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Sodium in PDB 2x0r: R207S, R292S Mutant of Malate Dehydrogenase From the Halophilic Archeon Haloarcula Marismortui (Holoform)

Enzymatic activity of R207S, R292S Mutant of Malate Dehydrogenase From the Halophilic Archeon Haloarcula Marismortui (Holoform)

All present enzymatic activity of R207S, R292S Mutant of Malate Dehydrogenase From the Halophilic Archeon Haloarcula Marismortui (Holoform):
1.1.1.37;

Protein crystallography data

The structure of R207S, R292S Mutant of Malate Dehydrogenase From the Halophilic Archeon Haloarcula Marismortui (Holoform), PDB code: 2x0r was solved by A.Irimia, C.Ebel, F.M.D.Vellieux, S.B.Richard, L.W.Cosenza, G.Zaccai, D.Madern, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.50 / 2.92
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 115.360, 125.910, 125.840, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 28.6

Other elements in 2x0r:

The structure of R207S, R292S Mutant of Malate Dehydrogenase From the Halophilic Archeon Haloarcula Marismortui (Holoform) also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the R207S, R292S Mutant of Malate Dehydrogenase From the Halophilic Archeon Haloarcula Marismortui (Holoform) (pdb code 2x0r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the R207S, R292S Mutant of Malate Dehydrogenase From the Halophilic Archeon Haloarcula Marismortui (Holoform), PDB code: 2x0r:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 2x0r

Go back to Sodium Binding Sites List in 2x0r
Sodium binding site 1 out of 5 in the R207S, R292S Mutant of Malate Dehydrogenase From the Halophilic Archeon Haloarcula Marismortui (Holoform)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of R207S, R292S Mutant of Malate Dehydrogenase From the Halophilic Archeon Haloarcula Marismortui (Holoform) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1007

b:63.5
occ:1.00
 OD1 A:ASP44 3.0 31.1 1.0
OD1 A:ASP47 3.3 42.9 1.0
O A:ALA46 3.5 40.4 1.0
O A:ASP44 3.5 25.2 1.0
CG A:ASP44 3.7 31.5 1.0
C A:ALA46 3.8 40.5 1.0
C A:ASP44 4.0 35.3 1.0
OD2 A:ASP44 4.1 26.2 1.0
N A:ASP47 4.2 36.6 1.0
N A:ALA46 4.2 30.9 1.0
CA A:ASP47 4.3 42.8 1.0
OG1 A:THR76 4.3 28.6 1.0
CG A:ASP47 4.4 45.0 1.0
CA A:ALA46 4.4 38.6 1.0
CA A:ASP44 4.5 44.4 1.0
O A:ASN75 4.6 49.5 1.0
C A:ILE45 4.6 34.3 1.0
C A:ASN75 4.6 42.1 1.0
N A:ILE45 4.6 34.9 1.0
CB A:ASP44 4.7 42.7 1.0
N A:THR76 4.7 38.1 1.0
CA A:ILE45 4.9 31.1 1.0
CA A:THR76 4.9 43.1 1.0
CB A:ASP47 5.0 41.8 1.0

Sodium binding site 2 out of 5 in 2x0r

Go back to Sodium Binding Sites List in 2x0r
Sodium binding site 2 out of 5 in the R207S, R292S Mutant of Malate Dehydrogenase From the Halophilic Archeon Haloarcula Marismortui (Holoform)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of R207S, R292S Mutant of Malate Dehydrogenase From the Halophilic Archeon Haloarcula Marismortui (Holoform) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1006

b:41.6
occ:1.00
 O B:HOH2054 3.1 16.3 1.0
O B:LYS205 3.5 22.0 1.0
CB B:SER207 3.6 45.2 1.0
OG B:SER207 3.9 53.1 1.0
OD1 B:ASP211 4.1 64.1 1.0
OE1 B:GLU188 4.3 98.7 1.0
C B:LYS205 4.5 23.5 1.0
CA B:SER207 4.7 36.5 1.0
N B:SER207 4.7 42.4 1.0
CA B:LYS205 5.0 23.3 1.0

Sodium binding site 3 out of 5 in 2x0r

Go back to Sodium Binding Sites List in 2x0r
Sodium binding site 3 out of 5 in the R207S, R292S Mutant of Malate Dehydrogenase From the Halophilic Archeon Haloarcula Marismortui (Holoform)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of R207S, R292S Mutant of Malate Dehydrogenase From the Halophilic Archeon Haloarcula Marismortui (Holoform) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1008

b:12.1
occ:1.00
 OG1 B:THR76 2.8 15.1 1.0
N B:ILE45 2.9 14.4 1.0
N B:ALA46 3.1 38.2 1.0
O B:ILE40 3.2 40.0 1.0
N B:ASP44 3.3 30.3 1.0
O B:ALA41 3.4 44.9 1.0
CG1 B:ILE45 3.5 23.2 1.0
CA B:ALA41 3.5 18.1 1.0
CA B:ASP44 3.5 39.4 1.0
O B:ALA46 3.5 37.8 1.0
C B:ASP44 3.7 47.1 1.0
CB B:THR76 3.8 33.4 1.0
C B:ALA41 3.8 30.7 1.0
CA B:ILE45 3.8 24.9 1.0
CG2 B:THR76 3.8 33.2 1.0
C B:ILE40 3.8 29.9 1.0
C B:ILE45 3.9 31.5 1.0
CA B:ALA46 3.9 43.1 1.0
N B:ALA41 4.0 27.0 1.0
CB B:ALA46 4.1 50.4 1.0
C B:ALA46 4.2 42.1 1.0
CB B:ILE45 4.2 25.6 1.0
C B:ARG43 4.3 35.6 1.0
CG2 B:ILE40 4.4 35.2 1.0
N B:ARG43 4.6 36.1 1.0
OG B:SER74 4.6 28.2 1.0
CD1 B:ILE45 4.7 14.4 1.0
CB B:ALA41 4.7 20.0 1.0
CG2 B:VAL49 4.8 34.0 1.0
CA B:ARG43 4.8 37.1 1.0
CG2 B:ILE45 4.8 28.2 1.0
O B:ASP44 4.9 45.0 1.0
N B:LEU42 4.9 22.8 1.0

Sodium binding site 4 out of 5 in 2x0r

Go back to Sodium Binding Sites List in 2x0r
Sodium binding site 4 out of 5 in the R207S, R292S Mutant of Malate Dehydrogenase From the Halophilic Archeon Haloarcula Marismortui (Holoform)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of R207S, R292S Mutant of Malate Dehydrogenase From the Halophilic Archeon Haloarcula Marismortui (Holoform) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1009

b:44.6
occ:1.00
 N B:GLN80 3.3 36.8 1.0
O B:GLN80 3.8 49.4 1.0
CB B:GLN80 3.8 20.1 1.0
CA B:GLN80 4.0 34.2 1.0
CA B:ARG79 4.1 35.1 1.0
C B:ARG79 4.2 39.2 1.0
CB B:ARG79 4.2 22.4 1.0
C B:GLN80 4.4 41.2 1.0
CG2 B:VAL60 4.6 21.7 1.0
NE2 B:GLN80 4.6 49.2 1.0

Sodium binding site 5 out of 5 in 2x0r

Go back to Sodium Binding Sites List in 2x0r
Sodium binding site 5 out of 5 in the R207S, R292S Mutant of Malate Dehydrogenase From the Halophilic Archeon Haloarcula Marismortui (Holoform)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of R207S, R292S Mutant of Malate Dehydrogenase From the Halophilic Archeon Haloarcula Marismortui (Holoform) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1010

b:27.7
occ:1.00
 OG B:SER272 2.9 28.7 1.0
O B:ASP143 3.2 29.0 1.0
CB B:ALA286 3.5 38.1 1.0
CB B:ASN146 3.5 37.7 1.0
O B:SER272 3.5 25.4 1.0
CB B:SER272 3.6 28.1 1.0
C B:SER272 3.6 21.0 1.0
N B:ARG147 3.7 49.7 1.0
OD1 B:ASN146 3.7 20.2 1.0
C B:ALA286 3.9 31.4 1.0
CA B:ASP143 3.9 30.4 1.0
C B:ASP143 4.0 36.1 1.0
N B:VAL273 4.0 22.2 1.0
O B:ALA286 4.0 31.6 1.0
CG B:ASN146 4.1 28.5 1.0
N B:PHE287 4.1 26.7 1.0
CA B:SER272 4.2 29.9 1.0
CA B:ALA286 4.2 42.1 1.0
C B:ASN146 4.2 48.9 1.0
CA B:VAL273 4.2 36.2 1.0
CA B:ARG147 4.4 49.7 1.0
C B:VAL273 4.4 42.5 1.0
CA B:ASN146 4.4 38.6 1.0
CB B:ARG147 4.5 47.7 1.0
CA B:PHE287 4.5 33.0 1.0
O B:VAL273 4.6 44.4 1.0
OD1 B:ASP143 4.6 37.4 1.0
CB B:ASP143 4.7 20.7 1.0
O B:VAL142 4.7 46.4 1.0
N B:LYS274 4.8 40.1 1.0
N B:ASN146 4.9 33.6 1.0
N B:ASP143 4.9 41.5 1.0

Reference:

A.Irimia, C.Ebel, D.Madern, S.B.Richard, L.W.Cosenza, G.Zaccai, F.M.D.Vellieux. The Oligomeric States of Haloarcula Marismortui Malate Dehydrogenase Are Modulated By Solvent Components As Shown By Crystallographic and Biochemical Studies J.Mol.Biol. V. 326 859 2003.
ISSN: ISSN 0022-2836
PubMed: 12581646
DOI: 10.1016/S0022-2836(02)01450-X
Page generated: Mon Oct 7 05:02:43 2024

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