Sodium in PDB 1o68: Crystal Structure of 3-Methyl-2-Oxobutanoate Hydroxymethyltransferase

All present enzymatic activity of Crystal Structure of 3-Methyl-2-Oxobutanoate Hydroxymethyltransferase:
2.1.2.11;

The structure of Crystal Structure of 3-Methyl-2-Oxobutanoate Hydroxymethyltransferase, PDB code: 1o68 was solved by Structural Genomix, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.00 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	164.419, 111.238, 98.807, 90.00, 122.93, 90.00
R / Rfree (%)	18.6 / 22.4

The binding sites of Sodium atom in the Crystal Structure of 3-Methyl-2-Oxobutanoate Hydroxymethyltransferase (pdb code 1o68). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of 3-Methyl-2-Oxobutanoate Hydroxymethyltransferase, PDB code: 1o68:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of 3-Methyl-2-Oxobutanoate Hydroxymethyltransferase


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 3-Methyl-2-Oxobutanoate Hydroxymethyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na274 b:35.7 occ:1.00 OD1 A:ASP43 2.2 21.9 1.0 O1 A:KIV275 2.3 32.7 1.0 O3 A:KIV275 2.3 33.2 1.0 O A:HOH327 2.4 20.9 1.0 OD2 A:ASP82 2.4 25.5 1.0 C1 A:KIV275 3.0 32.9 1.0 O A:HOH341 3.0 28.1 1.0 C2 A:KIV275 3.1 33.3 1.0 CG A:ASP43 3.3 22.1 1.0 NZ A:LYS111 3.3 17.8 1.0 CG A:ASP82 3.4 23.0 1.0 N A:ASP43 3.7 18.4 1.0 O A:HOH389 3.8 42.8 1.0 OD2 A:ASP43 3.8 24.9 1.0 OD1 A:ASP82 3.8 27.9 1.0 N A:SER44 4.1 18.0 1.0 OE1 A:GLU113 4.1 26.2 1.0 O2 A:KIV275 4.2 31.6 1.0 CB A:ASP43 4.3 20.0 1.0 CA A:ASP43 4.4 19.1 1.0 CE A:LYS111 4.4 20.2 1.0 CA A:GLY42 4.5 19.4 1.0 CB A:ASP82 4.5 17.6 1.0 C A:GLY42 4.5 19.5 1.0 C A:ASP43 4.6 18.6 1.0 C3 A:KIV275 4.6 33.1 1.0 ND1 A:HIS135 4.7 22.0 1.0 CE1 A:HIS135 4.7 24.2 1.0 C5 A:KIV275 4.9 33.6 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of 3-Methyl-2-Oxobutanoate Hydroxymethyltransferase


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 3-Methyl-2-Oxobutanoate Hydroxymethyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na274 b:31.1 occ:1.00 OD2 B:ASP82 2.2 25.2 1.0 O3 B:KIV275 2.3 29.6 1.0 O B:HOH314 2.3 22.2 1.0 O1 B:KIV275 2.3 28.7 1.0 OD1 B:ASP43 2.4 18.8 1.0 O B:HOH389 2.9 38.5 1.0 CG B:ASP82 3.1 22.1 1.0 C1 B:KIV275 3.1 29.6 1.0 C2 B:KIV275 3.1 29.9 1.0 CG B:ASP43 3.3 20.3 1.0 NZ B:LYS111 3.3 22.3 1.0 OD1 B:ASP82 3.5 25.4 1.0 N B:ASP43 3.6 18.0 1.0 OD2 B:ASP43 3.9 20.8 1.0 OE1 B:GLU113 4.2 22.5 1.0 CB B:ASP82 4.2 19.9 1.0 CB B:ASP43 4.3 17.1 1.0 O2 B:KIV275 4.3 30.5 1.0 CE B:LYS111 4.3 21.2 1.0 CA B:GLY42 4.3 16.9 1.0 CA B:ASP43 4.3 18.5 1.0 N B:SER44 4.3 18.1 1.0 C B:GLY42 4.4 17.8 1.0 C3 B:KIV275 4.6 30.6 1.0 O B:HOH321 4.7 19.4 1.0 C B:ASP43 4.7 18.7 1.0 ND1 B:HIS135 4.9 21.0 1.0 CE1 B:HIS135 5.0 19.8 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of 3-Methyl-2-Oxobutanoate Hydroxymethyltransferase


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 3-Methyl-2-Oxobutanoate Hydroxymethyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ D:Na274 b:32.7 occ:1.00 O D:HOH312 2.3 26.8 1.0 OD1 D:ASP43 2.3 18.6 1.0 OD2 D:ASP82 2.3 24.5 1.0 O1 D:KIV275 2.4 30.1 1.0 O3 D:KIV275 2.5 30.8 1.0 O D:HOH311 2.9 32.5 1.0 O D:HOH375 3.0 39.7 1.0 C1 D:KIV275 3.2 30.8 1.0 CG D:ASP82 3.3 21.8 1.0 CG D:ASP43 3.3 18.8 1.0 C2 D:KIV275 3.3 31.6 1.0 NZ D:LYS111 3.4 18.9 1.0 OD1 D:ASP82 3.7 23.9 1.0 N D:ASP43 3.7 13.8 1.0 OD2 D:ASP43 3.9 21.1 1.0 OE1 D:GLU113 4.0 19.9 1.0 CB D:ASP43 4.3 16.9 1.0 N D:SER44 4.3 13.5 1.0 O2 D:KIV275 4.4 30.6 1.0 CB D:ASP82 4.4 17.5 1.0 CA D:ASP43 4.4 14.7 1.0 CE D:LYS111 4.6 20.8 1.0 CA D:GLY42 4.6 13.2 1.0 C D:GLY42 4.7 14.2 1.0 C D:ASP43 4.7 14.1 1.0 ND1 D:HIS135 4.8 18.7 1.0 C3 D:KIV275 4.8 31.2 1.0 O D:HOH320 4.8 26.3 1.0 CE1 D:HIS135 4.9 18.4 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of 3-Methyl-2-Oxobutanoate Hydroxymethyltransferase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of 3-Methyl-2-Oxobutanoate Hydroxymethyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ E:Na274 b:40.4 occ:1.00 OD2 E:ASP82 2.4 28.5 1.0 OD1 E:ASP43 2.4 25.5 1.0 O E:HOH345 2.4 27.5 1.0 O1 E:KIV275 2.4 34.1 1.0 O3 E:KIV275 2.6 35.5 1.0 NZ E:LYS111 2.8 30.9 1.0 CG E:ASP82 3.2 25.6 1.0 C1 E:KIV275 3.2 35.0 1.0 CG E:ASP43 3.3 25.0 1.0 C2 E:KIV275 3.4 35.8 1.0 O E:HOH344 3.6 29.8 1.0 OD1 E:ASP82 3.6 28.4 1.0 N E:ASP43 3.7 19.3 1.0 OD2 E:ASP43 3.9 25.5 1.0 CE E:LYS111 4.0 29.9 1.0 OE1 E:GLU113 4.1 28.2 1.0 CB E:ASP43 4.3 22.7 1.0 N E:SER44 4.3 22.7 1.0 CA E:ASP43 4.4 22.4 1.0 CB E:ASP82 4.4 22.5 1.0 O2 E:KIV275 4.4 35.5 1.0 CA E:GLY42 4.5 18.4 1.0 C E:GLY42 4.5 19.3 1.0 C E:ASP43 4.6 22.8 1.0 O E:HOH329 4.7 27.2 1.0 ND1 E:HIS135 4.8 25.5 1.0 CE1 E:HIS135 4.9 25.1 1.0 C3 E:KIV275 4.9 35.5 1.0

J.Badger, J.M.Sauder, J.M.Adams, S.Antonysamy, K.Bain, M.G.Bergseid, S.G.Buchanan, M.D.Buchanan, Y.Batiyenko, J.A.Christopher, S.Emtage, A.Eroshkina, I.Feil, E.B.Furlong, K.S.Gajiwala, X.Gao, D.He, J.Hendle, A.Huber, K.Hoda, P.Kearins, C.Kissinger, B.Laubert, H.A.Lewis, J.Lin, K.Loomis, D.Lorimer, G.Louie, M.Maletic, C.D.Marsh, I.Miller, J.Molinari, H.J.Muller-Dieckmann, J.M.Newman, B.W.Noland, B.Pagarigan, F.Park, T.S.Peat, K.W.Post, S.Radojicic, A.Ramos, R.Romero, M.E.Rutter, W.E.Sanderson, K.D.Schwinn, J.Tresser, J.Winhoven, T.A.Wright, L.Wu, J.Xu, T.J.Harris. Structural Analysis of A Set of Proteins Resulting From A Bacterial Genomics Project Proteins V. 60 787 2005.
ISSN: ISSN 0887-3585
PubMed: 16021622
DOI: 10.1002/PROT.20541