Zinc in PDB 2nyd: Crystal Structure of Staphylococcus Aureus Hypothetical Protein SA1388

The structure of Crystal Structure of Staphylococcus Aureus Hypothetical Protein SA1388, PDB code: 2nyd was solved by K.S.Singh, X.Zhang, H.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.51 / 2.00
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	132.547, 132.547, 125.670, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 23.1

The binding sites of Zinc atom in the Crystal Structure of Staphylococcus Aureus Hypothetical Protein SA1388 (pdb code 2nyd). 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 Staphylococcus Aureus Hypothetical Protein SA1388, PDB code: 2nyd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Staphylococcus Aureus Hypothetical Protein SA1388


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 Staphylococcus Aureus Hypothetical Protein SA1388 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:50.3 occ:1.00 OE2 A:GLU329 2.1 17.2 1.0 OD1 A:ASP102 2.2 15.5 1.0 NE2 A:HIS64 2.2 15.4 1.0 O A:HOH604 2.3 13.6 1.0 OD2 A:ASP102 2.3 14.7 1.0 CG A:ASP102 2.6 15.8 1.0 CD A:GLU329 3.0 13.2 1.0 CD2 A:HIS64 3.1 14.6 1.0 CE1 A:HIS64 3.2 15.3 1.0 OE1 A:GLU329 3.3 18.2 1.0 ZN A:ZN402 3.6 48.0 1.0 CB A:ASP102 4.1 18.1 1.0 O A:HOH428 4.1 17.0 1.0 NE2 A:HIS98 4.2 17.8 1.0 CD2 A:HIS98 4.3 14.8 1.0 ND1 A:HIS64 4.3 13.8 1.0 CG A:HIS64 4.3 15.1 1.0 O A:GLY283 4.3 13.0 1.0 CG A:GLU329 4.4 14.2 1.0 CG2 A:VAL108 4.5 14.8 1.0 CG1 A:VAL108 4.7 17.1 1.0 NE2 A:HIS65 4.8 12.0 1.0 CA A:ASP102 4.9 18.5 1.0 CB A:VAL108 4.9 18.1 1.0 C A:GLY283 4.9 13.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Staphylococcus Aureus Hypothetical Protein SA1388


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 Staphylococcus Aureus Hypothetical Protein SA1388 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:48.0 occ:1.00 OE1 A:GLU329 2.2 18.2 1.0 O A:HOH604 2.2 13.6 1.0 NE2 A:HIS65 2.2 12.0 1.0 O B:HOH660 2.3 18.2 1.0 NE2 A:HIS326 2.4 11.4 1.0 CD2 A:HIS65 3.1 14.6 1.0 CE1 A:HIS65 3.2 11.0 1.0 CD A:GLU329 3.2 13.2 1.0 CE1 A:HIS326 3.3 7.5 1.0 CD2 A:HIS326 3.4 11.8 1.0 ZN A:ZN401 3.6 50.3 1.0 OE2 A:GLU329 3.7 17.2 1.0 NE2 A:HIS98 4.0 17.8 1.0 CA A:GLY284 4.2 14.7 1.0 CG A:HIS65 4.2 14.5 1.0 ND1 A:HIS65 4.3 13.4 1.0 NE2 B:HIS309 4.3 19.2 1.0 CD2 A:HIS64 4.3 14.6 1.0 O B:HOH444 4.3 13.1 1.0 ND1 A:HIS326 4.4 13.8 1.0 NE2 A:HIS64 4.5 15.4 1.0 CG A:GLU329 4.5 14.2 1.0 CG A:HIS326 4.5 11.9 1.0 CD2 A:HIS98 4.8 14.8 1.0 O B:HOH429 4.9 16.8 1.0 CE1 A:HIS98 5.0 15.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Staphylococcus Aureus Hypothetical Protein SA1388


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 Staphylococcus Aureus Hypothetical Protein SA1388 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:41.6 occ:1.00 OE2 B:GLU329 2.1 13.5 1.0 O B:HOH615 2.2 10.6 1.0 NE2 B:HIS65 2.3 14.2 1.0 NE2 B:HIS326 2.3 7.2 1.0 O A:HOH579 2.3 12.4 1.0 CD2 B:HIS65 3.1 10.1 1.0 CD B:GLU329 3.2 11.5 1.0 CE1 B:HIS326 3.2 9.3 1.0 CD2 B:HIS326 3.3 9.2 1.0 CE1 B:HIS65 3.3 10.3 1.0 ZN B:ZN402 3.5 47.4 1.0 OE1 B:GLU329 3.6 14.9 1.0 NE2 B:HIS98 4.1 14.9 1.0 CA B:GLY284 4.1 15.4 1.0 NE2 A:HIS309 4.3 12.7 1.0 O A:HOH674 4.3 17.4 1.0 CG B:HIS65 4.3 11.6 1.0 ND1 B:HIS326 4.3 10.8 1.0 CD2 B:HIS64 4.3 14.6 1.0 ND1 B:HIS65 4.3 11.2 1.0 CG B:HIS326 4.4 10.4 1.0 NE2 B:HIS64 4.4 13.3 1.0 CG B:GLU329 4.4 12.3 1.0 O A:HOH664 4.9 17.9 1.0 CD2 B:HIS98 4.9 12.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Staphylococcus Aureus Hypothetical Protein SA1388


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 Staphylococcus Aureus Hypothetical Protein SA1388 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:47.4 occ:1.00 OE1 B:GLU329 2.1 14.9 1.0 OD1 B:ASP102 2.2 13.7 1.0 O B:HOH615 2.2 10.6 1.0 NE2 B:HIS64 2.2 13.3 1.0 OD2 B:ASP102 2.4 12.9 1.0 CG B:ASP102 2.6 17.0 1.0 CD B:GLU329 3.0 11.5 1.0 CE1 B:HIS64 3.2 14.3 1.0 CD2 B:HIS64 3.2 14.6 1.0 OE2 B:GLU329 3.3 13.5 1.0 ZN B:ZN401 3.5 41.6 1.0 CB B:ASP102 4.1 16.2 1.0 O B:HOH668 4.1 14.9 1.0 NE2 B:HIS98 4.2 14.9 1.0 CD2 B:HIS98 4.3 12.4 1.0 ND1 B:HIS64 4.3 11.8 1.0 O B:GLY283 4.3 14.6 1.0 CG B:HIS64 4.3 13.0 1.0 CG B:GLU329 4.4 12.3 1.0 CG2 B:VAL108 4.6 14.2 1.0 NE2 B:HIS65 4.8 14.2 1.0 CG1 B:VAL108 4.8 14.6 1.0 CA B:ASP102 4.9 16.3 1.0 CB B:VAL108 4.9 13.6 1.0

K.Singh Saikatendu, X.Zhang, L.Kinch, M.Leybourne, N.V.Grishin, H.Zhang. Structure of A Conserved Hypothetical Protein SA1388 From S. Aureus Reveals A Capped Hexameric Toroid with Two Pii Domain Lids and A Dinuclear Metal Center. Bmc Struct.Biol. V. 6 27 2006.
ISSN: ESSN 1472-6807
PubMed: 17187687
DOI: 10.1186/1472-6807-6-27