Sodium in PDB 5bju: X-Ray Structure of the Pglf Dehydratase From Campylobacter Jejuni in Complex with Udp and Nad(H)

The structure of X-Ray Structure of the Pglf Dehydratase From Campylobacter Jejuni in Complex with Udp and Nad(H), PDB code: 5bju was solved by A.S.Riegert, J.B.Thoden, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.135, 107.882, 110.208, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.7

The binding sites of Sodium atom in the X-Ray Structure of the Pglf Dehydratase From Campylobacter Jejuni in Complex with Udp and Nad(H) (pdb code 5bju). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of the Pglf Dehydratase From Campylobacter Jejuni in Complex with Udp and Nad(H), PDB code: 5bju:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of the Pglf Dehydratase From Campylobacter Jejuni in Complex with Udp and Nad(H)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Pglf Dehydratase From Campylobacter Jejuni in Complex with Udp and Nad(H) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na704 b:34.0 occ:1.00 O B:HOH983 2.2 41.8 1.0 O B:ILE323 2.3 11.3 1.0 O B:HOH915 2.3 18.6 1.0 O B:LYS320 2.4 15.5 1.0 O B:HOH1005 2.6 35.9 1.0 O B:HOH990 2.9 25.3 1.0 C B:ILE323 3.4 11.5 1.0 C B:LYS320 3.5 15.4 1.0 CG1 B:ILE323 3.9 15.9 1.0 CA B:LYS320 4.1 16.0 1.0 O A:HOH854 4.2 22.5 1.0 N B:ILE323 4.2 12.6 1.0 CA B:ILE323 4.2 11.7 1.0 CB B:LYS320 4.3 18.6 1.0 CD B:PRO325 4.3 7.3 1.0 N B:THR324 4.4 10.2 1.0 N B:GLU321 4.6 15.6 1.0 CA B:THR324 4.6 9.0 1.0 O B:HOH835 4.7 27.1 1.0 CB B:ILE323 4.7 12.7 1.0 ND2 B:ASN313 4.8 8.5 1.0 CA B:GLU321 4.8 16.6 1.0 OE1 A:GLN362 4.9 23.1 1.0 CD1 B:ILE323 5.0 17.3 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of the Pglf Dehydratase From Campylobacter Jejuni in Complex with Udp and Nad(H)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of the Pglf Dehydratase From Campylobacter Jejuni in Complex with Udp and Nad(H) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na705 b:43.1 occ:1.00 OG B:SER263 2.4 16.7 1.0 OD1 B:ASP261 2.4 12.8 1.0 O B:HOH943 2.5 17.6 1.0 O B:HOH968 2.5 15.5 1.0 CB B:SER263 3.4 13.3 1.0 CG B:ASP261 3.4 14.4 1.0 N B:SER263 3.7 10.9 1.0 OD2 B:ASP261 4.0 18.3 1.0 CA B:SER263 4.0 11.5 1.0 N B:ALA264 4.3 8.9 1.0 N B:ASP262 4.5 10.4 1.0 CA B:ASP261 4.5 12.3 1.0 CB B:ASP261 4.5 12.9 1.0 C B:ASP261 4.5 10.9 1.0 O B:HOH924 4.6 23.4 1.0 C B:SER263 4.6 9.9 1.0 C B:ASP262 4.9 10.8 1.0

A.S.Riegert, J.B.Thoden, I.C.Schoenhofen, D.C.Watson, N.M.Young, P.A.Tipton, H.M.Holden. Structural and Biochemical Investigation of Pglf From Campylobacter Jejuni Reveals A New Mechanism For A Member of the Short Chain Dehydrogenase/Reductase Superfamily. Biochemistry V. 56 6030 2017.
ISSN: ISSN 1520-4995
PubMed: 29053280
DOI: 10.1021/ACS.BIOCHEM.7B00910