Sodium in PDB 5bjw: X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, T595S Variant, in Complex with Udp

The structure of X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, T595S Variant, in Complex with Udp, PDB code: 5bjw 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 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.168, 69.237, 101.544, 90.00, 100.41, 90.00
R / Rfree (%)	17.3 / 20.5

The binding sites of Sodium atom in the X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, T595S Variant, in Complex with Udp (pdb code 5bjw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, T595S Variant, in Complex with Udp, PDB code: 5bjw:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, T595S Variant, in Complex with Udp


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 4,6-Dehydratase From Campylobacter Jejuni, T595S Variant, in Complex with Udp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:22.5 occ:1.00 O A:LYS320 2.3 18.3 1.0 O B:HOH1033 2.3 45.1 1.0 O A:HOH1048 2.4 31.0 1.0 O A:HOH860 2.5 22.0 1.0 O A:ILE323 2.5 13.7 1.0 O A:HOH1045 2.9 38.3 1.0 C A:LYS320 3.4 15.6 1.0 C A:ILE323 3.6 12.7 1.0 CG1 A:ILE323 3.9 14.9 1.0 CA A:LYS320 3.9 16.8 1.0 CB A:LYS320 4.1 18.1 1.0 O A:HOH847 4.2 30.1 1.0 N A:ILE323 4.3 11.6 1.0 CA A:ILE323 4.4 11.9 1.0 O A:HOH1044 4.4 22.6 1.0 N A:GLU321 4.5 18.2 1.0 CD A:PRO325 4.5 12.9 1.0 N A:THR324 4.6 12.8 1.0 CA A:THR324 4.7 11.1 1.0 OD1 A:ASN313 4.7 12.3 1.0 CB A:ILE323 4.8 14.1 1.0 CA A:GLU321 4.9 20.1 1.0 CD1 A:ILE323 4.9 15.6 1.0 O B:HOH1057 4.9 37.1 1.0 CG A:LYS320 5.0 22.2 1.0

Sodium binding site 2 out of 4 in the X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, T595S Variant, in Complex with Udp


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 4,6-Dehydratase From Campylobacter Jejuni, T595S Variant, in Complex with Udp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na705 b:26.2 occ:1.00 O A:HOH1083 2.2 42.0 1.0 O A:HOH1023 2.3 39.2 1.0 O A:HOH937 2.5 18.5 1.0 O A:HOH896 2.5 16.7 1.0 O A:HOH1047 2.5 29.4 1.0 O A:HOH1013 2.5 17.7 1.0 NZ A:LYS289 3.8 12.9 1.0 O1 A:EDO703 3.9 34.0 1.0 O A:HOH911 4.0 14.9 1.0 O A:HOH1061 4.3 35.0 1.0 OD2 A:ASP315 4.5 16.1 1.0 NZ A:LYS311 4.6 17.0 1.0 O A:HOH1094 4.6 27.4 1.0 O A:HOH898 4.6 12.2 1.0 C1 A:EDO703 4.6 22.6 1.0 O A:HOH938 4.7 13.3 1.0 O A:HOH1067 4.7 27.1 1.0 CE A:LYS289 5.0 12.1 1.0

Sodium binding site 3 out of 4 in the X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, T595S Variant, in Complex with Udp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, T595S Variant, in Complex with Udp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na706 b:29.6 occ:1.00 OG B:SER263 2.2 18.2 1.0 O B:HOH954 2.3 26.2 1.0 O B:HOH1019 2.4 23.0 1.0 O B:HOH1054 2.4 33.7 1.0 OD1 B:ASP261 2.4 14.6 1.0 O B:HOH1110 2.5 43.2 1.0 CG B:ASP261 3.4 16.6 1.0 CB B:SER263 3.4 13.6 1.0 N B:SER263 3.8 11.3 1.0 OD2 B:ASP261 4.0 20.3 1.0 CA B:SER263 4.1 11.5 1.0 N B:ALA264 4.4 9.9 1.0 CA B:ASP261 4.5 11.7 1.0 CB B:ASP261 4.5 15.0 1.0 N B:ASP262 4.6 11.2 1.0 C B:ASP261 4.7 12.1 1.0 C B:SER263 4.7 10.3 1.0 O B:HOH1062 4.9 23.1 1.0 C B:ASP262 5.0 11.1 1.0

Sodium binding site 4 out of 4 in the X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, T595S Variant, in Complex with Udp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, T595S Variant, in Complex with Udp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na707 b:27.1 occ:1.00 O B:HOH1068 2.3 37.7 1.0 O B:HOH1078 2.4 27.4 1.0 O B:HOH953 2.4 17.7 1.0 O B:HOH1035 2.5 18.1 1.0 O B:HOH878 2.6 17.0 1.0 NZ B:LYS289 3.9 12.4 1.0 O1 B:EDO703 4.0 32.3 1.0 O B:HOH921 4.0 14.0 1.0 O B:HOH1101 4.4 33.3 1.0 OD2 B:ASP315 4.5 16.4 1.0 O B:HOH1149 4.5 24.3 1.0 NZ B:LYS311 4.6 16.9 1.0 O B:HOH959 4.6 11.9 1.0 O B:HOH906 4.6 13.0 1.0 C1 B:EDO703 4.7 21.1 1.0 O B:HOH1119 4.8 39.7 1.0 O B:HOH1096 4.8 28.4 1.0 O B:HOH1151 4.9 29.2 1.0 CE B:LYS289 5.0 12.0 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