Sodium in PDB 5bjv: X-Ray Structure of the Pglf Udp-N-Acetylglucosamine 4,6-Dehydratase From Campylobacterjejuni, D396N/K397A Variant in Complex with Udp-N- Acrtylglucosamine

The structure of X-Ray Structure of the Pglf Udp-N-Acetylglucosamine 4,6-Dehydratase From Campylobacterjejuni, D396N/K397A Variant in Complex with Udp-N- Acrtylglucosamine, PDB code: 5bjv 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 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.820, 108.468, 108.959, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 23.2

The binding sites of Sodium atom in the X-Ray Structure of the Pglf Udp-N-Acetylglucosamine 4,6-Dehydratase From Campylobacterjejuni, D396N/K397A Variant in Complex with Udp-N- Acrtylglucosamine (pdb code 5bjv). 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 Udp-N-Acetylglucosamine 4,6-Dehydratase From Campylobacterjejuni, D396N/K397A Variant in Complex with Udp-N- Acrtylglucosamine, PDB code: 5bjv:
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 Udp-N-Acetylglucosamine 4,6-Dehydratase From Campylobacterjejuni, D396N/K397A Variant in Complex with Udp-N- Acrtylglucosamine


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 Udp-N-Acetylglucosamine 4,6-Dehydratase From Campylobacterjejuni, D396N/K397A Variant in Complex with Udp-N- Acrtylglucosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na705 b:23.9 occ:1.00 O A:HOH1040 2.2 29.1 1.0 O A:ILE323 2.4 15.6 1.0 O A:LYS320 2.6 14.9 1.0 O A:HOH829 2.6 19.4 1.0 O A:HOH1043 2.7 32.9 1.0 O A:HOH1022 2.8 30.6 1.0 C A:ILE323 3.6 14.7 1.0 C A:LYS320 3.6 16.5 1.0 CG1 A:ILE323 3.9 13.9 1.0 O A:HOH917 3.9 30.4 1.0 CA A:LYS320 4.2 15.9 1.0 CB A:LYS320 4.2 20.2 1.0 N A:ILE323 4.4 14.1 1.0 O A:HOH1037 4.4 18.0 1.0 CA A:ILE323 4.4 13.9 1.0 CD A:PRO325 4.5 10.7 1.0 N A:THR324 4.5 12.1 1.0 O B:HOH1082 4.6 31.1 1.0 CA A:THR324 4.6 10.9 1.0 N A:GLU321 4.6 17.1 1.0 OD1 A:ASN313 4.7 8.6 1.0 CB A:ILE323 4.8 14.2 1.0 CA A:GLU321 4.8 18.7 1.0 CD1 A:ILE323 5.0 14.0 1.0 CG A:LYS320 5.0 23.3 1.0

Sodium binding site 2 out of 4 in the X-Ray Structure of the Pglf Udp-N-Acetylglucosamine 4,6-Dehydratase From Campylobacterjejuni, D396N/K397A Variant in Complex with Udp-N- Acrtylglucosamine


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 Udp-N-Acetylglucosamine 4,6-Dehydratase From Campylobacterjejuni, D396N/K397A Variant in Complex with Udp-N- Acrtylglucosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na706 b:43.3 occ:1.00 O A:HOH823 2.1 20.0 1.0 O A:HOH1036 2.3 35.8 1.0 O A:HOH1069 2.5 32.5 1.0 O1 A:EDO704 2.6 40.1 0.5 O A:HOH957 2.6 14.2 1.0 O A:HOH831 2.7 18.8 1.0 C1 A:EDO704 3.9 42.1 0.5 NZ A:LYS289 4.0 12.2 1.0 O A:HOH866 4.0 11.4 1.0 C1 A:EDO704 4.0 18.1 0.5 O A:HOH905 4.2 12.7 1.0 O A:HOH1055 4.4 35.7 1.0 OD2 A:ASP315 4.5 17.2 1.0 O A:HOH856 4.5 11.8 1.0 NZ A:LYS311 4.7 14.0 1.0 O A:HOH932 4.7 30.9 1.0 OG A:SER285 4.8 16.6 1.0 C2 A:EDO704 4.9 17.8 0.5 C2 A:EDO704 4.9 39.0 0.5 O A:HOH1089 4.9 27.8 1.0

Sodium binding site 3 out of 4 in the X-Ray Structure of the Pglf Udp-N-Acetylglucosamine 4,6-Dehydratase From Campylobacterjejuni, D396N/K397A Variant in Complex with Udp-N- Acrtylglucosamine


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 Udp-N-Acetylglucosamine 4,6-Dehydratase From Campylobacterjejuni, D396N/K397A Variant in Complex with Udp-N- Acrtylglucosamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na704 b:30.8 occ:1.00 O B:HOH1034 2.4 43.5 1.0 O B:LYS320 2.4 17.7 1.0 O B:HOH907 2.4 21.8 1.0 O B:ILE323 2.6 11.2 1.0 O B:HOH1041 2.6 39.2 1.0 O B:HOH1024 2.8 33.7 1.0 C B:LYS320 3.4 18.8 1.0 C B:ILE323 3.7 12.7 1.0 CG1 B:ILE323 3.9 13.7 1.0 CA B:LYS320 4.0 19.4 1.0 CB B:LYS320 4.1 26.9 1.0 O A:HOH1023 4.3 19.8 1.0 O B:HOH827 4.4 19.6 1.0 N B:ILE323 4.4 13.5 1.0 N B:GLU321 4.4 19.8 1.0 CA B:ILE323 4.6 13.2 1.0 N B:THR324 4.7 11.5 1.0 CD B:PRO325 4.7 10.0 1.0 CA B:GLU321 4.7 19.5 1.0 CA B:THR324 4.8 11.1 1.0 CD1 B:ILE323 4.8 13.5 1.0 ND2 B:ASN313 4.9 10.6 1.0 CB B:ILE323 4.9 13.9 1.0 C B:GLU321 4.9 15.9 1.0 CG B:LYS320 5.0 32.8 1.0

Sodium binding site 4 out of 4 in the X-Ray Structure of the Pglf Udp-N-Acetylglucosamine 4,6-Dehydratase From Campylobacterjejuni, D396N/K397A Variant in Complex with Udp-N- Acrtylglucosamine


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 Udp-N-Acetylglucosamine 4,6-Dehydratase From Campylobacterjejuni, D396N/K397A Variant in Complex with Udp-N- Acrtylglucosamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na705 b:31.8 occ:1.00 O B:HOH1071 2.3 37.1 1.0 O B:HOH911 2.4 19.3 1.0 O B:HOH1031 2.4 32.4 1.0 O B:HOH872 2.5 15.2 1.0 O B:HOH926 2.7 14.4 1.0 O B:HOH1057 3.0 40.2 1.0 NZ B:LYS289 3.8 12.7 1.0 O B:HOH845 4.2 8.4 1.0 O B:HOH904 4.5 15.8 1.0 NZ B:LYS311 4.5 9.4 1.0 O B:HOH871 4.6 14.7 1.0 OD2 B:ASP315 4.6 12.0 1.0 O B:HOH955 4.7 28.9 1.0 O B:HOH1104 4.7 33.4 1.0 O B:HOH1107 4.8 30.5 1.0 O B:HOH1095 4.8 25.4 1.0 O B:HOH1047 4.9 33.7 1.0 CE B:LYS289 4.9 11.6 1.0 OG B:SER285 5.0 7.8 0.5

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