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Sodium in PDB 5bjx: X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, Variant T395V, in Complex with Udp

Protein crystallography data

The structure of X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, Variant T395V, in Complex with Udp, PDB code: 5bjx 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 (°) 69.229, 108.251, 108.374, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 18.5

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, Variant T395V, in Complex with Udp (pdb code 5bjx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, Variant T395V, in Complex with Udp, PDB code: 5bjx:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 5bjx

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Sodium binding site 1 out of 8 in the X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, Variant T395V, 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, Variant T395V, in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na705

b:30.2
occ:1.00
 O A:HOH1148 2.2 40.0 1.0
O A:HOH1101 2.2 39.9 1.0
O A:HOH886 2.4 19.5 1.0
O A:HOH1069 2.4 29.0 1.0
O A:HOH936 2.5 17.5 1.0
O A:HOH968 2.5 18.1 1.0
O A:HOH1093 3.8 42.4 1.0
NZ A:LYS289 3.9 11.5 1.0
O A:HOH937 4.0 15.1 1.0
NZ A:LYS311 4.4 15.2 1.0
OD2 A:ASP315 4.4 16.4 1.0
O A:HOH1149 4.4 35.9 1.0
O A:HOH1123 4.6 27.3 1.0
O A:HOH1128 4.7 24.8 1.0
O A:HOH919 4.7 13.5 1.0
O A:HOH960 4.8 12.5 1.0
CE A:LYS289 5.0 11.2 1.0

Sodium binding site 2 out of 8 in 5bjx

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Sodium binding site 2 out of 8 in the X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, Variant T395V, 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, Variant T395V, in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na706

b:27.5
occ:1.00
 OG A:SER263 2.2 15.2 1.0
O A:HOH1077 2.3 41.3 1.0
O A:HOH977 2.3 22.4 1.0
OD1 A:ASP261 2.4 12.2 1.0
O A:HOH974 2.4 21.3 1.0
O A:HOH994 2.4 20.2 1.0
CG A:ASP261 3.4 14.5 1.0
CB A:SER263 3.4 12.2 1.0
N A:SER263 3.7 9.6 1.0
OD2 A:ASP261 3.9 16.8 1.0
CA A:SER263 4.0 10.1 1.0
N A:ALA264 4.3 8.7 1.0
O A:HOH963 4.4 43.8 1.0
CB A:ASP261 4.5 12.2 1.0
CA A:ASP261 4.5 11.2 1.0
N A:ASP262 4.6 10.1 1.0
C A:ASP261 4.6 11.3 1.0
C A:SER263 4.6 8.8 1.0
O A:HOH1021 4.9 22.1 1.0
C A:ASP262 4.9 9.8 1.0

Sodium binding site 3 out of 8 in 5bjx

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Sodium binding site 3 out of 8 in the X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, Variant T395V, 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, Variant T395V, in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na707

b:20.2
occ:1.00
 O B:HOH1056 2.3 42.4 1.0
O A:LYS320 2.4 15.9 1.0
O A:HOH864 2.5 20.7 1.0
O A:ILE323 2.5 13.0 1.0
O A:HOH1017 2.5 40.8 1.0
O A:HOH1042 2.8 44.6 1.0
C A:LYS320 3.4 15.9 1.0
C A:ILE323 3.6 12.1 1.0
CG1 A:ILE323 3.8 11.8 1.0
CA A:LYS320 4.0 14.9 1.0
O A:HOH893 4.1 33.5 1.0
CB A:LYS320 4.1 17.2 1.0
N A:ILE323 4.3 12.2 1.0
CA A:ILE323 4.4 10.2 1.0
CD A:PRO325 4.5 11.3 1.0
O A:HOH1064 4.5 21.2 1.0
N A:THR324 4.5 10.6 1.0
N A:GLU321 4.5 16.6 1.0
CA A:THR324 4.7 11.0 1.0
CB A:ILE323 4.7 12.0 1.0
OD1 A:ASN313 4.7 12.0 1.0
CA A:GLU321 4.8 18.5 1.0
CD1 A:ILE323 4.9 13.1 1.0
CG A:LYS320 4.9 21.5 1.0

Sodium binding site 4 out of 8 in 5bjx

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Sodium binding site 4 out of 8 in the X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, Variant T395V, 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, Variant T395V, in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na708

b:33.5
occ:1.00
 O B:HOH923 2.3 41.0 1.0
O A:HOH883 2.3 33.7 1.0
O A:HOH1013 2.6 38.3 1.0
O B:HOH1142 2.7 44.3 1.0
O A:HOH857 2.8 25.1 1.0
O B:HOH1051 3.3 35.7 1.0
O A:HOH1107 4.2 36.5 1.0
O B:HOH801 4.3 40.6 1.0
O A:ASP314 4.4 12.8 1.0
OE1 B:GLU453 4.4 28.8 1.0
CA A:ASP315 4.5 11.3 1.0
OD2 A:ASP314 4.5 17.3 1.0
NZ B:LYS444 4.5 22.3 1.0
O A:ASP315 4.6 14.2 1.0
OD1 A:ASP315 4.6 15.7 1.0
OE2 B:GLU453 4.7 26.4 1.0
C A:ASP315 5.0 11.1 1.0

Sodium binding site 5 out of 8 in 5bjx

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Sodium binding site 5 out of 8 in the X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, Variant T395V, 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 4,6-Dehydratase From Campylobacter Jejuni, Variant T395V, in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na709

b:39.3
occ:1.00
 O A:HOH1054 2.3 35.5 1.0
O A:HOH1141 2.3 48.9 1.0
O A:HOH1092 2.4 32.6 1.0
OD1 A:ASP555 2.5 19.0 1.0
O A:HOH1022 2.6 17.8 1.0
CG A:ASP555 3.2 18.0 1.0
OD2 A:ASP555 3.8 17.9 1.0
CA A:ASP555 4.0 13.1 1.0
CB A:ASP555 4.0 13.4 1.0
O A:HOH889 4.1 19.3 1.0
N A:LEU556 4.3 11.9 1.0
C A:ASP555 4.6 11.7 1.0
OD2 A:ASP557 4.7 18.6 1.0
N A:ASP557 4.9 13.1 1.0
O A:HOH992 5.0 20.6 1.0

Sodium binding site 6 out of 8 in 5bjx

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Sodium binding site 6 out of 8 in the X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, Variant T395V, 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 4,6-Dehydratase From Campylobacter Jejuni, Variant T395V, in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na706

b:24.8
occ:1.00
 O B:HOH1083 2.3 38.5 1.0
O B:HOH1091 2.4 29.8 1.0
O B:HOH1124 2.5 43.0 1.0
O B:HOH1030 2.5 17.3 1.0
O B:HOH885 2.5 17.8 1.0
O B:HOH945 2.5 16.2 1.0
NZ B:LYS289 3.9 12.2 1.0
O2 B:EDO703 3.9 35.6 1.0
O B:HOH970 4.0 15.9 1.0
NZ B:LYS311 4.4 14.1 1.0
OD2 B:ASP315 4.5 14.6 1.0
O B:HOH1120 4.5 38.8 1.0
C2 B:EDO703 4.6 26.3 1.0
O B:HOH1148 4.6 30.9 1.0
O B:HOH986 4.7 33.1 1.0
O B:HOH969 4.7 11.8 1.0
O B:HOH871 4.7 11.8 1.0
O B:HOH1100 4.8 29.1 1.0
O B:HOH1147 4.9 25.6 1.0
CE B:LYS289 5.0 11.2 1.0

Sodium binding site 7 out of 8 in 5bjx

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Sodium binding site 7 out of 8 in the X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, Variant T395V, in Complex with Udp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, Variant T395V, in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na707

b:19.6
occ:1.00
 O A:HOH1056 2.2 38.6 1.0
O B:LYS320 2.3 16.0 1.0
O B:ILE323 2.4 11.7 1.0
O B:HOH909 2.5 19.1 1.0
O B:HOH1088 2.5 36.3 1.0
O B:HOH1075 2.8 41.3 1.0
C B:LYS320 3.3 14.5 1.0
C B:ILE323 3.6 10.8 1.0
CG1 B:ILE323 3.8 12.3 1.0
CA B:LYS320 3.9 15.5 1.0
CB B:LYS320 4.1 17.2 1.0
O A:HOH1058 4.2 35.9 1.0
N B:ILE323 4.3 11.0 1.0
CA B:ILE323 4.4 11.1 1.0
O B:HOH884 4.4 29.9 1.0
N B:GLU321 4.5 14.6 1.0
CD B:PRO325 4.5 11.5 1.0
N B:THR324 4.5 9.7 1.0
O B:HOH1097 4.6 20.8 1.0
CA B:THR324 4.6 8.8 1.0
CB B:ILE323 4.7 11.2 1.0
CA B:GLU321 4.8 16.3 1.0
ND2 B:ASN313 4.8 8.5 1.0
CD1 B:ILE323 5.0 15.0 1.0

Sodium binding site 8 out of 8 in 5bjx

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Sodium binding site 8 out of 8 in the X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, Variant T395V, in Complex with Udp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of X-Ray Structure of the Pglf 4,6-Dehydratase From Campylobacter Jejuni, Variant T395V, in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na708

b:28.4
occ:1.00
 OG B:SER263 2.3 16.0 1.0
O B:HOH1108 2.3 42.2 1.0
O B:HOH983 2.3 29.3 1.0
OD1 B:ASP261 2.4 15.5 1.0
O B:HOH1022 2.4 23.7 1.0
O B:HOH1018 2.5 20.1 1.0
CG B:ASP261 3.3 16.8 1.0
CB B:SER263 3.4 13.0 1.0
N B:SER263 3.8 10.4 1.0
OD2 B:ASP261 3.9 18.6 1.0
CA B:SER263 4.1 10.0 1.0
N B:ALA264 4.4 7.9 1.0
CB B:ASP261 4.5 13.5 1.0
CA B:ASP261 4.5 12.6 1.0
N B:ASP262 4.6 10.4 1.0
C B:ASP261 4.6 10.9 1.0
C B:SER263 4.7 8.7 1.0
O B:HOH1067 4.8 24.5 1.0
C B:ASP262 4.9 11.1 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 20:05:26 2024

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