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Sodium in PDB 6oxn: 2.6 Angstrom Structure of W45F/H46S Glyoxylate/Hydroxypyruvate Reductase A From Escherichia Coli in Complex with Glyoxylate and Nadp

Enzymatic activity of 2.6 Angstrom Structure of W45F/H46S Glyoxylate/Hydroxypyruvate Reductase A From Escherichia Coli in Complex with Glyoxylate and Nadp

All present enzymatic activity of 2.6 Angstrom Structure of W45F/H46S Glyoxylate/Hydroxypyruvate Reductase A From Escherichia Coli in Complex with Glyoxylate and Nadp:
1.1.1.79; 1.1.1.81;

Protein crystallography data

The structure of 2.6 Angstrom Structure of W45F/H46S Glyoxylate/Hydroxypyruvate Reductase A From Escherichia Coli in Complex with Glyoxylate and Nadp, PDB code: 6oxn was solved by N.Vuksanovic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.48 / 2.61
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 158.960, 158.960, 94.540, 90.00, 90.00, 120.00
R / Rfree (%) 15.2 / 18.9

Sodium Binding Sites:

The binding sites of Sodium atom in the 2.6 Angstrom Structure of W45F/H46S Glyoxylate/Hydroxypyruvate Reductase A From Escherichia Coli in Complex with Glyoxylate and Nadp (pdb code 6oxn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the 2.6 Angstrom Structure of W45F/H46S Glyoxylate/Hydroxypyruvate Reductase A From Escherichia Coli in Complex with Glyoxylate and Nadp, PDB code: 6oxn:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6oxn

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Sodium binding site 1 out of 3 in the 2.6 Angstrom Structure of W45F/H46S Glyoxylate/Hydroxypyruvate Reductase A From Escherichia Coli in Complex with Glyoxylate and Nadp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.6 Angstrom Structure of W45F/H46S Glyoxylate/Hydroxypyruvate Reductase A From Escherichia Coli in Complex with Glyoxylate and Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:34.4
occ:1.00
 NH1 A:ARG134 3.6 34.9 1.0
N A:ARG134 3.8 29.0 1.0
CD A:ARG134 3.8 31.7 1.0
CG A:ARG134 4.2 25.5 1.0
CB A:ARG134 4.2 21.7 1.0
ND1 A:HIS133 4.2 56.7 1.0
CA A:HIS133 4.4 30.3 1.0
NH2 A:ARG159 4.5 24.0 1.0
CZ A:ARG134 4.6 32.5 1.0
C A:HIS133 4.6 25.4 1.0
CA A:ARG134 4.7 26.7 1.0
NE A:ARG134 4.7 30.1 1.0
CB A:HIS133 4.7 35.6 1.0
CZ A:PHE111 4.9 21.0 1.0
CG A:HIS133 4.9 54.4 1.0
O A:TYR132 5.0 29.4 1.0

Sodium binding site 2 out of 3 in 6oxn

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Sodium binding site 2 out of 3 in the 2.6 Angstrom Structure of W45F/H46S Glyoxylate/Hydroxypyruvate Reductase A From Escherichia Coli in Complex with Glyoxylate and Nadp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2.6 Angstrom Structure of W45F/H46S Glyoxylate/Hydroxypyruvate Reductase A From Escherichia Coli in Complex with Glyoxylate and Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:57.1
occ:1.00
 OG1 A:THR12 3.4 50.6 1.0
O A:HIS7 3.9 42.5 1.0
CD2 A:TYR6 4.0 37.6 1.0
N A:HIS7 4.0 32.3 1.0
CA A:TYR6 4.1 28.7 1.0
O A:PHE5 4.2 33.4 1.0
CG2 A:THR12 4.3 38.6 1.0
O A:TRP31 4.3 42.4 1.0
CB A:THR12 4.4 41.6 1.0
CB A:ALA30 4.4 35.9 1.0
CE A:LYS32 4.5 61.0 1.0
CE2 A:TYR6 4.5 39.5 1.0
CG A:TYR6 4.6 32.5 1.0
C A:TYR6 4.6 23.5 1.0
C A:HIS7 4.8 41.7 1.0
CB A:TYR6 4.8 24.2 1.0
CD1 A:PHE5 4.9 26.9 1.0
C A:PHE5 4.9 30.2 1.0
N A:TYR6 5.0 25.8 1.0
N A:TRP31 5.0 33.1 1.0

Sodium binding site 3 out of 3 in 6oxn

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Sodium binding site 3 out of 3 in the 2.6 Angstrom Structure of W45F/H46S Glyoxylate/Hydroxypyruvate Reductase A From Escherichia Coli in Complex with Glyoxylate and Nadp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 2.6 Angstrom Structure of W45F/H46S Glyoxylate/Hydroxypyruvate Reductase A From Escherichia Coli in Complex with Glyoxylate and Nadp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:66.8
occ:1.00
 O A:HOH542 2.8 46.0 1.0
CG1 A:ILE70 3.0 60.0 1.0
O A:HOH502 3.0 43.5 1.0
OG A:SER69 3.3 60.6 1.0
O A:GLY66 3.3 43.1 1.0
N A:ILE70 3.5 36.1 1.0
CA A:VAL67 3.6 30.0 1.0
N A:SER69 3.7 38.8 1.0
CB A:SER69 3.8 42.8 1.0
C A:VAL67 3.8 32.9 1.0
CD1 A:ILE70 3.9 72.4 1.0
C A:GLY66 4.1 36.6 1.0
CA A:SER69 4.1 39.1 1.0
CB A:ILE70 4.2 35.8 1.0
N A:ASP68 4.2 37.0 1.0
O A:VAL67 4.2 33.8 1.0
N A:VAL67 4.2 33.2 1.0
C A:SER69 4.3 38.8 1.0
CA A:ILE70 4.4 35.7 1.0
CE1 A:PHE45 4.5 45.4 1.0
CB A:VAL67 4.7 23.6 1.0
C A:ASP68 4.8 43.5 1.0
CD1 A:PHE45 4.9 46.9 1.0

Reference:

N.Vuksanovic, N.Vuksanovic. N/A N/A.
Page generated: Tue Dec 15 12:44:04 2020

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