Sodium in PDB 8joo: Crystal Structure of Cytochrome P450 Ikad From Streptomyces Sp. ZJ306, in Complex with the Substrate Ikarugamycin

The structure of Crystal Structure of Cytochrome P450 Ikad From Streptomyces Sp. ZJ306, in Complex with the Substrate Ikarugamycin, PDB code: 8joo was solved by Y.L.Zhang, L.P.Zhang, C.S.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.89 / 2.25
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.174, 82.121, 143.92, 90, 94.41, 90
R / Rfree (%)	21.7 / 26.4

The structure of Crystal Structure of Cytochrome P450 Ikad From Streptomyces Sp. ZJ306, in Complex with the Substrate Ikarugamycin also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Cytochrome P450 Ikad From Streptomyces Sp. ZJ306, in Complex with the Substrate Ikarugamycin (pdb code 8joo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Cytochrome P450 Ikad From Streptomyces Sp. ZJ306, in Complex with the Substrate Ikarugamycin, PDB code: 8joo:

Sodium binding site 1 out of 1 in the Crystal Structure of Cytochrome P450 Ikad From Streptomyces Sp. ZJ306, in Complex with the Substrate Ikarugamycin


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 Ikad From Streptomyces Sp. ZJ306, in Complex with the Substrate Ikarugamycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na506 b:27.4 occ:1.00 HE22 B:GLN253 1.4 10.7 1.0 NE2 B:GLN253 2.1 8.9 1.0 HE21 B:GLN253 2.2 10.7 1.0 H B:FMT503 2.4 42.7 1.0 HE3 B:MET286 2.8 8.9 1.0 O2 B:FMT503 2.9 21.3 1.0 C B:FMT503 2.9 35.6 1.0 HA B:MET286 3.1 15.1 1.0 HB B:ILE291 3.2 25.1 1.0 HB B:VAL289 3.2 11.3 1.0 CD B:GLN253 3.2 9.1 1.0 O B:MET286 3.3 8.7 1.0 HG21 B:ILE291 3.4 23.4 1.0 O B:VAL289 3.5 8.8 1.0 CE B:MET286 3.6 7.4 1.0 HE1 B:MET286 3.7 8.9 1.0 HO2 B:FMT503 3.8 25.6 1.0 OE1 B:GLN253 3.8 9.8 1.0 CA B:MET286 3.9 12.6 1.0 C B:MET286 4.0 11.1 1.0 HE1 B:PHE257 4.0 10.9 1.0 HD13 B:ILE291 4.0 21.5 1.0 CB B:ILE291 4.0 21.0 1.0 CG2 B:ILE291 4.0 19.5 1.0 SD B:MET286 4.0 9.3 1.0 H B:ILE291 4.0 12.0 1.0 O1 B:FMT503 4.1 19.9 1.0 HG22 B:ILE291 4.1 23.4 1.0 CB B:VAL289 4.2 9.4 1.0 HG12 B:VAL289 4.2 11.8 1.0 O B:LEU285 4.2 11.0 1.0 HG3 B:GLN253 4.3 12.3 1.0 HMBB B:HEM501 4.3 11.2 1.0 HE2 B:MET286 4.4 8.9 1.0 CG B:GLN253 4.4 10.2 1.0 HZ B:PHE257 4.4 11.4 1.0 C B:VAL289 4.4 12.0 1.0 HMBA B:HEM501 4.5 11.2 1.0 HB3 B:MET286 4.5 10.7 1.0 H B:VAL289 4.6 10.9 1.0 HMB B:HEM501 4.6 11.2 1.0 CG1 B:VAL289 4.6 9.9 1.0 O B:HOH640 4.6 10.7 1.0 N B:ILE291 4.7 10.0 1.0 CB B:MET286 4.7 8.9 1.0 CMB B:HEM501 4.7 9.3 1.0 CA B:VAL289 4.7 9.4 1.0 HA3 B:GLY349 4.7 8.6 1.0 CE1 B:PHE257 4.8 9.1 1.0 CD1 B:ILE291 4.8 17.9 1.0 HG11 B:VAL289 4.8 11.8 1.0 HG2 B:GLN253 4.8 12.3 1.0 HD12 B:ILE291 4.9 21.5 1.0 HG23 B:ILE291 4.9 23.4 1.0 N B:MET286 4.9 8.3 1.0 N B:VAL289 4.9 9.1 1.0 CA B:ILE291 4.9 15.3 1.0 CZ B:PHE257 5.0 9.5 1.0 CG B:MET286 5.0 9.5 1.0 C B:LEU285 5.0 8.3 1.0

P.Jiang, H.Jin, G.Zhang, W.Zhang, W.Liu, Y.Zhu, C.Zhang, L.Zhang. A Mechanistic Understanding of the Distinct Regio- and Chemoselectivity of Multifunctional P450S By Structural Comparison of Ikad and Cfta Complexed with Common Substrates. Angew.Chem.Int.Ed.Engl. 10728 2023.
ISSN: ESSN 1521-3773
PubMed: 37917570
DOI: 10.1002/ANIE.202310728