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Sodium in PDB 3rv4: Crystal Structure of E.Coli Biotin Carboxylase R16E Mutant in Complex with Mg-Adp and Bicarbonate

Enzymatic activity of Crystal Structure of E.Coli Biotin Carboxylase R16E Mutant in Complex with Mg-Adp and Bicarbonate

All present enzymatic activity of Crystal Structure of E.Coli Biotin Carboxylase R16E Mutant in Complex with Mg-Adp and Bicarbonate:
6.3.4.14; 6.4.1.2;

Protein crystallography data

The structure of Crystal Structure of E.Coli Biotin Carboxylase R16E Mutant in Complex with Mg-Adp and Bicarbonate, PDB code: 3rv4 was solved by C.Y.Chou, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 119.404, 51.171, 84.156, 90.00, 119.75, 90.00
R / Rfree (%) 17.9 / 21.9

Other elements in 3rv4:

The structure of Crystal Structure of E.Coli Biotin Carboxylase R16E Mutant in Complex with Mg-Adp and Bicarbonate also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Caesium (Cs) 1 atom
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of E.Coli Biotin Carboxylase R16E Mutant in Complex with Mg-Adp and Bicarbonate (pdb code 3rv4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of E.Coli Biotin Carboxylase R16E Mutant in Complex with Mg-Adp and Bicarbonate, PDB code: 3rv4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3rv4

Go back to Sodium Binding Sites List in 3rv4
Sodium binding site 1 out of 2 in the Crystal Structure of E.Coli Biotin Carboxylase R16E Mutant in Complex with Mg-Adp and Bicarbonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of E.Coli Biotin Carboxylase R16E Mutant in Complex with Mg-Adp and Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1012

b:16.3
occ:1.00
O A:HOH470 3.1 18.5 1.0
O A:GLN407 3.1 17.4 1.0
O A:LEU409 3.4 16.1 1.0
CG1 A:ILE410 3.9 14.5 1.0
O A:HOH630 3.9 47.5 1.0
C A:GLN407 4.0 16.9 1.0
C A:LEU409 4.3 15.3 1.0
O A:HOH766 4.5 42.7 1.0
O A:HOH795 4.5 33.9 1.0
C A:GLU408 4.6 16.0 1.0
O A:GLU408 4.6 16.1 1.0
CD1 A:ILE410 4.6 13.7 1.0
O A:HOH782 4.6 30.8 1.0
CA A:GLN407 4.7 17.0 1.0
CA A:ILE410 4.7 15.0 1.0
N A:GLU408 4.8 16.2 1.0
O A:HOH802 4.8 61.4 1.0
N A:LEU409 4.8 15.2 1.0
N A:ILE410 4.9 15.4 1.0
CB A:ILE410 4.9 15.0 1.0
CA A:GLU408 4.9 16.2 1.0

Sodium binding site 2 out of 2 in 3rv4

Go back to Sodium Binding Sites List in 3rv4
Sodium binding site 2 out of 2 in the Crystal Structure of E.Coli Biotin Carboxylase R16E Mutant in Complex with Mg-Adp and Bicarbonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of E.Coli Biotin Carboxylase R16E Mutant in Complex with Mg-Adp and Bicarbonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na450

b:13.0
occ:1.00
O A:HOH671 2.1 25.8 1.0
O A:ASP382 2.6 22.5 1.0
O A:PRO378 3.0 22.6 1.0
O A:HOH662 3.2 26.2 1.0
O A:HOH679 3.2 30.6 1.0
CG1 A:VAL377 3.6 20.0 1.0
C A:ASP382 3.9 22.3 1.0
CB A:PRO349 4.1 22.1 1.0
C A:PRO378 4.2 21.9 1.0
CD A:PRO378 4.4 20.7 1.0
N A:ASP382 4.5 23.1 1.0
CA A:SER383 4.5 20.8 1.0
CG A:PRO378 4.6 20.8 1.0
N A:PRO378 4.6 20.5 1.0
N A:SER383 4.7 21.3 1.0
C A:TYR381 4.7 23.1 1.0
CG A:PRO349 4.8 21.6 1.0
CA A:ASP382 4.8 23.5 1.0
N A:TYR381 4.8 22.9 1.0
CB A:TYR381 4.9 21.7 1.0
CB A:VAL377 4.9 19.8 1.0
CA A:PRO378 4.9 21.2 1.0
C A:SER383 5.0 19.9 1.0
C A:VAL377 5.0 20.1 1.0

Reference:

C.Y.Chou, L.Tong. Structural and Biochemical Studies on the Regulation of Biotin Carboxylase By Substrate Inhibition and Dimerization. J.Biol.Chem. V. 286 24417 2011.
ISSN: ISSN 0021-9258
PubMed: 21592965
DOI: 10.1074/JBC.M111.220517
Page generated: Tue Dec 15 06:24:12 2020

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