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Sodium in PDB 4qoq: Structure of Bacillus Pumilus Catalase with Guaiacol Bound

Enzymatic activity of Structure of Bacillus Pumilus Catalase with Guaiacol Bound

All present enzymatic activity of Structure of Bacillus Pumilus Catalase with Guaiacol Bound:
1.11.1.6;

Protein crystallography data

The structure of Structure of Bacillus Pumilus Catalase with Guaiacol Bound, PDB code: 4qoq 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) 103.35 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.790, 108.109, 103.409, 90.00, 91.98, 90.00
R / Rfree (%) 16.2 / 19

Other elements in 4qoq:

The structure of Structure of Bacillus Pumilus Catalase with Guaiacol Bound also contains other interesting chemical elements:

Iron (Fe) 8 atoms
Chlorine (Cl) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Bacillus Pumilus Catalase with Guaiacol Bound (pdb code 4qoq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Bacillus Pumilus Catalase with Guaiacol Bound, PDB code: 4qoq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4qoq

Go back to Sodium Binding Sites List in 4qoq
Sodium binding site 1 out of 2 in the Structure of Bacillus Pumilus Catalase with Guaiacol Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Bacillus Pumilus Catalase with Guaiacol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:6.1
occ:1.00
O A:HOH843 1.6 22.2 1.0
O A:HOH845 1.8 23.1 1.0
O A:HOH844 1.9 25.1 1.0
OE2 A:GLU85 1.9 28.8 1.0
OG A:SER72 2.1 21.9 1.0
O A:HOH842 2.2 28.0 1.0
CD A:GLU85 2.9 29.1 1.0
CB A:SER72 3.2 22.9 1.0
OE1 A:GLU85 3.2 28.8 1.0
O A:HOH846 3.7 42.0 1.0
N A:SER72 3.8 21.8 1.0
CA A:SER72 3.9 22.0 1.0
OE1 A:GLU74 4.1 28.4 1.0
OE2 A:GLU74 4.1 27.7 1.0
O A:SER72 4.2 20.8 1.0
CG A:GLU85 4.3 28.6 1.0
C A:SER72 4.4 22.6 1.0
CD A:GLU74 4.5 29.5 1.0
C A:ASN71 4.9 21.1 1.0

Sodium binding site 2 out of 2 in 4qoq

Go back to Sodium Binding Sites List in 4qoq
Sodium binding site 2 out of 2 in the Structure of Bacillus Pumilus Catalase with Guaiacol Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Bacillus Pumilus Catalase with Guaiacol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na506

b:19.3
occ:1.00
OE2 B:GLU85 1.9 42.4 1.0
O B:HOH981 2.0 31.1 1.0
O B:HOH1004 2.0 34.5 1.0
OG B:SER72 2.3 24.1 1.0
O B:HOH961 2.3 42.1 1.0
CD B:GLU85 2.8 46.6 1.0
OE1 B:GLU85 3.2 49.6 1.0
CB B:SER72 3.4 24.4 1.0
N B:SER72 3.9 23.2 1.0
CA B:SER72 4.1 22.1 1.0
CG B:GLU85 4.2 39.8 1.0
OE2 B:GLU74 4.2 31.3 1.0
OE1 B:GLU74 4.3 28.0 1.0
O B:SER72 4.4 24.1 1.0
C B:SER72 4.7 21.9 1.0
CD B:GLU74 4.7 26.8 1.0

Reference:

P.C.Loewen, J.Villanueva, J.Switala, L.J.Donald, A.Ivancich. Unprecedented Access of Phenolic Substrates to the Heme Active Site of A Catalase: Substrate Binding and Peroxidase-Like Reactivity of Bacillus Pumilus Catalase Monitored By X-Ray Crystallography and Epr Spectroscopy. Proteins 2015.
ISSN: ESSN 1097-0134
PubMed: 25663126
DOI: 10.1002/PROT.24777
Page generated: Tue Dec 15 07:06:16 2020

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