Sodium in PDB 6vbb: 2.60 Angstrom Resolution Crystal Structure of Peptidase S41 From Acinetobacter Baumannii

The structure of 2.60 Angstrom Resolution Crystal Structure of Peptidase S41 From Acinetobacter Baumannii, PDB code: 6vbb was solved by G.Minasov, Z.Wawrzak, L.Shuvalova, O.Kiryukhina, I.Dubrovska, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.43 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.311, 102.525, 68.035, 90.00, 116.28, 90.00
R / Rfree (%)	18.3 / 23.7

The structure of 2.60 Angstrom Resolution Crystal Structure of Peptidase S41 From Acinetobacter Baumannii also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the 2.60 Angstrom Resolution Crystal Structure of Peptidase S41 From Acinetobacter Baumannii (pdb code 6vbb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 2.60 Angstrom Resolution Crystal Structure of Peptidase S41 From Acinetobacter Baumannii, PDB code: 6vbb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the 2.60 Angstrom Resolution Crystal Structure of Peptidase S41 From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.60 Angstrom Resolution Crystal Structure of Peptidase S41 From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:48.9 occ:1.00 O A:LEU285 2.3 56.9 1.0 O A:LEU264 2.3 49.2 1.0 O A:ASP261 2.3 42.4 1.0 OD1 A:ASP261 2.3 46.8 1.0 O A:HOH562 2.5 47.3 1.0 CG A:ASP261 3.3 46.0 1.0 C A:ASP261 3.4 40.8 1.0 C A:LEU285 3.4 59.4 1.0 C A:LEU264 3.5 48.0 1.0 N A:LEU285 3.5 52.8 1.0 CA A:ASP261 3.9 44.7 1.0 CA A:LEU285 4.0 59.2 1.0 CB A:ASP261 4.1 46.7 1.0 OD2 A:ASP261 4.1 50.7 1.0 CA A:ASN265 4.3 54.0 1.0 N A:ASN265 4.3 51.0 1.0 O A:HOH572 4.4 51.4 1.0 CB A:LEU285 4.4 62.9 1.0 N A:LEU264 4.4 42.9 1.0 O A:GLY287 4.4 0.7 1.0 CA A:LEU264 4.5 42.1 1.0 OD1 A:ASN265 4.5 61.9 1.0 N A:LEU262 4.5 39.1 1.0 N A:PRO286 4.5 65.3 1.0 C A:PRO286 4.6 68.7 1.0 O A:PRO286 4.6 61.8 1.0 C A:ALA284 4.7 48.8 1.0 CB A:ALA284 4.7 51.3 1.0 N A:GLY287 4.9 89.4 1.0 CA A:PRO286 4.9 67.3 1.0 CA A:LEU262 4.9 41.0 1.0 C A:LEU262 4.9 39.2 1.0 C A:ASN265 5.0 57.2 1.0 CA A:ALA284 5.0 50.7 1.0

Sodium binding site 2 out of 2 in the 2.60 Angstrom Resolution Crystal Structure of Peptidase S41 From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2.60 Angstrom Resolution Crystal Structure of Peptidase S41 From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:65.9 occ:1.00 O B:ASP261 2.3 71.0 1.0 O B:LEU285 2.3 80.9 1.0 O B:LEU264 2.3 73.6 1.0 OD1 B:ASP261 2.3 70.5 1.0 CG B:ASP261 3.3 62.8 1.0 C B:ASP261 3.4 61.3 1.0 C B:LEU285 3.4 81.3 1.0 C B:LEU264 3.5 71.9 1.0 N B:LEU285 3.6 73.8 1.0 CA B:ASP261 3.9 59.0 1.0 CA B:LEU285 4.0 81.5 1.0 CB B:ASP261 4.1 60.4 1.0 OD2 B:ASP261 4.2 71.5 1.0 CA B:ASN265 4.3 81.8 1.0 N B:ASN265 4.3 77.1 1.0 N B:LEU264 4.4 64.3 1.0 CB B:LEU285 4.4 85.9 1.0 C B:PRO286 4.5 94.0 1.0 CA B:LEU264 4.5 68.4 1.0 N B:PRO286 4.5 89.0 1.0 N B:LEU262 4.5 61.4 1.0 O B:PRO286 4.5 91.8 1.0 O B:GLY287 4.7 95.2 1.0 C B:ALA284 4.7 72.0 1.0 CB B:ALA284 4.7 65.9 1.0 N B:GLY287 4.8 0.2 1.0 CA B:PRO286 4.8 89.8 1.0 C B:LEU262 4.9 63.8 1.0 CA B:LEU262 4.9 64.7 1.0 C B:ASN265 5.0 82.0 1.0 CA B:ALA284 5.0 68.1 1.0

G.Minasov, Z.Wawrzak, L.Shuvalova, O.Kiryukhina, I.Dubrovska, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid). 2.60 Angstrom Resolution Crystal Structure of Peptidase S41 From Acinetobacter Baumannii To Be Published.