Zinc in PDB 2y7i: Structural Basis For High Arginine Specificity in Salmonella Typhimurium Periplasmic Binding Protein STM4351.

The structure of Structural Basis For High Arginine Specificity in Salmonella Typhimurium Periplasmic Binding Protein STM4351., PDB code: 2y7i was solved by A.L.Stamp, P.Owen, K.El Omari, M.Lockyer, H.K.Lamb, I.G.Charles, A.R.Hawkins, D.K.Stammers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.28 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.317, 56.331, 88.370, 90.00, 100.17, 90.00
R / Rfree (%)	19.805 / 22.602

The binding sites of Zinc atom in the Structural Basis For High Arginine Specificity in Salmonella Typhimurium Periplasmic Binding Protein STM4351. (pdb code 2y7i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structural Basis For High Arginine Specificity in Salmonella Typhimurium Periplasmic Binding Protein STM4351., PDB code: 2y7i:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Structural Basis For High Arginine Specificity in Salmonella Typhimurium Periplasmic Binding Protein STM4351.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis For High Arginine Specificity in Salmonella Typhimurium Periplasmic Binding Protein STM4351. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1246 b:16.2 occ:1.00 OD2 A:ASP157 1.8 16.8 1.0 OD2 A:ASP72 2.1 19.1 1.0 CG A:ASP157 2.7 19.0 1.0 CG A:ASP72 2.7 15.7 1.0 OD1 A:ASP72 2.8 13.9 1.0 OD1 A:ASP157 2.8 18.0 1.0 OG A:SER70 3.9 18.0 1.0 CB A:ASP157 4.1 19.5 1.0 CB A:ASP72 4.2 15.0 1.0 ND2 A:ASN136 4.2 21.3 0.5 CB A:SER70 4.4 16.2 1.0 ND2 A:ASN136 4.4 14.9 0.5 CB A:ASN136 4.7 16.3 0.5 O A:HOH2067 4.8 12.6 1.0 CB A:ASN136 4.9 17.0 0.5 CG A:ASN136 5.0 16.6 0.5

Zinc binding site 2 out of 6 in the Structural Basis For High Arginine Specificity in Salmonella Typhimurium Periplasmic Binding Protein STM4351.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis For High Arginine Specificity in Salmonella Typhimurium Periplasmic Binding Protein STM4351. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1247 b:35.8 occ:1.00 OD2 A:ASP84 2.1 24.7 1.0 ND1 A:HIS26 2.1 27.3 1.0 O A:HOH2150 2.2 38.6 1.0 CG A:ASP84 2.8 23.5 1.0 OD1 A:ASP84 2.9 26.0 1.0 CE1 A:HIS26 2.9 28.9 1.0 CG A:HIS26 3.2 26.4 1.0 CB A:HIS26 3.6 24.6 1.0 O A:THR24 3.8 30.1 1.0 N A:HIS26 3.9 24.7 1.0 NE2 A:HIS26 4.1 28.7 1.0 CB A:ASP84 4.2 22.6 1.0 CD2 A:HIS26 4.2 27.5 1.0 CA A:HIS26 4.4 23.4 1.0 N A:ASP84 4.6 22.6 1.0 C A:LEU25 4.9 25.3 1.0 CA A:ASP84 4.9 21.8 1.0 C A:THR24 4.9 29.8 1.0 CA A:LEU25 5.0 26.5 1.0

Zinc binding site 3 out of 6 in the Structural Basis For High Arginine Specificity in Salmonella Typhimurium Periplasmic Binding Protein STM4351.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis For High Arginine Specificity in Salmonella Typhimurium Periplasmic Binding Protein STM4351. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1248 b:33.5 occ:1.00 OD1 A:ASP42 1.9 37.9 1.0 OD2 A:ASP40 2.1 32.1 1.0 CG A:ASP40 2.8 30.2 1.0 CG A:ASP42 2.9 36.9 1.0 OD1 A:ASP40 3.1 31.2 1.0 OD2 A:ASP42 3.4 38.3 1.0 CB A:LYS44 4.0 28.6 1.0 CG A:LYS44 4.0 31.2 1.0 CB A:ASP40 4.1 28.5 1.0 CB A:ASP42 4.2 37.1 1.0 N A:ASP42 4.3 34.4 1.0 CA A:ASP42 4.7 35.5 1.0 N A:LYS44 4.9 29.3 1.0 C A:ASP42 5.0 34.1 1.0

Zinc binding site 4 out of 6 in the Structural Basis For High Arginine Specificity in Salmonella Typhimurium Periplasmic Binding Protein STM4351.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis For High Arginine Specificity in Salmonella Typhimurium Periplasmic Binding Protein STM4351. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2246 b:49.0 occ:1.00 OD2 B:ASP72 2.0 39.7 1.0 OD1 B:ASP157 2.1 46.6 1.0 O B:HOH2069 2.2 49.5 1.0 CG B:ASP72 2.8 39.1 1.0 OD1 B:ASP72 2.9 38.1 1.0 CG B:ASP157 3.2 45.8 1.0 OD2 B:ASP157 3.6 49.6 1.0 ND2 B:ASN136 4.1 41.8 1.0 OG B:SER70 4.2 40.1 1.0 CB B:ASP72 4.3 38.0 1.0 CB B:ASP157 4.5 42.4 1.0 CB B:ASN136 4.7 38.4 1.0 CA B:ASP157 4.8 40.3 1.0 CG B:ASN136 4.9 40.8 1.0 CB B:SER70 4.9 37.9 1.0 O B:HOH2034 5.0 33.9 1.0

Zinc binding site 5 out of 6 in the Structural Basis For High Arginine Specificity in Salmonella Typhimurium Periplasmic Binding Protein STM4351.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural Basis For High Arginine Specificity in Salmonella Typhimurium Periplasmic Binding Protein STM4351. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2247 b:47.9 occ:1.00 ND1 B:HIS26 2.1 36.7 1.0 OD2 B:ASP84 2.2 37.0 1.0 O B:HOH2070 2.5 43.2 1.0 OD1 B:ASP84 2.8 36.8 1.0 CG B:ASP84 2.8 35.1 1.0 CE1 B:HIS26 2.8 39.3 1.0 CG B:HIS26 3.2 37.0 1.0 CB B:HIS26 3.7 35.8 1.0 N B:HIS26 4.0 33.5 1.0 NE2 B:HIS26 4.0 40.2 1.0 O B:THR24 4.1 37.1 1.0 CD2 B:HIS26 4.2 38.3 1.0 CB B:ASP84 4.3 32.1 1.0 CA B:HIS26 4.5 33.4 1.0 N B:ASP84 4.6 33.2 1.0 C B:LEU25 4.9 32.9 1.0 CA B:LEU25 5.0 33.2 1.0 C B:THR24 5.0 35.8 1.0 CA B:ASP84 5.0 32.5 1.0

Zinc binding site 6 out of 6 in the Structural Basis For High Arginine Specificity in Salmonella Typhimurium Periplasmic Binding Protein STM4351.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural Basis For High Arginine Specificity in Salmonella Typhimurium Periplasmic Binding Protein STM4351. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2250 b:43.8 occ:1.00 O B:HOH2067 2.1 32.5 1.0 O B:HOH2068 2.3 47.4 1.0 O B:HOH2064 2.4 29.3 1.0 O B:HOH2065 2.4 34.5 1.0 O B:HOH2066 2.5 39.7 1.0 OD2 A:ASP228 3.8 22.1 1.0 OD2 B:ASP228 3.9 29.4 1.0 OD1 A:ASP228 4.1 20.7 1.0 OD1 B:ASP228 4.1 25.2 1.0 CG A:ASP228 4.4 20.1 1.0 CG B:ASP228 4.4 25.1 1.0 NE2 A:GLN104 4.5 23.9 1.0 NE2 B:GLN104 4.7 24.2 1.0

A.L.Stamp, P.Owen, K.El Omari, M.Lockyer, H.K.Lamb, I.G.Charles, A.R.Hawkins, D.K.Stammers. Crystallographic and Microcalorimetric Analyses Reveal the Structural Basis For High Arginine Specificity in the Salmonella Enterica Serovar Typhimurium Periplasmic Binding Protein STM4351. Proteins V. 79 2352 2011.
ISSN: ISSN 0887-3585
PubMed: 21560168
DOI: 10.1002/PROT.23060