Calcium in PDB 7y9o: Crystal Structure of A CYP109B4 Variant From Bacillus Sonorensis

The structure of Crystal Structure of A CYP109B4 Variant From Bacillus Sonorensis, PDB code: 7y9o was solved by P.P.Shen, J.-W.Huang, X.Li, W.D.Liu, C.-C.Chen, R.-T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.06 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.87, 62.602, 140.526, 90, 90, 90
R / Rfree (%)	19.1 / 22.2

The structure of Crystal Structure of A CYP109B4 Variant From Bacillus Sonorensis also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Calcium atom in the Crystal Structure of A CYP109B4 Variant From Bacillus Sonorensis (pdb code 7y9o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of A CYP109B4 Variant From Bacillus Sonorensis, PDB code: 7y9o:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of A CYP109B4 Variant From Bacillus Sonorensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A CYP109B4 Variant From Bacillus Sonorensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:31.1 occ:1.00 O A:SER85 2.3 18.5 1.0 O A:HOH922 2.6 30.5 1.0 NE2 A:GLN69 3.3 32.5 1.0 CD A:GLN69 3.3 30.2 1.0 C A:SER85 3.4 19.2 1.0 CG A:GLN69 3.5 28.6 1.0 OE1 A:GLN69 3.8 36.5 1.0 CB A:GLN69 3.8 27.3 1.0 CB A:SER85 4.0 23.2 1.0 O A:ALA80 4.0 34.5 1.0 CA A:GLN69 4.2 24.0 1.0 CA A:MET86 4.3 15.7 1.0 N A:MET86 4.3 15.6 1.0 CA A:SER85 4.4 18.6 1.0 O A:HOH861 4.5 38.8 1.0 O A:HOH910 4.5 48.9 1.0 CG A:MET86 4.6 15.8 1.0 O A:HOH608 4.7 47.6 1.0 CB A:MET86 5.0 16.1 1.0 C A:GLN69 5.0 28.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of A CYP109B4 Variant From Bacillus Sonorensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A CYP109B4 Variant From Bacillus Sonorensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:22.5 occ:1.00 O A:GLU220 2.3 18.4 1.0 O A:GLY223 2.4 19.5 1.0 O A:HOH740 2.4 17.6 1.0 O A:HOH658 2.4 24.9 1.0 OD1 A:ASP224 3.0 27.2 1.0 C A:GLU220 3.5 18.8 1.0 C A:GLY223 3.5 21.6 1.0 CG A:ASP224 4.0 24.5 1.0 CA A:ASP224 4.1 21.3 1.0 N A:ASP224 4.2 20.5 1.0 CA A:GLU220 4.4 20.0 1.0 OE2 A:GLU220 4.4 36.6 1.0 O A:GLU221 4.4 21.6 1.0 O A:LEU226 4.4 16.7 1.0 N A:GLU221 4.5 18.8 1.0 CG A:GLU220 4.6 24.8 1.0 CA A:GLU221 4.6 19.4 1.0 C A:GLU221 4.6 20.6 1.0 CB A:ASP224 4.6 23.3 1.0 CA A:GLY223 4.6 23.3 1.0 N A:GLY223 4.7 21.3 1.0 CD A:GLU220 4.8 28.6 1.0 O A:HOH827 4.8 36.6 1.0 O A:HOH898 4.9 32.3 1.0 OD2 A:ASP224 5.0 23.8 1.0

X.Zhang, P.Shen, J.Zhao, Y.Chen, X.Li, J.W.Huang, L.Zhang, Q.Li, C.Gao, Q.Xing, C.C.Chen, R.T.Guo, A.Li. Rationally Controlling Selective Steroid Hydroxylation Via Scaffold Sampling of A P450 Family Acs Catalysis V. 13 1280 2023.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.2C04906