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Chlorine in PDB 5v53: Crystal Structure of the D141A/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound

Enzymatic activity of Crystal Structure of the D141A/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound

All present enzymatic activity of Crystal Structure of the D141A/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound:
1.11.1.21;

Protein crystallography data

The structure of Crystal Structure of the D141A/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound, PDB code: 5v53 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) 46.23 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.842, 115.825, 174.775, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 17.2

Other elements in 5v53:

The structure of Crystal Structure of the D141A/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound 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/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound (pdb code 5v53). 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/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound, PDB code: 5v53:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5v53

Go back to Chlorine Binding Sites List in 5v53
Chlorine binding site 1 out of 2 in the Crystal Structure of the D141A/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound


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/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl803

b:44.4
occ:1.00
 O A:HOH1589 2.9 21.0 1.0
O A:HOH1457 3.1 25.2 1.0
O A:HOH1499 3.1 23.0 1.0
CB A:GLU198 3.3 36.4 1.0
CG A:GLU198 3.4 52.4 1.0
N A:GLY124 3.4 18.4 1.0
CG2 A:VAL200 3.5 26.6 1.0
CA A:GLY124 4.0 18.5 1.0
O A:HOH1443 4.2 34.4 1.0
OE1 A:GLU128 4.4 30.7 1.0
CB A:ARG123 4.5 21.7 1.0
O A:HOH908 4.5 47.4 1.0
C A:ARG123 4.5 17.5 1.0
CA A:ARG123 4.5 18.6 1.0
O A:HOH1224 4.6 22.4 1.0
OE2 A:GLU128 4.7 36.2 1.0
CD A:GLU198 4.7 56.3 1.0
CG A:GLN130 4.7 18.8 1.0
NA A:NA802 4.7 20.1 1.0
C A:GLY124 4.7 19.7 1.0
O A:GLY124 4.8 17.5 1.0
CA A:GLU198 4.8 27.8 1.0
CD A:GLU128 4.8 33.5 1.0
CB A:VAL200 4.9 24.2 1.0
O A:HOH1083 4.9 18.5 1.0
CG A:ARG123 5.0 19.6 1.0

Chlorine binding site 2 out of 2 in 5v53

Go back to Chlorine Binding Sites List in 5v53
Chlorine binding site 2 out of 2 in the Crystal Structure of the D141A/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound


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/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl803

b:28.3
occ:0.50
 OE1 B:GLU198 1.1 25.7 0.5
CD B:GLU198 1.4 23.8 0.5
OE2 B:GLU198 1.7 22.8 0.5
CG B:GLU198 2.7 23.0 0.5
O B:HOH1315 2.9 18.3 1.0
O B:HOH1346 3.0 22.0 1.0
O B:HOH1003 3.1 24.8 1.0
N B:GLY124 3.1 19.0 1.0
CB B:GLU198 3.4 23.0 0.5
CG2 B:VAL200 3.5 21.1 1.0
CB B:GLU198 3.7 30.9 0.5
CA B:GLY124 3.7 18.4 1.0
CG B:GLU198 4.0 32.3 0.5
C B:ARG123 4.2 17.3 1.0
CB B:ARG123 4.3 18.0 1.0
CA B:ARG123 4.3 17.1 1.0
OE1 B:GLU128 4.3 32.7 1.0
O B:HOH1163 4.4 40.6 1.0
C B:GLY124 4.5 19.9 1.0
O B:HOH1004 4.6 41.4 1.0
O B:GLY124 4.6 17.6 1.0
NA B:NA802 4.6 20.2 1.0
OE2 B:GLU128 4.7 35.3 1.0
CG B:GLN130 4.7 19.2 1.0
O B:HOH1214 4.8 20.6 1.0
CD B:GLU128 4.8 33.6 1.0
O B:HOH1173 4.8 17.4 1.0
CG B:ARG123 4.9 18.1 1.0
CD B:GLU198 4.9 37.1 0.5
CB B:VAL200 4.9 21.2 1.0
CA B:GLU198 4.9 22.0 0.5

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: Fri Jul 26 18:37:20 2024

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