Sodium in PDB 9end: Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 3

The structure of Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 3, PDB code: 9end was solved by S.Coquille, J.Roche, E.Girard, D.Madern, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.78 / 1.95
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.82, 78.82, 251.51, 90, 90, 90
R / Rfree (%)	19.5 / 23

The structure of Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 3 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 3 (pdb code 9end). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 3, PDB code: 9end:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 3


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 Methanopyrus Kandleri Malate Dehydrogenase Mutant 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:29.7 occ:1.00 O A:LEU24 2.5 40.6 1.0 O A:ASP59 2.6 44.9 1.0 O A:VAL27 2.7 44.5 1.0 O A:ALA22 2.7 37.5 1.0 O A:HOH552 2.9 47.6 0.9 O A:HOH529 2.9 42.7 0.8 HB1 A:ALA60 3.0 44.6 1.0 C A:LEU24 3.6 42.1 1.0 HA A:ASP25 3.7 51.4 1.0 C A:ASP59 3.8 45.7 1.0 C A:ALA22 3.8 36.7 1.0 CB A:ALA60 3.9 37.2 1.0 C A:VAL27 3.9 41.7 1.0 HB A:VAL27 4.0 50.2 1.0 HB3 A:ALA60 4.0 44.6 1.0 H A:VAL27 4.0 52.7 1.0 HA A:ALA60 4.1 53.2 1.0 HA A:ASN28 4.2 53.2 1.0 C A:LEU23 4.2 40.0 1.0 O A:HOH575 4.2 52.8 0.9 H A:ASP59 4.2 58.1 1.0 N A:LEU24 4.3 36.3 1.0 CA A:ASP25 4.3 42.8 1.0 HA A:LEU23 4.3 46.2 1.0 HB3 A:LYS58 4.3 55.2 1.0 HA A:ALA22 4.3 40.6 1.0 N A:ASP25 4.4 39.1 1.0 CA A:ALA60 4.4 44.2 1.0 O A:LEU23 4.4 41.3 1.0 HD22 A:LEU53 4.5 55.0 1.0 N A:ALA60 4.5 44.0 1.0 H A:LEU24 4.5 43.7 1.0 O A:ASP25 4.5 47.9 1.0 C A:ASP25 4.6 46.3 1.0 HB2 A:ALA60 4.6 44.6 1.0 CA A:LEU24 4.6 40.0 1.0 N A:VAL27 4.6 43.9 1.0 CA A:VAL27 4.6 42.0 1.0 CA A:LEU23 4.7 38.5 1.0 HG13 A:VAL27 4.7 48.5 1.0 N A:LEU23 4.7 37.7 1.0 CB A:VAL27 4.7 41.8 1.0 CA A:ALA22 4.7 33.8 1.0 N A:ASP59 4.7 48.4 1.0 HD3 A:LYS58 4.8 65.9 1.0 N A:ASN28 4.8 41.2 1.0 HD21 A:LEU53 4.8 55.0 1.0 CA A:ASP59 4.9 47.1 1.0 CA A:ASN28 4.9 44.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Methanopyrus Kandleri Malate Dehydrogenase Mutant 3


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 Methanopyrus Kandleri Malate Dehydrogenase Mutant 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:22.5 occ:1.00 O B:VAL27 2.6 29.5 1.0 O B:LEU24 2.6 33.0 1.0 O B:ASP59 2.6 33.4 1.0 O B:HOH622 2.7 44.5 0.9 O B:ALA22 2.8 30.9 1.0 HB3 B:ALA60 3.0 37.7 1.0 O B:HOH602 3.0 46.0 0.8 C B:LEU24 3.6 30.4 1.0 HA B:ASP25 3.7 41.7 1.0 C B:VAL27 3.8 38.9 1.0 C B:ASP59 3.8 36.8 1.0 HB B:VAL27 3.8 37.0 1.0 H B:VAL27 3.8 37.4 1.0 H B:ASP59 3.9 44.4 1.0 C B:ALA22 3.9 31.2 1.0 CB B:ALA60 3.9 31.4 1.0 HB2 B:ALA60 4.1 37.7 1.0 C B:LEU23 4.2 33.8 1.0 HA B:ALA60 4.2 41.5 1.0 HA B:ASN28 4.3 39.5 1.0 O B:HOH611 4.3 42.8 0.7 HA B:ALA22 4.3 35.7 1.0 N B:LEU24 4.3 33.1 1.0 O B:LEU23 4.3 32.7 1.0 CA B:ASP25 4.4 34.7 1.0 N B:ASP25 4.4 31.4 1.0 HA B:LEU23 4.4 38.7 1.0 HB3 B:LYS58 4.4 42.5 1.0 N B:VAL27 4.4 31.1 1.0 CA B:ALA60 4.5 34.5 1.0 CA B:VAL27 4.5 27.7 1.0 H B:LEU24 4.5 39.8 1.0 HB1 B:ALA60 4.5 37.7 1.0 HG12 B:VAL27 4.6 35.6 1.0 CA B:LEU24 4.6 32.4 1.0 CB B:VAL27 4.6 30.8 1.0 N B:ALA60 4.6 34.0 1.0 C B:ASP25 4.6 35.9 1.0 N B:ASP59 4.6 36.9 1.0 CA B:LEU23 4.7 32.2 1.0 CA B:ALA22 4.7 29.7 1.0 N B:LEU23 4.7 28.7 1.0 O B:ASP25 4.7 34.2 1.0 N B:ASN28 4.8 30.0 1.0 HD22 B:LEU53 4.8 53.4 1.0 CA B:ASP59 4.9 37.0 1.0 CA B:ASN28 4.9 32.9 1.0 HB2 B:LEU24 5.0 34.8 1.0

S.Coquille, C.Simoes Pereira, C.Brochier-Armanet, J.Roche, G.Santoni, N.Coquelle, E.Girard, F.Sterpone, D.Madern. Navigating the Conformational Landscape of An Enzyme. Stabilization of A Low Populated Conformer By Evolutionary Mutations Triggers Allostery Into A Non-Allosteric Enzyme. To Be Published.