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Sodium in PDB 1uxj: Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface

Enzymatic activity of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface

All present enzymatic activity of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface:
1.1.1.37;

Protein crystallography data

The structure of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface, PDB code: 1uxj 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 (°) 105.247, 105.247, 102.196, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 21.1

Other elements in 1uxj:

The structure of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface also contains other interesting chemical elements:

Cadmium (Cd) 9 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface (pdb code 1uxj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface, PDB code: 1uxj:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 1uxj

Go back to Sodium Binding Sites List in 1uxj
Sodium binding site 1 out of 3 in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations 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 Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1314

b:30.7
occ:0.50
ND1 A:HIS19 2.7 16.0 1.0
O A:HOH2017 2.7 15.5 1.0
CE1 A:HIS19 3.4 15.7 1.0
CG A:HIS19 3.7 16.3 1.0
CE1 A:TYR227 3.8 14.1 1.0
CG2 A:THR16 4.1 12.7 1.0
CB A:HIS19 4.1 14.8 1.0
CD1 A:TYR227 4.4 12.8 1.0
OG1 A:THR16 4.5 13.2 1.0
NE2 A:HIS19 4.5 18.3 1.0
CB A:THR16 4.7 13.2 1.0
CA A:THR16 4.7 11.9 1.0
CD2 A:HIS19 4.7 18.5 1.0
CZ A:TYR227 4.7 13.1 1.0
OH A:TYR227 4.8 13.9 1.0
NA A:NA1315 4.8 24.6 0.5

Sodium binding site 2 out of 3 in 1uxj

Go back to Sodium Binding Sites List in 1uxj
Sodium binding site 2 out of 3 in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations 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 Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1315

b:24.6
occ:0.50
O A:HOH2251 2.8 22.9 1.0
O A:HOH2017 3.2 15.5 1.0
CE2 A:TYR226 3.7 13.9 1.0
CD1 A:PHE12 4.2 18.7 1.0
CE1 A:PHE12 4.3 21.6 1.0
OH A:TYR227 4.4 13.9 1.0
CZ A:TYR226 4.4 17.1 1.0
OH A:TYR226 4.4 19.0 1.0
CD2 A:TYR226 4.4 14.2 1.0
OG1 A:THR16 4.5 13.2 1.0
NA A:NA1314 4.8 30.7 0.5
O A:HOH2055 5.0 23.4 1.0

Sodium binding site 3 out of 3 in 1uxj

Go back to Sodium Binding Sites List in 1uxj
Sodium binding site 3 out of 3 in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations 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 3 of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1315

b:14.2
occ:1.00
OE2 C:GLU238 2.2 28.6 1.0
OE1 C:GLU238 2.7 28.9 1.0
CD C:GLU238 2.8 25.5 1.0
NZ A:LYS165 4.0 29.3 1.0
O A:HOH2186 4.2 33.6 1.0
NZ C:LYS24 4.2 36.2 1.0
CG C:GLU238 4.3 21.3 1.0
CE C:LYS244 4.5 26.6 1.0
NZ C:LYS242 4.9 28.5 1.0
NZ C:LYS244 4.9 24.7 1.0

Reference:

A.Bjork, B.Dalhus, D.Mantzilas, R.Sirevag, V.G.H.Eijsink. Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface. J.Mol.Biol. V. 341 1215 2004.
ISSN: ISSN 0022-2836
PubMed: 15321717
DOI: 10.1016/J.JMB.2004.06.079
Page generated: Sun Oct 6 22:47:41 2024

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