Zinc in PDB 2zkt: Structure of PH0037 Protein From Pyrococcus Horikoshii

All present enzymatic activity of Structure of PH0037 Protein From Pyrococcus Horikoshii:
5.4.2.1;

The structure of Structure of PH0037 Protein From Pyrococcus Horikoshii, PDB code: 2zkt was solved by N.K.Lokanath, K.J.Pampa, N.Kunishima, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.40
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	155.900, 155.900, 230.857, 90.00, 90.00, 120.00
R / Rfree (%)	27.7 / 28.6

The structure of Structure of PH0037 Protein From Pyrococcus Horikoshii also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Structure of PH0037 Protein From Pyrococcus Horikoshii (pdb code 2zkt). 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 PH0037 Protein From Pyrococcus Horikoshii, PDB code: 2zkt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of PH0037 Protein From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of PH0037 Protein From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn414 b:50.2 occ:1.00 OG A:SER60 2.2 61.5 1.0 OD2 A:ASP346 2.3 60.3 1.0 OD1 A:ASP13 2.3 57.5 1.0 NE2 A:HIS347 2.3 48.5 1.0 OD2 A:ASP13 2.7 55.6 1.0 CG A:ASP13 2.8 51.9 1.0 CB A:SER60 2.9 51.3 1.0 CD2 A:HIS347 3.1 45.2 1.0 CG A:ASP346 3.3 51.5 1.0 CA A:SER60 3.4 50.3 1.0 CE1 A:HIS347 3.4 43.3 1.0 OD1 A:ASP346 3.6 54.0 1.0 N A:SER60 4.2 49.5 1.0 CB A:ASP13 4.3 49.5 1.0 CE1 A:HIS356 4.3 50.8 1.0 CG A:HIS347 4.4 45.0 1.0 ND1 A:HIS347 4.5 42.9 1.0 OD2 A:ASP305 4.5 58.6 1.0 C A:SER60 4.6 48.8 1.0 ZN A:ZN415 4.6 52.9 1.0 NE2 A:HIS356 4.6 53.3 1.0 CB A:ASP346 4.6 44.8 1.0 CG A:ASP305 4.7 54.7 1.0 CE1 A:HIS64 4.7 45.0 1.0 O A:SER60 4.7 49.8 1.0 CA A:ASP13 4.8 48.7 1.0 N A:GLY14 4.8 46.8 1.0 OD1 A:ASP305 4.9 48.9 1.0 ND1 A:HIS64 5.0 46.2 1.0

Zinc binding site 2 out of 4 in the Structure of PH0037 Protein From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of PH0037 Protein From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn415 b:52.9 occ:1.00 OD2 A:ASP305 2.2 58.6 1.0 NE2 A:HIS356 2.3 53.3 1.0 NE2 A:HIS309 2.4 56.5 1.0 CG A:ASP305 2.9 54.7 1.0 OD1 A:ASP305 3.0 48.9 1.0 CE1 A:HIS356 3.3 50.8 1.0 CD2 A:HIS309 3.3 54.7 1.0 CE1 A:HIS309 3.4 56.2 1.0 CD2 A:HIS356 3.4 51.6 1.0 CE1 A:HIS347 4.4 43.3 1.0 CB A:ASP305 4.4 53.0 1.0 ND1 A:HIS356 4.4 54.2 1.0 CG A:HIS309 4.5 55.5 1.0 ND1 A:HIS309 4.5 56.2 1.0 CG A:HIS356 4.5 52.3 1.0 OD1 A:ASP13 4.5 57.5 1.0 NE2 A:HIS347 4.5 48.5 1.0 NZ A:LYS302 4.6 63.8 1.0 ZN A:ZN414 4.6 50.2 1.0 OG1 A:THR349 4.8 44.8 1.0 CE A:LYS302 5.0 57.5 1.0

Zinc binding site 3 out of 4 in the Structure of PH0037 Protein From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of PH0037 Protein From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn414 b:55.0 occ:1.00 OD2 B:ASP346 2.3 64.6 1.0 OD1 B:ASP13 2.3 56.6 1.0 NE2 B:HIS347 2.4 58.0 1.0 OG B:SER60 2.6 60.4 1.0 OD2 B:ASP13 2.7 59.3 1.0 CG B:ASP13 2.7 50.4 1.0 CD2 B:HIS347 3.1 52.0 1.0 CG B:ASP346 3.3 51.9 1.0 CB B:SER60 3.5 52.7 1.0 CE1 B:HIS347 3.5 51.7 1.0 OD1 B:ASP346 3.6 54.0 1.0 CA B:SER60 4.0 51.0 1.0 CB B:ASP13 4.2 46.0 1.0 CE1 B:HIS356 4.2 37.4 1.0 CG B:HIS347 4.3 49.3 1.0 NE2 B:HIS356 4.4 44.8 1.0 ZN B:ZN415 4.5 61.7 1.0 CG B:ASP305 4.5 58.0 1.0 ND1 B:HIS347 4.6 53.5 1.0 OD2 B:ASP305 4.6 63.2 1.0 N B:GLY14 4.6 44.3 1.0 CB B:ASP346 4.6 46.4 1.0 CA B:ASP13 4.6 45.8 1.0 OD1 B:ASP305 4.7 54.3 1.0 CE B:LYS302 4.7 66.7 1.0 CE1 B:HIS64 4.7 43.7 1.0 N B:SER60 4.8 49.9 1.0 CD B:LYS302 4.9 63.3 1.0 C B:ASP13 5.0 45.2 1.0

Zinc binding site 4 out of 4 in the Structure of PH0037 Protein From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of PH0037 Protein From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn415 b:61.7 occ:1.00 OD2 B:ASP305 2.1 63.2 1.0 NE2 B:HIS356 2.3 44.8 1.0 NE2 B:HIS309 2.4 61.4 1.0 CG B:ASP305 2.8 58.0 1.0 OD1 B:ASP305 2.8 54.3 1.0 CD2 B:HIS309 3.0 56.9 1.0 CD2 B:HIS356 3.1 44.7 1.0 CE1 B:HIS356 3.4 37.4 1.0 CE1 B:HIS309 3.6 62.4 1.0 CE1 B:HIS347 4.2 51.7 1.0 CB B:ASP305 4.2 53.9 1.0 NE2 B:HIS347 4.2 58.0 1.0 CG B:HIS309 4.3 57.3 1.0 CG B:HIS356 4.3 47.0 1.0 ND1 B:HIS356 4.4 47.7 1.0 OD1 B:ASP13 4.4 56.6 1.0 OG1 B:THR349 4.5 41.7 1.0 ZN B:ZN414 4.5 55.0 1.0 ND1 B:HIS309 4.5 60.5 1.0 NZ B:LYS302 4.6 68.9 1.0 O B:ASP305 4.8 51.1 1.0 CE B:LYS302 4.9 66.7 1.0

N.K.Lokanath, K.J.Pampa, N.Kunishima. Structure of PH0037 Protein From Pyrococcus Horikoshii To Be Published.