Zinc in PDB 1xtm: Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis.

The structure of Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis., PDB code: 1xtm was solved by V.Calderone, S.Mangani, L.Banci, M.Benvenuti, I.Bertini, A.Fantoni, M.S.Viezzoli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.60 / 1.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	52.462, 104.350, 58.756, 90.00, 90.00, 90.00
R / Rfree (%)	25.3 / 26.6

The structure of Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis. also contains other interesting chemical elements:

Copper

(Cu)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis. (pdb code 1xtm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis., PDB code: 1xtm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis.


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 Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:20.3 occ:1.00 OD2 B:ASP124 2.0 8.8 1.0 ND1 B:HIS104 2.0 13.3 1.0 ND1 B:HIS121 2.0 17.5 1.0 ND1 B:HIS112 2.1 12.1 1.0 CE1 B:HIS104 2.8 19.3 1.0 CG B:ASP124 2.8 14.5 1.0 CE1 B:HIS112 2.9 10.6 1.0 CE1 B:HIS121 2.9 13.4 1.0 OD1 B:ASP124 2.9 15.9 1.0 CG B:HIS121 3.1 13.8 1.0 CG B:HIS104 3.1 15.5 1.0 CG B:HIS112 3.2 15.6 1.0 CB B:HIS121 3.5 12.7 1.0 CB B:HIS104 3.6 14.8 1.0 CB B:HIS112 3.6 17.7 1.0 O B:PRO176 3.8 25.9 1.0 NE2 B:HIS104 4.0 18.5 1.0 CA B:HIS112 4.0 17.3 1.0 NE2 B:HIS121 4.1 17.5 1.0 NE2 B:HIS112 4.1 12.0 1.0 CD2 B:HIS104 4.2 15.6 1.0 CD2 B:HIS121 4.2 16.8 1.0 CD2 B:HIS112 4.2 15.4 1.0 CB B:ASP124 4.3 11.4 1.0 N B:HIS121 4.7 13.7 1.0 N B:GLY113 4.7 16.7 1.0 CA B:HIS121 4.7 12.9 1.0 CA B:ASP124 4.8 11.4 1.0 C B:HIS112 4.9 16.3 1.0 C B:PRO176 4.9 26.7 1.0 O B:HOH567 4.9 34.9 1.0 CD2 B:HIS86 4.9 16.1 1.0 N B:ASP124 5.0 10.5 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis.


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 Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:21.4 occ:1.00 OD1 B:ASP137 1.9 13.2 1.0 NE2 B:HIS71 2.2 19.3 1.0 CG B:ASP137 2.8 14.0 1.0 OD2 B:ASP137 2.9 18.5 1.0 CE1 B:HIS71 3.0 19.3 1.0 CD2 B:HIS71 3.2 16.6 1.0 ND1 B:HIS71 4.2 18.0 1.0 CB B:ASP137 4.2 16.6 1.0 CB B:SER73 4.2 14.7 1.0 OG B:SER73 4.3 16.9 1.0 CG B:HIS71 4.3 16.9 1.0 C B:ASP137 4.6 16.3 1.0 CA B:ASP137 4.7 15.8 1.0 O B:ASP137 4.8 15.1 1.0 N B:VAL138 4.8 16.5 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis.


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 Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn505 b:26.9 occ:0.30 O B:HOH553 2.0 28.8 1.0 O B:HOH642 2.0 39.8 1.0 OD2 B:ASP144 2.2 15.0 1.0 NE2 B:HIS120 2.3 24.5 1.0 CE1 B:HIS120 3.0 23.6 1.0 CG B:ASP144 3.1 15.0 1.0 CD2 B:HIS120 3.4 21.2 1.0 OD1 B:ASP144 3.7 15.0 1.0 CB B:ASP144 4.0 15.0 1.0 ND1 B:HIS120 4.2 21.7 1.0 O B:HOH523 4.3 20.2 1.0 O B:HOH530 4.3 18.1 1.0 CG B:HIS120 4.4 18.7 1.0 CG B:PRO143 4.6 19.3 1.0 N B:ASP144 5.0 15.0 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis.


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 Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn506 b:22.0 occ:0.50 OD2 B:ASP157 2.3 27.2 1.0 OD1 B:ASP157 2.5 26.2 1.0 O B:HOH628 2.5 24.9 1.0 O B:GLY160 2.5 16.3 1.0 O B:GLU89 2.5 17.1 1.0 CG B:ASP157 2.8 26.3 1.0 CB B:ASP159 3.1 15.0 1.0 O B:HOH609 3.4 28.2 1.0 C B:GLY160 3.5 15.4 1.0 C B:GLU89 3.7 15.6 1.0 N B:GLY160 3.9 18.8 1.0 CA B:ASP159 4.1 15.0 1.0 C B:ASP159 4.1 15.0 1.0 OG B:SER161 4.1 16.2 1.0 CG B:ASP159 4.2 15.0 1.0 CA B:GLY160 4.2 16.1 1.0 O B:HOH631 4.3 41.5 1.0 CB B:ASP157 4.3 24.0 1.0 OD2 B:ASP159 4.3 15.0 1.0 CA B:GLU89 4.5 15.4 1.0 N B:ASP159 4.5 15.0 1.0 N B:LYS90 4.6 16.2 1.0 N B:SER161 4.6 13.2 1.0 O B:ASP159 4.6 20.3 1.0 CA B:LYS90 4.7 16.6 1.0 CA B:SER161 4.8 12.9 1.0 O B:ILE155 4.9 17.3 1.0 O B:HOH613 4.9 28.8 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Double Mutant Y88H-P104H of A Sod-Like Protein From Bacillus Subtilis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:33.0 occ:0.80 ND1 A:HIS121 1.9 36.5 1.0 OD2 A:ASP124 2.0 27.5 1.0 ND1 A:HIS104 2.1 32.1 1.0 ND1 A:HIS112 2.1 32.9 1.0 CE1 A:HIS121 2.7 35.9 1.0 CG A:ASP124 2.9 28.1 1.0 CE1 A:HIS104 2.9 31.6 1.0 CG A:HIS121 3.0 35.5 1.0 OD1 A:ASP124 3.1 29.9 1.0 CE1 A:HIS112 3.1 32.8 1.0 CG A:HIS112 3.2 35.0 1.0 CG A:HIS104 3.2 34.8 1.0 CB A:HIS112 3.5 35.0 1.0 CB A:HIS121 3.5 35.5 1.0 CB A:HIS104 3.6 38.1 1.0 O A:PRO176 3.8 31.9 1.0 NE2 A:HIS121 3.9 35.3 1.0 CA A:HIS112 4.0 35.1 1.0 CD2 A:HIS121 4.1 36.0 1.0 NE2 A:HIS104 4.1 33.5 1.0 NE2 A:HIS112 4.2 32.5 1.0 CD2 A:HIS104 4.2 33.6 1.0 CD2 A:HIS86 4.3 27.9 1.0 CD2 A:HIS112 4.3 33.0 1.0 CB A:ASP124 4.4 28.2 1.0 N A:GLY113 4.8 33.9 1.0 CA A:HIS121 4.8 35.6 1.0 NE2 A:HIS86 4.8 28.0 1.0 N A:HIS121 4.8 36.2 1.0 CA A:ASP124 4.9 27.8 1.0 CG A:HIS86 4.9 27.1 1.0 C A:HIS112 4.9 34.7 1.0 C A:PRO176 4.9 31.6 1.0 N A:HIS112 5.0 35.9 1.0

L.Banci, M.Benvenuti, I.Bertini, D.E.Cabelli, V.Calderone, A.Fantoni, S.Mangani, M.Migliardi, M.S.Viezzoli. From An Inactive Prokaryotic Sod Homologue to An Active Protein Through Site-Directed Mutagenesis. J.Am.Chem.Soc. V. 127 13287 2005.
ISSN: ISSN 0002-7863
PubMed: 16173759
DOI: 10.1021/JA052790O