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Sodium in PDB 1ur5: Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface

Enzymatic activity of Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface

All present enzymatic activity of Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface:
1.1.1.37;

Protein crystallography data

The structure of Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface, PDB code: 1ur5 was solved by A.Bjork, B.Dalhus, D.Mantzilas, V.G.H.Eijsink, R.Sirevag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.75
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.575, 105.575, 102.531, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 22.3

Other elements in 1ur5:

The structure of Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface also contains other interesting chemical elements:

Cadmium (Cd) 6 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface (pdb code 1ur5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface, PDB code: 1ur5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1ur5

Go back to Sodium Binding Sites List in 1ur5
Sodium binding site 1 out of 2 in the Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1313

b:28.5
occ:0.50
ND1 A:HIS19 3.0 31.0 1.0
O A:HOH2205 3.7 19.9 1.0
CE1 A:HIS19 3.8 31.8 1.0
O A:HOH2013 3.9 44.2 1.0
CG A:HIS19 4.0 28.4 1.0
CE1 A:TYR227 4.1 18.7 1.0
CG2 A:THR16 4.2 16.6 1.0
CB A:HIS19 4.3 22.3 1.0
CD1 A:TYR227 4.6 17.9 1.0
CA A:THR16 4.9 13.8 1.0
OG1 A:THR16 4.9 14.0 1.0
CB A:THR16 5.0 12.7 1.0
NE2 A:HIS19 5.0 32.2 1.0

Sodium binding site 2 out of 2 in 1ur5

Go back to Sodium Binding Sites List in 1ur5
Sodium binding site 2 out of 2 in the Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1313

b:28.5
occ:0.50
ND1 C:HIS19 3.2 29.6 1.0
CE1 C:HIS19 3.9 30.2 1.0
O C:HOH2005 4.0 34.6 1.0
CG2 C:THR16 4.1 17.3 1.0
CE1 C:TYR227 4.1 27.2 1.0
CG C:HIS19 4.2 26.6 1.0
CB C:HIS19 4.5 22.7 1.0
CD1 C:TYR227 4.7 24.2 1.0
OG1 C:THR16 4.9 17.8 1.0
CB C:THR16 4.9 15.5 1.0
CA C:THR16 4.9 16.4 1.0

Reference:

A.Bjork, B.Dalhus, D.Mantzilas, V.G.H.Eijsink, R.Sirevag. Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer-Dimer Interface J.Mol.Biol. V. 334 811 2003.
ISSN: ISSN 0022-2836
PubMed: 14636605
DOI: 10.1016/J.JMB.2003.10.006
Page generated: Sun Oct 6 22:47:14 2024

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