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Sodium in PDB 5kqq: Crystal Structure of the W153F Variant of Catalase-Peroxidase From B. Pseudomallei Treated

Enzymatic activity of Crystal Structure of the W153F Variant of Catalase-Peroxidase From B. Pseudomallei Treated

All present enzymatic activity of Crystal Structure of the W153F Variant of Catalase-Peroxidase From B. Pseudomallei Treated:
1.11.1.21;

Protein crystallography data

The structure of Crystal Structure of the W153F Variant of Catalase-Peroxidase From B. Pseudomallei Treated, PDB code: 5kqq 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) 96.90 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.922, 116.130, 175.788, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 17.5

Other elements in 5kqq:

The structure of Crystal Structure of the W153F Variant of Catalase-Peroxidase From B. Pseudomallei Treated also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the W153F Variant of Catalase-Peroxidase From B. Pseudomallei Treated (pdb code 5kqq). 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 W153F Variant of Catalase-Peroxidase From B. Pseudomallei Treated, PDB code: 5kqq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5kqq

Go back to Sodium Binding Sites List in 5kqq
Sodium binding site 1 out of 2 in the Crystal Structure of the W153F Variant of Catalase-Peroxidase From B. Pseudomallei Treated


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 W153F Variant of Catalase-Peroxidase From B. Pseudomallei Treated within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:18.9
occ:1.00
O A:GLY124 2.3 17.5 1.0
O A:HOH949 2.3 21.4 1.0
O A:SER494 2.3 19.8 1.0
O A:GLY122 2.4 16.2 1.0
O A:HOH1083 2.4 21.2 1.0
C A:SER494 3.2 18.8 1.0
C A:GLY124 3.5 19.1 1.0
C A:GLY122 3.5 16.0 1.0
C A:ARG123 3.6 16.7 1.0
N A:GLY124 3.6 17.2 1.0
CA A:ARG123 3.6 18.3 1.0
O A:HOH939 3.9 34.3 1.0
CA A:SER494 4.0 18.7 1.0
O A:HOH1346 4.0 20.4 1.0
N A:ARG123 4.0 16.8 1.0
OD2 A:ASP427 4.1 17.7 1.0
N A:ASP495 4.1 17.5 1.0
CB A:ASP427 4.1 20.2 1.0
CA A:GLY124 4.1 19.1 1.0
O A:ARG123 4.2 16.8 1.0
CB A:SER494 4.2 17.9 1.0
CA A:ASP495 4.4 20.2 1.0
CB A:ASP495 4.6 18.6 1.0
CD1 A:TYR117 4.6 17.4 1.0
N A:GLY125 4.6 17.2 1.0
CG A:ASP427 4.7 20.3 1.0
OE2 A:GLU198 4.7 42.7 1.0
CA A:GLY122 4.7 16.7 1.0
OE2 A:GLU128 4.8 38.0 1.0
CE1 A:TYR117 4.9 16.3 1.0
CB A:ARG123 4.9 19.5 1.0
OE1 A:GLU198 4.9 28.7 1.0
CA A:GLY125 5.0 17.8 1.0
OG A:SER494 5.0 16.7 1.0

Sodium binding site 2 out of 2 in 5kqq

Go back to Sodium Binding Sites List in 5kqq
Sodium binding site 2 out of 2 in the Crystal Structure of the W153F Variant of Catalase-Peroxidase From B. Pseudomallei Treated


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 W153F Variant of Catalase-Peroxidase From B. Pseudomallei Treated within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na802

b:20.3
occ:1.00
O B:HOH1005 2.3 23.6 1.0
O B:GLY124 2.4 17.4 1.0
O B:GLY122 2.4 17.1 1.0
O B:SER494 2.4 17.8 1.0
O B:HOH1144 2.4 24.8 1.0
C B:SER494 3.2 18.8 1.0
C B:GLY122 3.5 15.8 1.0
C B:GLY124 3.5 17.2 1.0
C B:ARG123 3.6 16.4 1.0
CA B:ARG123 3.6 16.3 1.0
N B:GLY124 3.6 17.4 1.0
CA B:SER494 4.0 17.0 1.0
N B:ARG123 4.0 16.6 1.0
O B:HOH1286 4.0 23.8 1.0
O B:HOH1111 4.1 28.9 1.0
N B:ASP495 4.2 15.8 1.0
OD2 B:ASP427 4.2 21.4 1.0
CA B:GLY124 4.2 16.3 1.0
CB B:ASP427 4.2 20.6 1.0
CB B:SER494 4.2 18.2 1.0
O B:ARG123 4.2 16.6 1.0
CA B:ASP495 4.5 16.1 1.0
CB B:ASP495 4.6 15.8 1.0
CD1 B:TYR117 4.6 18.5 1.0
OE2 B:GLU198 4.6 37.2 1.0
N B:GLY125 4.6 16.3 1.0
OE2 B:GLU128 4.7 35.2 1.0
CG B:ASP427 4.7 21.7 1.0
CA B:GLY122 4.8 17.0 1.0
CE1 B:TYR117 4.9 18.3 1.0
OE1 B:GLU198 4.9 28.9 1.0
CB B:ARG123 4.9 17.0 1.0
CA B:GLY125 5.0 16.6 1.0
OG B:SER494 5.0 16.0 1.0

Reference:

P.C.Loewen, P.C.Loewen. N/A N/A.
Page generated: Tue Dec 15 11:11:05 2020

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