Sodium in PDB 5br7: Structure of Udp-Galactopyranose Mutase From Corynebacterium Diphtheriae in Complex with Citrate Ion

All present enzymatic activity of Structure of Udp-Galactopyranose Mutase From Corynebacterium Diphtheriae in Complex with Citrate Ion:
5.4.99.9;

The structure of Structure of Udp-Galactopyranose Mutase From Corynebacterium Diphtheriae in Complex with Citrate Ion, PDB code: 5br7 was solved by K.Wangkanont, L.L.Kiessling, K.T.Forest, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.72 / 1.95
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.278, 98.278, 126.223, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 19

The binding sites of Sodium atom in the Structure of Udp-Galactopyranose Mutase From Corynebacterium Diphtheriae in Complex with Citrate Ion (pdb code 5br7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Udp-Galactopyranose Mutase From Corynebacterium Diphtheriae in Complex with Citrate Ion, PDB code: 5br7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Udp-Galactopyranose Mutase From Corynebacterium Diphtheriae in Complex with Citrate Ion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Udp-Galactopyranose Mutase From Corynebacterium Diphtheriae in Complex with Citrate Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:29.4 occ:1.00 O A:ILE129 2.3 31.8 1.0 O A:SER143 2.3 30.6 1.0 O A:HOH649 2.3 31.9 1.0 O A:SER126 2.4 33.7 1.0 O A:HOH808 2.5 33.8 1.0 O A:HOH588 2.5 34.0 1.0 C A:SER143 3.3 32.6 1.0 C A:ILE129 3.4 41.7 1.0 C A:SER126 3.5 31.4 1.0 O A:HOH933 3.6 46.9 1.0 CA A:SER143 3.7 30.1 1.0 CB A:SER126 3.9 27.3 1.0 OG A:SER126 3.9 30.9 1.0 CA A:ASP130 4.0 36.1 0.5 CA A:ASP130 4.0 36.1 0.5 CB A:SER143 4.0 30.6 1.0 N A:ASP130 4.1 32.8 0.5 N A:ASP130 4.1 32.9 0.5 O A:HOH827 4.1 51.0 1.0 CA A:SER126 4.3 29.9 1.0 N A:SER131 4.3 36.2 0.5 N A:SER131 4.3 36.2 0.5 O A:HOH739 4.4 43.6 1.0 N A:ALA127 4.5 31.6 1.0 O A:ALA127 4.5 40.9 1.0 N A:ILE129 4.5 31.1 1.0 CA A:ILE129 4.5 28.8 1.0 N A:LEU144 4.5 26.4 1.0 OD1 A:ASP130 4.5 44.0 0.5 C A:ASP130 4.5 33.2 0.5 C A:ALA127 4.6 40.7 1.0 C A:ASP130 4.6 33.2 0.5 CA A:ALA127 4.6 37.5 1.0 O A:HOH686 4.6 35.5 1.0 OG A:SER131 4.7 36.9 0.5 OG A:SER143 4.8 33.3 1.0

Sodium binding site 2 out of 2 in the Structure of Udp-Galactopyranose Mutase From Corynebacterium Diphtheriae in Complex with Citrate Ion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Udp-Galactopyranose Mutase From Corynebacterium Diphtheriae in Complex with Citrate Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:31.0 occ:1.00 O4 A:FAD401 2.3 23.1 1.0 OB1 A:FLC411 2.3 29.7 0.9 O A:ALA60 2.4 24.6 1.0 OHB A:FLC411 2.5 33.8 0.9 OA1 A:FLC411 2.5 26.5 0.9 N5 A:FAD401 2.6 26.8 1.0 CBC A:FLC411 3.0 31.6 0.9 C4 A:FAD401 3.1 24.2 1.0 CB A:FLC411 3.2 32.0 0.9 C4X A:FAD401 3.3 25.7 1.0 CAC A:FLC411 3.4 32.3 0.9 C A:ALA60 3.6 27.2 1.0 C5X A:FAD401 3.8 28.9 1.0 CA A:FLC411 3.8 31.1 0.9 C6 A:FAD401 4.0 29.4 1.0 OB2 A:FLC411 4.1 32.6 0.9 CD2 A:LEU62 4.1 21.6 0.6 O A:HOH596 4.2 32.8 1.0 O A:HOH553 4.2 38.2 1.0 O A:HOH768 4.3 32.3 1.0 CA A:HIS61 4.3 21.0 1.0 OG1 A:FLC411 4.3 35.2 0.9 N A:HIS61 4.4 22.9 1.0 N A:LEU62 4.4 22.7 0.6 N3 A:FAD401 4.4 22.5 1.0 N A:LEU62 4.5 22.7 0.4 OA2 A:FLC411 4.5 25.9 0.9 CA A:ALA60 4.6 25.5 1.0 CG A:FLC411 4.6 32.2 0.9 CG A:LEU62 4.6 23.6 0.4 N A:ALA60 4.7 25.0 1.0 CD1 A:LEU62 4.7 22.1 0.4 C10 A:FAD401 4.8 25.0 1.0 CB A:ALA60 4.8 22.4 1.0 C A:HIS61 4.9 22.4 1.0 CGC A:FLC411 4.9 35.5 0.9

K.Wangkanont, V.J.Winton, K.T.Forest, L.L.Kiessling. Conformational Control of Udp-Galactopyranose Mutase Inhibition. Biochemistry V. 56 3983 2017.
ISSN: ISSN 1520-4995
PubMed: 28608671
DOI: 10.1021/ACS.BIOCHEM.7B00189