Sodium in PDB 6vza: Crystal Structure of Cytochrome P450 NASF5053 Q65I-A86G Mutant Variant From Streptomyces Sp. Nrrl F-5053 in the Cyclo-L-Trp-L-Pro-Bound State

The structure of Crystal Structure of Cytochrome P450 NASF5053 Q65I-A86G Mutant Variant From Streptomyces Sp. Nrrl F-5053 in the Cyclo-L-Trp-L-Pro-Bound State, PDB code: 6vza was solved by Z.Luo, X.Jia, C.Sun, X.Qu, B.Kobe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.23 / 1.47
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.228, 91.310, 93.808, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 18

The structure of Crystal Structure of Cytochrome P450 NASF5053 Q65I-A86G Mutant Variant From Streptomyces Sp. Nrrl F-5053 in the Cyclo-L-Trp-L-Pro-Bound State also contains other interesting chemical elements:

Iron	(Fe)	1 atom
Calcium	(Ca)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Cytochrome P450 NASF5053 Q65I-A86G Mutant Variant From Streptomyces Sp. Nrrl F-5053 in the Cyclo-L-Trp-L-Pro-Bound State (pdb code 6vza). 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 Cytochrome P450 NASF5053 Q65I-A86G Mutant Variant From Streptomyces Sp. Nrrl F-5053 in the Cyclo-L-Trp-L-Pro-Bound State, PDB code: 6vza:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Cytochrome P450 NASF5053 Q65I-A86G Mutant Variant From Streptomyces Sp. Nrrl F-5053 in the Cyclo-L-Trp-L-Pro-Bound 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 Cytochrome P450 NASF5053 Q65I-A86G Mutant Variant From Streptomyces Sp. Nrrl F-5053 in the Cyclo-L-Trp-L-Pro-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:35.3 occ:1.00 HD2 A:ARG345 3.3 42.9 1.0 HB2 A:ARG345 3.6 28.4 1.0 HB3 A:ARG345 3.8 28.4 1.0 CB A:ARG345 4.1 23.7 1.0 CD A:ARG345 4.2 35.8 1.0 HD3 A:ARG345 4.5 42.9 1.0 HH21 A:ARG96 4.5 57.9 1.0 O A:HOH521 4.7 34.5 1.0 CG A:ARG345 4.7 31.4 1.0 HG3 A:ARG345 4.9 37.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Cytochrome P450 NASF5053 Q65I-A86G Mutant Variant From Streptomyces Sp. Nrrl F-5053 in the Cyclo-L-Trp-L-Pro-Bound 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 Cytochrome P450 NASF5053 Q65I-A86G Mutant Variant From Streptomyces Sp. Nrrl F-5053 in the Cyclo-L-Trp-L-Pro-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:30.4 occ:1.00 O A:ALA48 2.7 16.8 1.0 O A:HOH886 2.7 38.7 1.0 HG3 A:LYS52 2.8 37.6 1.0 O A:HOH892 2.9 29.8 1.0 O A:HOH897 2.9 30.6 1.0 HB A:VAL51 3.0 17.7 1.0 HA A:ALA48 3.0 18.6 1.0 HE3 A:LYS52 3.0 67.0 1.0 HB1 A:ALA48 3.2 21.5 1.0 C A:ALA48 3.5 14.8 1.0 CA A:ALA48 3.6 15.5 1.0 CG A:LYS52 3.7 31.3 1.0 HG12 A:VAL51 3.8 18.9 1.0 CE A:LYS52 3.8 55.8 1.0 CB A:ALA48 3.8 17.9 1.0 CB A:VAL51 3.8 14.7 1.0 HE2 A:LYS52 3.9 67.0 1.0 H A:LYS52 3.9 17.2 1.0 HG11 A:VAL51 4.0 18.9 1.0 HG2 A:LYS52 4.1 37.6 1.0 CG1 A:VAL51 4.1 15.7 1.0 CD A:LYS52 4.2 54.0 1.0 HB2 A:ALA48 4.2 21.5 1.0 HD2 A:LYS52 4.2 64.8 1.0 O A:HOH894 4.3 42.6 1.0 HG21 A:VAL51 4.3 17.1 1.0 N A:LYS52 4.4 14.3 1.0 O A:HOH863 4.4 46.3 1.0 HB3 A:ALA48 4.6 21.5 1.0 CG2 A:VAL51 4.6 14.2 1.0 O A:HOH773 4.6 36.7 1.0 H A:VAL51 4.7 15.7 1.0 N A:THR49 4.7 13.7 1.0 CB A:LYS52 4.8 21.6 1.0 HG23 A:VAL51 4.8 17.1 1.0 HB2 A:LYS52 4.8 25.9 1.0 CA A:VAL51 4.9 13.8 1.0 C A:VAL51 4.9 15.4 1.0 N A:ALA48 4.9 13.8 1.0

C.Sun, Z.Luo, W.Zhang, Z.Deng, M.Mobli, B.Kobe, X.Jia, X.Qu. Molecular Basis of Regio- and Stereo-Specificity in Biosynthesis of Bacterial Heterodimeric Diketopiperazines To Be Published.