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Sodium in PDB 5bjy: X-Ray Structure of the Pglf 4,5-Dehydratase From Campylobacter Jejuni, Variant M405Y, in Complex with Udp

Protein crystallography data

The structure of X-Ray Structure of the Pglf 4,5-Dehydratase From Campylobacter Jejuni, Variant M405Y, in Complex with Udp, PDB code: 5bjy 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) 31.00 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.508, 108.273, 109.657, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.6

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Pglf 4,5-Dehydratase From Campylobacter Jejuni, Variant M405Y, in Complex with Udp (pdb code 5bjy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the X-Ray Structure of the Pglf 4,5-Dehydratase From Campylobacter Jejuni, Variant M405Y, in Complex with Udp, PDB code: 5bjy:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5bjy

Go back to Sodium Binding Sites List in 5bjy
Sodium binding site 1 out of 6 in the X-Ray Structure of the Pglf 4,5-Dehydratase From Campylobacter Jejuni, Variant M405Y, 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 4,5-Dehydratase From Campylobacter Jejuni, Variant M405Y, in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na706

b:28.0
occ:1.00
 O A:HOH1087 2.3 42.8 1.0
OG A:SER263 2.3 17.4 1.0
OD1 A:ASP261 2.4 18.2 1.0
O A:HOH1026 2.4 19.9 1.0
O A:HOH1062 2.4 24.1 1.0
O A:HOH934 2.6 28.4 1.0
CG A:ASP261 3.4 17.3 1.0
CB A:SER263 3.5 15.2 1.0
N A:SER263 3.8 13.5 1.0
OD2 A:ASP261 3.9 19.7 1.0
CA A:SER263 4.1 14.5 1.0
N A:ALA264 4.4 13.2 1.0
CA A:ASP261 4.4 15.1 1.0
CB A:ASP261 4.5 15.0 1.0
N A:ASP262 4.5 13.6 1.0
C A:ASP261 4.6 14.3 1.0
O A:HOH1053 4.6 25.5 1.0
C A:SER263 4.6 13.5 1.0
C A:ASP262 4.9 12.7 1.0

Sodium binding site 2 out of 6 in 5bjy

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Sodium binding site 2 out of 6 in the X-Ray Structure of the Pglf 4,5-Dehydratase From Campylobacter Jejuni, Variant M405Y, 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 4,5-Dehydratase From Campylobacter Jejuni, Variant M405Y, in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na707

b:24.8
occ:1.00
 O A:HOH1088 2.2 40.8 1.0
O A:HOH1090 2.2 44.3 1.0
O A:LYS320 2.5 20.4 1.0
O A:HOH865 2.5 23.2 1.0
O A:ILE323 2.5 17.5 1.0
O A:HOH1081 2.7 49.0 1.0
C A:LYS320 3.5 20.0 1.0
C A:ILE323 3.6 16.9 1.0
CG1 A:ILE323 3.9 16.9 1.0
CA A:LYS320 4.1 17.7 1.0
O A:HOH840 4.1 33.4 1.0
CB A:LYS320 4.2 21.5 1.0
N A:ILE323 4.4 16.4 1.0
O A:HOH1071 4.4 25.1 1.0
CD A:PRO325 4.5 15.5 1.0
CA A:ILE323 4.5 15.5 1.0
N A:THR324 4.5 14.9 1.0
N A:GLU321 4.6 21.1 1.0
O B:HOH953 4.6 39.5 1.0
CA A:THR324 4.6 12.2 1.0
OD1 A:ASN313 4.8 14.5 1.0
CA A:GLU321 4.8 21.9 1.0
CB A:ILE323 4.9 17.3 1.0
CG A:LYS320 4.9 25.8 1.0
O B:HOH1020 5.0 45.1 1.0
CD1 A:ILE323 5.0 18.2 1.0

Sodium binding site 3 out of 6 in 5bjy

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Sodium binding site 3 out of 6 in the X-Ray Structure of the Pglf 4,5-Dehydratase From Campylobacter Jejuni, Variant M405Y, 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 4,5-Dehydratase From Campylobacter Jejuni, Variant M405Y, in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na708

b:32.9
occ:1.00
 O A:HOH1080 2.3 44.7 1.0
O A:HOH971 2.4 21.8 1.0
O A:HOH1136 2.4 48.5 1.0
O A:HOH1084 2.5 32.8 1.0
O A:HOH910 2.6 24.0 1.0
O A:HOH996 2.7 22.5 1.0
O1 A:EDO703 3.9 35.8 1.0
NZ A:LYS289 3.9 17.1 1.0
O A:HOH948 4.1 16.0 1.0
O A:HOH1096 4.3 33.8 1.0
O A:HOH965 4.5 14.7 1.0
O A:HOH1150 4.5 29.6 1.0
O A:HOH939 4.6 15.8 1.0
OD2 A:ASP315 4.6 21.7 1.0
NZ A:LYS311 4.6 23.8 1.0
O A:HOH1072 4.7 32.3 1.0
O A:HOH1153 4.8 33.2 1.0
C1 A:EDO703 4.8 25.4 1.0

Sodium binding site 4 out of 6 in 5bjy

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Sodium binding site 4 out of 6 in the X-Ray Structure of the Pglf 4,5-Dehydratase From Campylobacter Jejuni, Variant M405Y, 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 4,5-Dehydratase From Campylobacter Jejuni, Variant M405Y, in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na705

b:27.2
occ:1.00
 O B:HOH1074 2.2 39.9 1.0
OG B:SER263 2.3 18.0 1.0
OD1 B:ASP261 2.3 16.2 1.0
O B:HOH972 2.4 33.3 1.0
O B:HOH1034 2.4 24.8 1.0
O B:HOH1027 2.4 20.4 1.0
CG B:ASP261 3.3 18.8 1.0
CB B:SER263 3.5 15.9 1.0
N B:SER263 3.8 13.9 1.0
OD2 B:ASP261 3.9 22.1 1.0
CA B:SER263 4.1 13.4 1.0
N B:ALA264 4.4 12.3 1.0
CB B:ASP261 4.4 16.3 1.0
CA B:ASP261 4.4 16.3 1.0
N B:ASP262 4.5 15.6 1.0
C B:ASP261 4.6 14.6 1.0
C B:SER263 4.7 11.8 1.0
O B:HOH1038 4.7 22.7 1.0
C B:ASP262 4.9 14.8 1.0

Sodium binding site 5 out of 6 in 5bjy

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Sodium binding site 5 out of 6 in the X-Ray Structure of the Pglf 4,5-Dehydratase From Campylobacter Jejuni, Variant M405Y, in Complex with Udp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of X-Ray Structure of the Pglf 4,5-Dehydratase From Campylobacter Jejuni, Variant M405Y, in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na706

b:31.4
occ:1.00
 O B:HOH1119 2.4 46.2 1.0
O B:HOH1031 2.4 48.2 1.0
O B:HOH925 2.5 21.8 1.0
O B:HOH1083 2.5 34.7 1.0
O B:HOH870 2.6 21.9 1.0
O B:HOH1012 2.6 21.4 1.0
O2 B:EDO703 3.8 34.7 1.0
NZ B:LYS289 3.9 17.0 1.0
O B:HOH922 4.0 16.8 1.0
O B:HOH1080 4.3 43.7 1.0
OD2 B:ASP315 4.5 19.2 1.0
O B:HOH905 4.6 15.5 1.0
O B:HOH927 4.6 17.0 1.0
NZ B:LYS311 4.6 20.7 1.0
O B:HOH1133 4.6 34.1 1.0
C2 B:EDO703 4.7 23.8 1.0
O B:HOH1069 4.7 29.6 1.0
O B:HOH1131 4.8 35.8 1.0
CE B:LYS289 5.0 17.0 1.0

Sodium binding site 6 out of 6 in 5bjy

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Sodium binding site 6 out of 6 in the X-Ray Structure of the Pglf 4,5-Dehydratase From Campylobacter Jejuni, Variant M405Y, in Complex with Udp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of X-Ray Structure of the Pglf 4,5-Dehydratase From Campylobacter Jejuni, Variant M405Y, in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na707

b:24.9
occ:1.00
 O B:LYS320 2.3 21.7 1.0
O B:HOH895 2.5 23.4 1.0
O B:ILE323 2.5 15.2 1.0
O B:HOH1079 2.6 47.3 1.0
O B:HOH1084 2.8 40.6 1.0
C B:LYS320 3.4 21.1 1.0
C B:ILE323 3.6 15.7 1.0
CG1 B:ILE323 3.9 16.6 1.0
CA B:LYS320 3.9 18.3 1.0
CB B:LYS320 4.0 24.0 1.0
N B:ILE323 4.3 13.1 1.0
O A:HOH1066 4.4 26.0 1.0
CA B:ILE323 4.4 14.2 1.0
O B:HOH827 4.5 36.5 1.0
CD B:PRO325 4.5 14.6 1.0
N B:GLU321 4.5 18.8 1.0
N B:THR324 4.6 12.4 1.0
CA B:THR324 4.7 12.9 1.0
CA B:GLU321 4.8 22.4 1.0
CB B:ILE323 4.8 15.1 1.0
ND2 B:ASN313 4.8 11.3 1.0
O A:HOH1047 4.9 39.1 1.0
CD1 B:ILE323 4.9 18.9 1.0

Reference:

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
Page generated: Mon Oct 7 20:05:30 2024

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