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Sodium in PDB 1uxk: 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: 1uxk 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 / 1.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.405, 105.405, 102.305, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 21.4

Other elements in 1uxk:

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) 10 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 1uxk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 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: 1uxk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 1uxk

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Sodium binding site 1 out of 6 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:42.0
occ:0.50
 ND1 A:HIS19 2.7 15.5 1.0
O A:HOH2008 2.8 18.0 1.0
CE1 A:HIS19 3.4 14.4 1.0
CG A:HIS19 3.7 14.0 1.0
CE1 A:TYR227 3.8 16.8 1.0
CG2 A:THR16 4.1 12.5 1.0
CB A:HIS19 4.1 15.3 1.0
CD1 A:TYR227 4.4 16.0 1.0
NE2 A:HIS19 4.5 16.1 1.0
OG1 A:THR16 4.5 12.7 1.0
CD2 A:HIS19 4.7 16.9 1.0
CB A:THR16 4.7 13.5 1.0
CA A:THR16 4.7 12.7 1.0
CZ A:TYR227 4.8 15.9 1.0
OH A:TYR227 4.8 14.3 1.0

Sodium binding site 2 out of 6 in 1uxk

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Sodium binding site 2 out of 6 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:47.1
occ:0.50
 O A:HOH2007 2.7 20.3 1.0
O A:HOH2008 3.3 18.0 1.0
CE2 A:TYR226 3.7 15.9 1.0
CD1 A:PHE12 4.0 21.8 1.0
CE1 A:PHE12 4.0 24.0 1.0
CD2 A:TYR226 4.4 16.7 1.0
CZ A:TYR226 4.4 19.9 1.0
OH A:TYR226 4.4 19.5 1.0
OH A:TYR227 4.5 14.3 1.0
OG1 A:THR16 4.6 12.7 1.0
O A:HOH2044 4.9 22.7 1.0

Sodium binding site 3 out of 6 in 1uxk

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Sodium binding site 3 out of 6 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
A:Na1316

b:36.5
occ:1.00
 N A:LYS3 2.8 22.4 1.0
O A:HOH2019 3.2 28.3 1.0
O A:LEU26 3.3 20.1 1.0
CA A:ARG2 3.4 26.6 1.0
CB A:ARG2 3.5 25.5 1.0
CG A:LYS3 3.6 25.4 1.0
C A:ARG2 3.6 24.5 1.0
O A:HOH2023 3.7 33.1 1.0
CB A:LYS3 3.7 21.5 1.0
CA A:LYS3 3.8 21.6 1.0
CA A:GLY27 3.9 15.7 1.0
C A:LEU26 4.0 19.3 1.0
CG A:ARG2 4.1 21.7 1.0
N A:GLY27 4.3 17.6 1.0
O A:LYS3 4.5 18.1 1.0
O A:HOH2020 4.6 28.6 1.0
C A:LYS3 4.7 19.9 1.0
N A:ARG2 4.8 30.8 1.0
O A:ARG2 4.8 24.2 1.0
CD A:LYS3 4.8 26.4 1.0
CD A:ARG2 4.9 21.4 1.0

Sodium binding site 4 out of 6 in 1uxk

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Sodium binding site 4 out of 6 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 4 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:Na1318

b:16.6
occ:1.00
 O A:HOH2184 2.2 39.8 1.0
O A:HOH2188 2.3 37.1 1.0
O A:HOH2078 2.3 48.5 1.0
O A:HOH2079 2.4 39.5 1.0
O A:HOH2024 4.7 42.8 1.0
O A:HOH2077 4.8 16.8 1.0
O A:HIS175 4.8 20.1 1.0

Sodium binding site 5 out of 6 in 1uxk

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Sodium binding site 5 out of 6 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 5 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:Na1319

b:46.9
occ:0.50
 O C:HOH2251 2.9 20.0 1.0
O C:HOH2250 2.9 20.9 1.0
CE2 C:TYR226 3.7 19.9 1.0
CD1 C:PHE12 4.1 25.3 1.0
CE1 C:PHE12 4.2 27.8 1.0
OH C:TYR227 4.4 18.2 1.0
CD2 C:TYR226 4.4 18.3 1.0
CZ C:TYR226 4.4 19.4 1.0
OG1 C:THR16 4.4 14.9 1.0
OH C:TYR226 4.4 20.5 1.0
O C:HOH2010 4.7 44.0 0.5
CZ C:TYR227 5.0 16.7 1.0

Sodium binding site 6 out of 6 in 1uxk

Go back to Sodium Binding Sites List in 1uxk
Sodium binding site 6 out of 6 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 6 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:30.5
occ:1.00
 CD A:CD1308 4.7 16.6 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 22:48:01 2024

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