Atomistry » Sodium » PDB 5b15-5bph » 5bjx
Atomistry »
  Sodium »
    PDB 5b15-5bph »
      5bjx »

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

Go back to Sodium Binding Sites List in 5bjx
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

Go back to Sodium Binding Sites List in 5bjx
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

Go back to Sodium Binding Sites List in 5bjx
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

Go back to Sodium Binding Sites List in 5bjx
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

Go back to Sodium Binding Sites List in 5bjx
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

Go back to Sodium Binding Sites List in 5bjx
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

Go back to Sodium Binding Sites List in 5bjx
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

Go back to Sodium Binding Sites List in 5bjx
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy