN 1932-6203
PubMed: 24586487
DOI: 10.1371/JOURNAL.PONE.0089027