Zinc in PDB 1eqw: Crystal Structure of Salmonella Typhimurium Cu,Zn Superoxide Dismutase

All present enzymatic activity of Crystal Structure of Salmonella Typhimurium Cu,Zn Superoxide Dismutase:
1.15.1.1;

The structure of Crystal Structure of Salmonella Typhimurium Cu,Zn Superoxide Dismutase, PDB code: 1eqw was solved by A.Pesce, A.Battistoni, M.E.Stroppolo, F.Polizio, M.Nardini, J.S.Kroll, P.R.Langford, P.O'neill, M.Sette, A.Desideri, M.Bolognesi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.60 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	142.140, 40.659, 114.254, 90.00, 107.73, 90.00
R / Rfree (%)	22.6 / 28.3

The structure of Crystal Structure of Salmonella Typhimurium Cu,Zn Superoxide Dismutase also contains other interesting chemical elements:

Copper

(Cu)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Salmonella Typhimurium Cu,Zn Superoxide Dismutase (pdb code 1eqw). 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 Salmonella Typhimurium Cu,Zn Superoxide Dismutase, PDB code: 1eqw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Salmonella Typhimurium Cu,Zn Superoxide Dismutase


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 Salmonella Typhimurium Cu,Zn Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:43.9 occ:1.00 ND1 A:HIS69 1.9 43.0 1.0 ND1 A:HIS78 2.1 50.5 1.0 ND1 A:HIS61 2.1 41.5 1.0 OD1 A:ASP81 2.1 46.6 1.0 CE1 A:HIS69 2.8 39.0 1.0 CG A:ASP81 2.9 47.1 1.0 CG A:HIS78 3.0 49.0 1.0 CG A:HIS69 3.0 43.6 1.0 CE1 A:HIS61 3.0 48.1 1.0 CE1 A:HIS78 3.0 51.0 1.0 OD2 A:ASP81 3.1 43.6 1.0 CG A:HIS61 3.2 39.0 1.0 CB A:HIS78 3.3 44.3 1.0 CB A:HIS69 3.5 43.6 1.0 CB A:HIS61 3.5 40.9 1.0 NE2 A:HIS69 3.9 41.3 1.0 CA A:HIS69 4.0 46.1 1.0 CD2 A:HIS69 4.0 44.7 1.0 CD2 A:HIS78 4.1 47.9 1.0 NE2 A:HIS78 4.1 45.6 1.0 NE2 A:HIS61 4.2 48.6 1.0 CD2 A:HIS61 4.3 50.4 1.0 CB A:ASP81 4.4 39.7 1.0 CD2 A:HIS44 4.7 38.9 1.0 CA A:HIS78 4.7 38.4 1.0 CA A:ASP81 4.8 36.3 1.0 CG A:HIS44 4.8 35.4 1.0 N A:HIS69 4.9 44.0 1.0 C A:HIS69 5.0 45.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Salmonella Typhimurium Cu,Zn Superoxide Dismutase


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 Salmonella Typhimurium Cu,Zn Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:46.8 occ:1.00 ND1 B:HIS69 2.0 53.2 1.0 OD1 B:ASP81 2.1 39.8 1.0 ND1 B:HIS61 2.2 44.7 1.0 ND1 B:HIS78 2.3 46.9 1.0 CG B:ASP81 2.8 45.5 1.0 CE1 B:HIS69 2.9 53.5 1.0 OD2 B:ASP81 2.9 45.0 1.0 CG B:HIS78 3.1 49.2 1.0 CE1 B:HIS61 3.1 46.6 1.0 CG B:HIS69 3.1 53.9 1.0 CB B:HIS78 3.2 48.6 1.0 CG B:HIS61 3.2 46.5 1.0 CE1 B:HIS78 3.4 53.0 1.0 CB B:HIS69 3.6 53.7 1.0 CB B:HIS61 3.6 45.2 1.0 CA B:HIS69 3.9 55.3 1.0 NE2 B:HIS69 4.1 55.7 1.0 CD2 B:HIS69 4.2 52.1 1.0 CD2 B:HIS78 4.2 51.1 1.0 NE2 B:HIS61 4.2 48.4 1.0 CB B:ASP81 4.3 39.7 1.0 CD2 B:HIS61 4.3 44.6 1.0 NE2 B:HIS78 4.3 53.9 1.0 CD2 B:LEU135 4.5 53.4 1.0 CA B:HIS78 4.6 47.2 1.0 CA B:ASP81 4.8 42.6 1.0 O B:LYS68A 4.8 50.5 1.0 C B:HIS69 4.9 52.5 1.0 N B:ASP81 4.9 44.0 1.0 N B:HIS69 5.0 55.6 1.0 CD2 B:HIS44 5.0 39.8 1.0 N B:HIS78 5.0 44.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Salmonella Typhimurium Cu,Zn Superoxide Dismutase


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 Salmonella Typhimurium Cu,Zn Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn505 b:42.0 occ:1.00 ND1 C:HIS61 1.9 32.6 1.0 ND1 C:HIS78 2.0 61.9 1.0 ND1 C:HIS69 2.0 48.3 1.0 OD1 C:ASP81 2.0 39.7 1.0 CE1 C:HIS69 2.8 50.7 1.0 CE1 C:HIS61 2.8 44.5 1.0 CG C:ASP81 2.8 36.7 1.0 CG C:HIS78 2.9 60.1 1.0 OD2 C:ASP81 3.0 35.4 1.0 CE1 C:HIS78 3.0 62.5 1.0 CG C:HIS61 3.1 40.3 1.0 CG C:HIS69 3.1 52.3 1.0 CB C:HIS78 3.2 49.5 1.0 CB C:HIS61 3.5 39.6 1.0 CB C:HIS69 3.7 46.4 1.0 NE2 C:HIS61 3.9 42.7 1.0 NE2 C:HIS69 4.0 53.8 1.0 CA C:HIS69 4.0 48.5 1.0 CD2 C:HIS78 4.1 63.6 1.0 NE2 C:HIS78 4.1 62.2 1.0 CD2 C:HIS61 4.1 42.0 1.0 CD2 C:HIS69 4.2 54.5 1.0 CB C:ASP81 4.3 35.5 1.0 CA C:HIS78 4.6 40.2 1.0 CA C:ASP81 4.7 33.2 1.0 CD2 C:HIS44 4.8 34.6 1.0 N C:HIS78 4.9 35.3 1.0 N C:ASP81 4.9 32.1 1.0 N C:HIS69 4.9 49.6 1.0 O C:LYS68A 4.9 48.5 1.0 CG C:HIS44 5.0 34.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Salmonella Typhimurium Cu,Zn Superoxide Dismutase


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 Salmonella Typhimurium Cu,Zn Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn507 b:53.6 occ:1.00 OD1 D:ASP81 2.0 41.9 1.0 ND1 D:HIS69 2.0 62.1 1.0 ND1 D:HIS61 2.3 56.2 1.0 ND1 D:HIS78 2.3 50.7 1.0 CE1 D:HIS69 2.8 60.9 1.0 CG D:ASP81 2.8 40.9 1.0 OD2 D:ASP81 2.9 49.2 1.0 CG D:HIS78 3.1 50.2 1.0 CE1 D:HIS61 3.1 58.8 1.0 CG D:HIS69 3.2 62.4 1.0 CB D:HIS78 3.3 47.7 1.0 CE1 D:HIS78 3.3 51.4 1.0 CG D:HIS61 3.4 59.3 1.0 CB D:HIS69 3.7 56.7 1.0 CB D:HIS61 3.8 56.4 1.0 NE2 D:HIS69 3.9 61.0 1.0 CA D:HIS69 4.0 57.2 1.0 CD2 D:HIS69 4.2 60.7 1.0 CB D:ASP81 4.2 39.2 1.0 CD2 D:HIS78 4.3 50.3 1.0 NE2 D:HIS61 4.3 59.6 1.0 NE2 D:HIS78 4.4 56.1 1.0 CD2 D:HIS61 4.4 56.2 1.0 CA D:HIS78 4.6 48.5 1.0 CA D:ASP81 4.7 40.9 1.0 CD2 D:HIS44 4.8 43.4 1.0 N D:ASP81 4.9 45.2 1.0 N D:HIS78 4.9 50.1 1.0 O D:LYS68A 5.0 56.0 1.0 CG D:HIS44 5.0 45.6 1.0 C D:HIS69 5.0 58.4 1.0

A.Pesce, A.Battistoni, M.E.Stroppolo, F.Polizio, M.Nardini, J.S.Kroll, P.R.Langford, P.O'neill, M.Sette, A.Desideri, M.Bolognesi. Functional and Crystallographic Characterization of Salmonella Typhimurium Cu,Zn Superoxide Dismutase Coded By the Sodci Virulence Gene. J.Mol.Biol. V. 302 465 2000.
ISSN: ISSN 0022-2836
PubMed: 10970746
DOI: 10.1006/JMBI.2000.4074