Sodium in PDB 3r9b: Crystal Structure of Mycobacterium Smegmatis CYP164A2 in Ligand Free State

The structure of Crystal Structure of Mycobacterium Smegmatis CYP164A2 in Ligand Free State, PDB code: 3r9b was solved by C.R.J.Agnew, A.G.S.Warrilow, S.L.Kelly, R.L.Brady, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	92.45 / 1.89
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	178.396, 102.776, 92.412, 90.00, 90.06, 90.00
R / Rfree (%)	18.3 / 20.2

The structure of Crystal Structure of Mycobacterium Smegmatis CYP164A2 in Ligand Free State also contains other interesting chemical elements:

Potassium	(K)	3 atoms
Iron	(Fe)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of Mycobacterium Smegmatis CYP164A2 in Ligand Free State (pdb code 3r9b). 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 Mycobacterium Smegmatis CYP164A2 in Ligand Free State, PDB code: 3r9b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Mycobacterium Smegmatis CYP164A2 in Ligand Free State


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 Mycobacterium Smegmatis CYP164A2 in Ligand Free State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:40.9 occ:1.00 O2 A:PO4503 2.5 28.2 0.5 O A:HOH835 2.8 9.6 1.0 OG A:SER113 3.3 16.2 1.0 CA A:GLY110 3.4 7.6 1.0 P A:PO4503 3.6 29.9 0.5 N A:GLY110 3.7 7.5 1.0 O A:HOH744 3.7 24.0 1.0 CB A:SER113 3.7 12.3 1.0 O4 A:PO4503 3.8 29.1 0.5 O B:HOH667 4.0 12.0 1.0 C A:ARG109 4.0 8.2 1.0 O A:ARG109 4.0 8.1 1.0 CG A:ARG109 4.1 6.8 1.0 C2 A:EDO508 4.1 35.4 1.0 CD A:ARG109 4.1 8.5 1.0 O3 A:PO4503 4.1 30.9 0.5 O A:HOH771 4.2 26.6 1.0 NE A:ARG109 4.2 12.8 1.0 O2 A:EDO508 4.3 35.3 1.0 CB A:ARG109 4.6 7.8 1.0 C A:GLY110 4.6 7.9 1.0 O A:GLY110 4.8 8.0 1.0 O A:THR106 4.9 6.2 1.0 O1 A:PO4503 4.9 29.6 0.5 CA A:ARG109 5.0 7.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Mycobacterium Smegmatis CYP164A2 in Ligand Free State


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 Mycobacterium Smegmatis CYP164A2 in Ligand Free State within 5.0Å range: probe atom residue distance (Å) B Occ C:Na511 b:40.6 occ:1.00 O3 C:PO4503 2.4 26.6 0.5 O C:HOH825 2.9 28.1 1.0 P C:PO4503 3.5 29.3 0.5 O C:HOH772 3.6 24.0 1.0 O1 C:PO4503 3.8 28.4 0.5 O2 C:PO4503 4.0 29.9 0.5 O C:HOH655 4.0 12.1 1.0 C2 C:EDO507 4.1 36.7 1.0 O2 C:EDO507 4.4 35.1 1.0 O4 C:PO4503 4.8 27.8 0.5

C.R.Agnew, A.G.Warrilow, N.M.Burton, D.C.Lamb, S.L.Kelly, R.L.Brady. An Enlarged, Adaptable Active Site in CYP164 Family P450 Enzymes, the Sole P450 in Mycobacterium Leprae. Antimicrob.Agents Chemother. V. 56 391 2012.
ISSN: ISSN 0066-4804
PubMed: 22037849
DOI: 10.1128/AAC.05227-11