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Sodium in PDB 8b6d: Crystal Structure of Udp-Glucose Pyrophosphorylase From Thermocrispum Agreste Dsm 44070 in Complex with Udp

Enzymatic activity of Crystal Structure of Udp-Glucose Pyrophosphorylase From Thermocrispum Agreste Dsm 44070 in Complex with Udp

All present enzymatic activity of Crystal Structure of Udp-Glucose Pyrophosphorylase From Thermocrispum Agreste Dsm 44070 in Complex with Udp:
2.7.7.9;

Protein crystallography data

The structure of Crystal Structure of Udp-Glucose Pyrophosphorylase From Thermocrispum Agreste Dsm 44070 in Complex with Udp, PDB code: 8b6d was solved by J.Laustsen, A.Kumpf, I.Bento, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.52 / 2.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 65.752, 65.752, 329.552, 90, 90, 90
R / Rfree (%) 17.5 / 22.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Udp-Glucose Pyrophosphorylase From Thermocrispum Agreste Dsm 44070 in Complex with Udp (pdb code 8b6d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Udp-Glucose Pyrophosphorylase From Thermocrispum Agreste Dsm 44070 in Complex with Udp, PDB code: 8b6d:

Sodium binding site 1 out of 1 in 8b6d

Go back to Sodium Binding Sites List in 8b6d
Sodium binding site 1 out of 1 in the Crystal Structure of Udp-Glucose Pyrophosphorylase From Thermocrispum Agreste Dsm 44070 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 Crystal Structure of Udp-Glucose Pyrophosphorylase From Thermocrispum Agreste Dsm 44070 in Complex with Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:49.0
occ:1.00
 O A:HOH465 2.6 47.1 1.0
OE2 A:GLU45 2.7 40.8 1.0
O A:HOH536 2.7 53.6 1.0
HG3 B:PRO26 2.7 38.5 1.0
O A:LYS95 2.8 39.5 1.0
HB3 A:ARG98 2.9 49.3 1.0
HA A:LYS95 3.0 40.5 1.0
HD3 A:ARG98 3.2 65.7 1.0
HG2 A:ARG98 3.4 56.5 1.0
CD A:GLU45 3.5 41.6 1.0
C A:LYS95 3.6 39.5 1.0
OE1 A:GLU45 3.6 38.3 1.0
HB3 A:LYS95 3.6 42.5 1.0
CB A:ARG98 3.6 49.2 1.0
CA A:LYS95 3.6 41.3 1.0
O A:HOH439 3.6 31.9 1.0
CG B:PRO26 3.7 37.0 1.0
CG A:ARG98 3.8 58.1 1.0
HB2 A:ARG98 3.8 50.4 1.0
HD3 B:PRO26 3.9 37.7 1.0
HG2 A:LYS95 3.9 46.2 1.0
CD A:ARG98 3.9 66.8 1.0
CB A:LYS95 4.0 43.2 1.0
HG2 B:PRO26 4.2 36.4 1.0
HB3 B:PRO26 4.2 39.1 1.0
HG21 A:THR41 4.2 38.4 1.0
HG1 A:THR41 4.2 30.0 0.0
CD B:PRO26 4.3 36.8 1.0
HD2 A:ARG98 4.4 66.8 1.0
CG A:LYS95 4.5 46.3 1.0
O A:HOH433 4.5 58.3 1.0
CB B:PRO26 4.5 37.7 1.0
HG22 A:THR41 4.5 38.2 1.0
H A:ARG98 4.6 42.2 1.0
H A:ALA99 4.6 42.4 1.0
HD3 A:LYS95 4.7 49.4 1.0
HG3 A:ARG98 4.8 57.3 1.0
HD2 B:PRO26 4.8 35.7 1.0
OG1 A:THR41 4.8 34.2 1.0
CG2 A:THR41 4.8 40.1 1.0
N A:ILE96 4.9 38.0 1.0
O A:ALA94 4.9 36.2 1.0
HE A:ARG98 4.9 71.8 1.0
HB2 A:LYS95 4.9 43.8 1.0
HB2 B:PRO26 4.9 37.8 1.0
N A:LYS95 4.9 40.0 1.0
HA A:ILE96 4.9 38.1 1.0
CA A:ARG98 4.9 43.8 1.0
NE A:ARG98 5.0 72.3 1.0
CG A:GLU45 5.0 38.7 1.0

Reference:

A.Kumpf, A.Maier, J.U.Laustsen, C.M.Jeffries, I.Bento, D.Tischler. Crystal Structure Determination of A Highly Active Udp-Glucose Pyrophosphorylase From Thermocrispum Agreste Dsm 44070 To Be Published.
Page generated: Mon Aug 18 13:13:16 2025

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