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Sodium in PDB 5kqi: Crystal Structure of the L326D Variant of Catalase-Peroxidase From B. Pseudomallei

Enzymatic activity of Crystal Structure of the L326D Variant of Catalase-Peroxidase From B. Pseudomallei

All present enzymatic activity of Crystal Structure of the L326D Variant of Catalase-Peroxidase From B. Pseudomallei:
1.11.1.21;

Protein crystallography data

The structure of Crystal Structure of the L326D Variant of Catalase-Peroxidase From B. Pseudomallei, PDB code: 5kqi was solved by P.C.Loewen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.42 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.793, 115.227, 174.543, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19.8

Other elements in 5kqi:

The structure of Crystal Structure of the L326D Variant of Catalase-Peroxidase From B. Pseudomallei also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the L326D Variant of Catalase-Peroxidase From B. Pseudomallei (pdb code 5kqi). 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 the L326D Variant of Catalase-Peroxidase From B. Pseudomallei, PDB code: 5kqi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5kqi

Go back to Sodium Binding Sites List in 5kqi
Sodium binding site 1 out of 2 in the Crystal Structure of the L326D Variant of Catalase-Peroxidase From B. Pseudomallei


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 the L326D Variant of Catalase-Peroxidase From B. Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:20.9
occ:1.00
O A:HOH1012 2.3 23.6 1.0
O A:GLY124 2.3 17.7 1.0
O A:GLY122 2.4 18.6 1.0
O A:SER494 2.4 20.4 1.0
O A:HOH1379 2.4 26.5 1.0
C A:SER494 3.3 17.3 1.0
C A:GLY124 3.4 17.6 1.0
C A:GLY122 3.4 18.9 1.0
C A:ARG123 3.5 17.7 1.0
CA A:ARG123 3.5 19.0 1.0
N A:GLY124 3.5 19.1 1.0
O A:HOH1430 3.9 25.0 1.0
N A:ARG123 4.0 19.4 1.0
OD2 A:ASP427 4.0 23.8 1.0
CA A:SER494 4.0 19.1 1.0
O A:HOH1130 4.0 34.8 1.0
CA A:GLY124 4.1 19.1 1.0
O A:ARG123 4.1 18.6 1.0
CB A:ASP427 4.1 22.0 1.0
CB A:SER494 4.2 19.9 1.0
N A:ASP495 4.2 18.6 1.0
CA A:ASP495 4.5 18.2 1.0
N A:GLY125 4.5 18.4 1.0
CG A:ASP427 4.6 24.5 1.0
CD1 A:TYR117 4.6 19.6 1.0
CB A:ASP495 4.6 18.2 1.0
CL A:CL803 4.6 45.2 1.0
CA A:GLY122 4.8 18.5 1.0
CA A:GLY125 4.9 18.5 1.0
CB A:ARG123 4.9 18.5 1.0
CE1 A:TYR117 4.9 17.6 1.0

Sodium binding site 2 out of 2 in 5kqi

Go back to Sodium Binding Sites List in 5kqi
Sodium binding site 2 out of 2 in the Crystal Structure of the L326D Variant of Catalase-Peroxidase From B. Pseudomallei


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 the L326D Variant of Catalase-Peroxidase From B. Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na802

b:20.1
occ:1.00
O B:HOH1217 2.2 26.1 1.0
O B:GLY122 2.3 18.6 1.0
O B:SER494 2.4 20.9 1.0
O B:GLY124 2.4 20.4 1.0
O B:HOH929 2.4 25.8 1.0
C B:SER494 3.2 19.5 1.0
C B:GLY122 3.5 20.3 1.0
C B:GLY124 3.5 19.3 1.0
N B:GLY124 3.7 20.0 1.0
C B:ARG123 3.7 21.0 1.0
CA B:ARG123 3.7 20.8 1.0
O B:HOH936 3.8 41.3 1.0
O B:HOH1412 3.9 25.8 1.0
CA B:SER494 4.0 19.5 1.0
OD2 B:ASP427 4.0 23.4 1.0
N B:ARG123 4.0 18.9 1.0
N B:ASP495 4.1 19.6 1.0
CB B:SER494 4.1 19.7 1.0
CA B:GLY124 4.2 19.0 1.0
CB B:ASP427 4.2 21.2 1.0
O B:ARG123 4.2 18.9 1.0
CA B:ASP495 4.4 20.0 1.0
CB B:ASP495 4.4 20.2 1.0
CD1 B:TYR117 4.6 20.5 1.0
CL B:CL803 4.6 28.1 0.5
N B:GLY125 4.6 18.9 1.0
OE2 B:GLU128 4.7 45.2 1.0
CG B:ASP427 4.7 22.9 1.0
CA B:GLY122 4.7 18.4 1.0
CE1 B:TYR117 4.8 19.8 1.0
OE2 B:GLU198 4.9 31.4 0.5
OG B:SER494 4.9 21.1 1.0
CA B:GLY125 4.9 17.1 1.0
CB B:ARG123 5.0 21.2 1.0

Reference:

M.Machuqueiro, B.Victor, J.Switala, J.Villanueva, C.Rovira, I.Fita, P.C.Loewen. The Catalase Activity of Catalase-Peroxidases Is Modulated By Changes in the Pka of the Distal Histidine. Biochemistry V. 56 2271 2017.
ISSN: ISSN 1520-4995
PubMed: 28409923
DOI: 10.1021/ACS.BIOCHEM.6B01276
Page generated: Tue Dec 15 11:10:56 2020

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