Sodium in PDB 4qom: Bacillus Pumilus Catalase with Pyrogallol Bound

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

The structure of Bacillus Pumilus Catalase with Pyrogallol Bound, PDB code: 4qom 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)	103.29 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	91.853, 109.424, 103.368, 90.00, 92.21, 90.00
R / Rfree (%)	17.8 / 21

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

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

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

Sodium binding site 1 out of 2 in the Bacillus Pumilus Catalase with Pyrogallol Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bacillus Pumilus Catalase with Pyrogallol Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:14.7 occ:1.00 O A:HOH843 1.8 26.6 1.0 O A:HOH842 1.9 23.8 1.0 O A:HOH841 2.1 26.8 1.0 OE2 A:GLU85 2.2 32.7 1.0 OG A:SER72 2.3 32.1 1.0 O A:HOH840 2.3 41.9 1.0 CD A:GLU85 3.2 34.0 1.0 OE1 A:GLU85 3.4 36.8 1.0 O A:HOH844 3.4 46.4 1.0 CB A:SER72 3.5 31.4 1.0 N A:SER72 3.8 32.5 1.0 OE1 A:GLU74 4.0 40.2 1.0 O A:SER72 4.0 29.8 1.0 OE2 A:GLU74 4.0 36.9 1.0 CA A:SER72 4.0 32.6 1.0 C A:SER72 4.4 30.3 1.0 CD A:GLU74 4.5 38.4 1.0 CG A:GLU85 4.6 33.0 1.0 C A:ASN71 4.8 31.7 1.0

Sodium binding site 2 out of 2 in the Bacillus Pumilus Catalase with Pyrogallol Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bacillus Pumilus Catalase with Pyrogallol Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Na506 b:23.2 occ:1.00 O B:HOH961 1.9 37.4 1.0 OE2 B:GLU85 2.0 46.0 1.0 OG B:SER72 2.5 28.4 1.0 CD B:GLU85 2.7 40.5 1.0 OE1 B:GLU85 2.8 42.4 1.0 CB B:SER72 3.6 26.1 1.0 N B:SER72 4.0 23.9 1.0 CG B:GLU85 4.2 38.5 1.0 O B:HOH998 4.2 34.3 1.0 CA B:SER72 4.3 23.9 1.0 OE2 B:GLU74 4.4 29.4 1.0 OE1 B:GLU74 4.4 30.7 1.0 O B:SER72 4.6 28.7 1.0 CD B:GLU74 4.9 27.5 1.0 C B:SER72 4.9 25.4 1.0

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