Zinc in PDB 4q8r: Crystal Structure of A Phosphate Binding Protein (Pbp-1) From Clostridium Perfringens

The structure of Crystal Structure of A Phosphate Binding Protein (Pbp-1) From Clostridium Perfringens, PDB code: 4q8r was solved by D.Gonzalez, M.Richez, C.Bergonzi, E.Chabriere, M.Elias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.56 / 1.65
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	70.780, 105.730, 146.450, 90.00, 90.00, 90.00
R / Rfree (%)	13.2 / 17.8

The binding sites of Zinc atom in the Crystal Structure of A Phosphate Binding Protein (Pbp-1) From Clostridium Perfringens (pdb code 4q8r). 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 A Phosphate Binding Protein (Pbp-1) From Clostridium Perfringens, PDB code: 4q8r:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A Phosphate Binding Protein (Pbp-1) From Clostridium Perfringens


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 A Phosphate Binding Protein (Pbp-1) From Clostridium Perfringens within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:94.8 occ:1.00 NE2 A:HIS241 2.3 55.6 1.0 O A:HOH518 2.9 56.9 1.0 CD2 A:HIS241 3.2 51.6 1.0 CE1 A:HIS241 3.3 53.7 1.0 O A:HOH547 3.3 51.9 1.0 O A:HOH489 3.8 45.9 1.0 ND1 A:HIS241 4.4 47.1 1.0 CG A:HIS241 4.4 44.8 1.0 O A:LYS239 4.7 35.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Phosphate Binding Protein (Pbp-1) From Clostridium Perfringens


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 A Phosphate Binding Protein (Pbp-1) From Clostridium Perfringens within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:46.3 occ:0.50 OE2 A:GLU231 1.8 51.9 0.3 OE2 A:GLU231 2.0 42.6 0.7 OD2 A:ASP235 2.0 38.1 1.0 CG A:ASP235 2.7 38.9 1.0 OD1 A:ASP235 2.7 43.8 1.0 CD A:GLU231 2.8 41.8 0.7 CD A:GLU231 3.0 43.0 0.3 OE1 A:GLU231 3.0 37.4 0.7 CG A:GLU231 3.7 43.6 0.3 OE1 A:GLU231 3.9 40.1 0.3 O A:HOH583 4.1 62.6 1.0 CB A:ASP235 4.2 34.4 1.0 O A:HOH466 4.2 54.0 1.0 CG A:GLU231 4.2 40.5 0.7 O A:GLU231 4.4 45.7 1.0 O A:HOH442 4.5 50.4 1.0 NZ A:LYS244 4.7 40.9 1.0 O A:HOH503 5.0 56.8 1.0 C A:GLU231 5.0 44.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Phosphate Binding Protein (Pbp-1) From Clostridium Perfringens


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 A Phosphate Binding Protein (Pbp-1) From Clostridium Perfringens within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:36.6 occ:1.00 O A:HOH551 2.0 39.0 1.0 NE2 A:HIS86 2.1 31.0 1.0 O A:HOH566 2.2 38.8 1.0 O A:HOH552 2.7 63.1 1.0 CD2 A:HIS86 3.0 30.1 1.0 CE1 A:HIS86 3.1 28.9 1.0 CG A:GLU167 4.1 33.8 1.0 ND1 A:HIS86 4.2 30.1 1.0 CG A:HIS86 4.2 28.3 1.0 O A:HOH553 4.2 38.9 1.0 OE2 A:GLU167 4.2 37.8 1.0 O A:HOH423 4.3 33.9 1.0 CD A:GLU167 4.6 37.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Phosphate Binding Protein (Pbp-1) From Clostridium Perfringens


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 A Phosphate Binding Protein (Pbp-1) From Clostridium Perfringens within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:35.6 occ:0.80 O A:HOH550 1.8 57.8 1.0 OE2 A:GLU73 1.8 31.4 0.4 OD1 A:ASP61 2.0 43.8 1.0 OE2 A:GLU73 2.2 42.5 0.6 CD A:GLU73 2.4 40.3 0.4 OE1 A:GLU73 2.5 50.5 0.4 OE1 A:GLU73 2.8 55.0 0.6 CD A:GLU73 2.8 41.2 0.6 CG A:ASP61 2.9 39.7 1.0 OD2 A:ASP61 3.1 47.9 1.0 O A:HOH557 3.1 68.1 1.0 O A:HOH574 3.2 38.5 1.0 CG A:GLU73 3.8 42.5 0.4 N A:LEU62 4.1 38.2 1.0 CG A:GLU73 4.3 40.8 0.6 CB A:ASP61 4.3 38.4 1.0 CB A:LEU62 4.6 35.8 1.0 CB A:GLU73 4.6 38.6 0.4 CD1 A:LEU209 4.6 34.2 1.0 CA A:ASP61 4.7 33.1 1.0 CB A:GLU73 4.8 40.2 0.6 CG A:LEU62 4.8 29.9 1.0 O A:LEU62 4.9 42.0 1.0 CA A:LEU62 4.9 36.2 1.0 C A:ASP61 4.9 34.5 1.0

D.Gonzalez, M.Richez, C.Bergonzi, E.Chabriere, M.Elias. Crystal Structure of the Phosphate-Binding Protein (Pbp-1) of An Abc-Type Phosphate Transporter From Clostridium Perfringens. Sci Rep V. 4 6636 2014.
ISSN: ESSN 2045-2322
PubMed: 25338617
DOI: 10.1038/SREP06636