Sodium in PDB 2o34: Crystal Structure of Protein DVU1097 From Desulfovibrio Vulgaris Hildenborough, Pfam DUF375

The structure of Crystal Structure of Protein DVU1097 From Desulfovibrio Vulgaris Hildenborough, Pfam DUF375, PDB code: 2o34 was solved by V.N.Malashkevich, R.Toro, J.M.Sauder, K.D.Schwinn, D.A.Thompson, M.E.Rutter, M.Dickey, C.Groshong, K.T.Bain, J.M.Adams, C.Reyes, I.Rooney, A.Powell, A.Boice, T.Gheyi, S.Ozyurt, S.Atwell, S.R.Wasserman, S.Emtage, S.K.Burley, S.C.Almo, New York Sgx Research Center For Structuralgenomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.98 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.480, 81.480, 151.170, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 27.3

The binding sites of Sodium atom in the Crystal Structure of Protein DVU1097 From Desulfovibrio Vulgaris Hildenborough, Pfam DUF375 (pdb code 2o34). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Protein DVU1097 From Desulfovibrio Vulgaris Hildenborough, Pfam DUF375, PDB code: 2o34:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Protein DVU1097 From Desulfovibrio Vulgaris Hildenborough, Pfam DUF375


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Protein DVU1097 From Desulfovibrio Vulgaris Hildenborough, Pfam DUF375 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:34.5 occ:1.00 OD1 A:ASP196 2.2 32.8 1.0 O A:HOH615 2.3 38.0 1.0 OG1 A:THR200 2.3 35.0 1.0 O A:HOH639 2.4 37.5 1.0 O A:ALA102 2.4 34.6 1.0 O A:ASP196 2.4 31.6 1.0 CG A:ASP196 3.2 32.8 1.0 C A:ASP196 3.3 32.5 1.0 O A:HOH714 3.4 51.8 1.0 C A:ALA102 3.5 34.4 1.0 CB A:THR200 3.6 34.6 1.0 OD2 A:ASP196 3.9 31.6 1.0 CA A:ASP196 4.0 32.1 1.0 CA A:ALA102 4.0 34.7 1.0 N A:THR200 4.0 34.3 1.0 O A:HOH565 4.1 44.1 1.0 N A:ALA197 4.1 32.4 1.0 CB A:ASP196 4.1 32.2 1.0 CB A:ALA102 4.2 34.1 1.0 O A:HOH504 4.2 58.1 1.0 CA A:THR200 4.3 35.0 1.0 CA A:ALA197 4.5 32.7 1.0 N A:ALA103 4.6 34.4 1.0 O A:HOH721 4.6 53.0 1.0 CG2 A:THR200 4.7 34.0 1.0 CB A:ALA199 4.8 30.7 1.0 C A:ALA199 4.9 33.1 1.0 C A:ALA197 5.0 33.1 1.0 CA A:ALA103 5.0 34.1 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Protein DVU1097 From Desulfovibrio Vulgaris Hildenborough, Pfam DUF375


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Protein DVU1097 From Desulfovibrio Vulgaris Hildenborough, Pfam DUF375 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:43.6 occ:1.00 O A:GLY128 2.1 35.5 1.0 OE2 A:GLU126 2.4 41.9 1.0 O A:SER0 2.4 50.8 1.0 O A:MSE3 2.5 48.4 1.0 O A:PRO2 2.6 49.2 1.0 CD A:GLU126 3.1 42.2 1.0 C A:GLY128 3.3 34.6 1.0 C A:SER0 3.3 51.4 1.0 C A:MSE3 3.4 48.6 1.0 CG A:GLU126 3.4 36.5 1.0 C A:PRO2 3.7 49.6 1.0 CA A:SER0 3.9 51.5 1.0 N A:SER0 4.0 51.2 1.0 CB A:SER0 4.0 51.8 1.0 CA A:MSE3 4.0 48.7 1.0 CB A:MSE3 4.0 48.3 1.0 OE1 A:GLU126 4.1 45.8 1.0 N A:GLY129 4.2 34.6 1.0 CA A:GLY128 4.2 34.1 1.0 N A:MSE3 4.2 48.8 1.0 CA A:GLY129 4.2 34.9 1.0 N A:GLN4 4.3 48.9 1.0 N A:LEU1 4.3 51.5 1.0 CA A:LEU1 4.6 51.5 1.0 N A:GLY128 4.7 34.1 1.0 C A:LEU1 4.7 51.4 1.0 O A:HOH626 4.7 54.0 1.0 CA A:GLN4 4.7 49.8 1.0 N A:PRO2 4.8 50.7 1.0 CA A:PRO2 4.8 50.2 1.0 CB A:GLN4 4.9 50.1 1.0 O A:ALA171 4.9 69.6 1.0 C A:GLY129 4.9 35.8 1.0 CB A:GLU126 4.9 32.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Protein DVU1097 From Desulfovibrio Vulgaris Hildenborough, Pfam DUF375


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Protein DVU1097 From Desulfovibrio Vulgaris Hildenborough, Pfam DUF375 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:37.2 occ:1.00 OG1 B:THR200 2.2 36.7 1.0 OD1 B:ASP196 2.4 38.5 1.0 O B:ALA102 2.4 34.8 1.0 O B:ASP196 2.4 34.1 1.0 O B:HOH571 2.5 41.2 1.0 C B:ASP196 3.3 35.2 1.0 CG B:ASP196 3.3 38.7 1.0 C B:ALA102 3.4 34.6 1.0 CB B:THR200 3.6 37.2 1.0 O B:HOH581 3.7 62.0 1.0 O B:HOH508 3.9 44.3 1.0 CA B:ALA102 3.9 34.7 1.0 N B:THR200 3.9 37.0 1.0 OD2 B:ASP196 4.0 41.2 1.0 O B:HOH582 4.0 52.3 1.0 CA B:ASP196 4.0 35.5 1.0 CB B:ALA102 4.1 33.7 1.0 N B:ALA197 4.1 34.4 1.0 CB B:ASP196 4.2 36.7 1.0 CA B:THR200 4.2 37.0 1.0 CA B:ALA197 4.4 33.6 1.0 N B:ALA103 4.6 33.7 1.0 CG2 B:THR200 4.6 36.2 1.0 C B:ALA197 4.9 34.5 1.0 C B:ALA199 4.9 36.1 1.0 O B:ALA197 4.9 33.5 1.0 CA B:ALA103 5.0 33.6 1.0

V.N.Malashkevich, R.Toro, J.M.Sauder, D.A.Thompson, M.E.Rutter, M.Dickey, C.Groshong, K.T.Bain, J.M.Adams, C.Reyes, I.Rooney, A.Powell, A.Boice, T.Gheyi, S.Ozyurt, S.Atwell, S.R.Wasserman, K.D.Schwinn, S.Emtage, S.K.Burley, S.C.Almo. Crystal Structure of the Hypothetical Protein From Desulfovibrio Vulgaris Hildenborough To Be Published.