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Chlorine in PDB 5ksf: Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate

Enzymatic activity of Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate

All present enzymatic activity of Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate:
1.11.1.21;

Protein crystallography data

The structure of Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate, PDB code: 5ksf 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) 48.38 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.692, 115.474, 174.586, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 17.5

Other elements in 5ksf:

The structure of Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate (pdb code 5ksf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate, PDB code: 5ksf:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5ksf

Go back to Chlorine Binding Sites List in 5ksf
Chlorine binding site 1 out of 2 in the Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl803

b:38.3
occ:1.00
O A:HOH1565 2.9 23.1 1.0
O A:HOH1443 3.0 27.1 1.0
O A:HOH1492 3.1 25.4 1.0
N A:GLY124 3.3 18.9 1.0
O A:HOH1488 3.4 43.2 1.0
CG2 A:VAL200 3.5 29.8 1.0
CB A:GLU198 3.7 41.3 1.0
CG A:GLU198 3.8 48.6 1.0
CA A:GLY124 3.9 19.8 1.0
CB A:ARG123 4.2 22.0 1.0
C A:ARG123 4.3 19.4 1.0
CA A:ARG123 4.4 20.2 1.0
OE1 A:GLU128 4.5 31.8 1.0
C A:GLY124 4.6 22.0 1.0
NA A:NA802 4.6 22.9 1.0
O A:GLY124 4.6 19.6 1.0
CD A:GLU198 4.6 56.3 1.0
O A:HOH1180 4.7 25.3 1.0
CG A:ARG123 4.8 21.5 1.0
CG A:GLN130 4.8 21.3 1.0
CB A:VAL200 4.9 29.5 1.0
O A:HOH1006 4.9 21.7 1.0

Chlorine binding site 2 out of 2 in 5ksf

Go back to Chlorine Binding Sites List in 5ksf
Chlorine binding site 2 out of 2 in the Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl803

b:37.8
occ:1.00
O B:HOH1457 2.9 24.8 1.0
O B:HOH1567 3.1 18.0 1.0
O B:HOH1493 3.2 24.5 1.0
N B:GLY124 3.2 20.5 1.0
O B:HOH1479 3.5 34.5 1.0
CG2 B:VAL200 3.5 24.6 1.0
CB B:GLU198 3.7 35.8 1.0
CG B:GLU198 3.8 39.6 1.0
CA B:GLY124 3.9 19.7 1.0
CB B:ARG123 4.2 17.7 1.0
C B:ARG123 4.3 19.5 1.0
CA B:ARG123 4.3 17.8 1.0
OE1 B:GLU128 4.3 33.9 1.0
CD B:GLU198 4.5 49.9 1.0
NA B:NA802 4.6 21.6 1.0
O B:GLY124 4.7 19.8 1.0
CG B:ARG123 4.7 19.4 1.0
C B:GLY124 4.7 19.7 1.0
CD B:GLU128 4.8 34.4 1.0
OE2 B:GLU128 4.9 37.3 1.0
CG B:GLN130 4.9 20.6 1.0
O B:HOH1162 4.9 21.6 1.0
CB B:VAL200 4.9 24.3 1.0
OE1 B:GLU198 4.9 48.3 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: Sat Dec 12 11:57:26 2020

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