Magnesium in PDB 3nc5: CYP134A1 Structure with An Open Substrate Binding Loop

The structure of CYP134A1 Structure with An Open Substrate Binding Loop, PDB code: 3nc5 was solved by M.J.Cryle, I.Schlichting, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.62 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.800, 105.400, 143.900, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 30.6

The structure of CYP134A1 Structure with An Open Substrate Binding Loop also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Magnesium atom in the CYP134A1 Structure with An Open Substrate Binding Loop (pdb code 3nc5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the CYP134A1 Structure with An Open Substrate Binding Loop, PDB code: 3nc5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the CYP134A1 Structure with An Open Substrate Binding Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of CYP134A1 Structure with An Open Substrate Binding Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:54.8 occ:1.00 OG1 A:THR166 2.5 44.6 1.0 OD1 A:ASP163 2.7 50.8 1.0 OG A:SER167 3.1 49.7 1.0 CB A:THR166 3.6 43.2 1.0 CG A:ASP163 3.8 49.5 1.0 CA A:ASP163 3.8 44.4 1.0 O A:ASP163 4.0 46.2 1.0 N A:SER167 4.0 47.1 1.0 CB A:ASP163 4.2 45.6 1.0 CB A:SER167 4.2 49.6 1.0 CA A:SER167 4.3 48.7 1.0 C A:THR166 4.3 46.3 1.0 C A:ASP163 4.4 45.6 1.0 CA A:THR166 4.5 44.7 1.0 O A:ALA162 4.6 42.1 1.0 CG2 A:THR166 4.7 42.2 1.0 O A:HOH414 4.8 55.7 1.0 N A:ASP163 4.8 42.8 1.0 OD2 A:ASP163 4.8 53.4 1.0 N A:THR166 5.0 44.7 1.0

Magnesium binding site 2 out of 3 in the CYP134A1 Structure with An Open Substrate Binding Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of CYP134A1 Structure with An Open Substrate Binding Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg409 b:43.1 occ:1.00 O A:GLN281 2.6 40.0 1.0 N A:GLY309 2.9 34.9 1.0 N A:ILE308 3.3 38.6 1.0 NE2 A:GLN281 3.3 38.6 1.0 C A:MET307 3.4 40.9 1.0 CA A:MET307 3.5 43.3 1.0 CA A:GLY309 3.5 34.6 1.0 C A:GLN281 3.6 38.6 1.0 CB A:MET307 3.6 45.0 1.0 CZ A:PHE23 3.8 47.0 1.0 C A:ILE308 3.9 35.4 1.0 CB A:GLN281 4.0 36.8 1.0 N A:ALA310 4.0 39.4 1.0 CA A:GLN281 4.0 36.6 1.0 CD A:GLN281 4.1 36.4 1.0 O A:MET307 4.1 41.6 1.0 CA A:ILE308 4.1 36.5 1.0 CE A:MET307 4.2 47.6 1.0 CE1 A:PHE23 4.2 48.4 1.0 C A:GLY309 4.3 36.9 1.0 CD2 A:LEU282 4.4 43.3 1.0 CG A:MET307 4.6 48.9 1.0 CG A:GLN281 4.6 36.2 1.0 CE2 A:PHE23 4.7 46.8 1.0 OE1 A:GLN281 4.7 36.5 1.0 CB A:ILE308 4.8 34.6 1.0 N A:MET307 4.8 45.1 1.0 N A:LEU282 4.8 38.8 1.0 CG A:LEU282 5.0 42.4 1.0

Magnesium binding site 3 out of 3 in the CYP134A1 Structure with An Open Substrate Binding Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of CYP134A1 Structure with An Open Substrate Binding Loop within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg408 b:41.0 occ:1.00 O B:VAL354 3.0 37.7 1.0 N B:ALA357 3.1 35.3 1.0 CA B:GLY355 3.1 35.9 1.0 C B:GLY355 3.2 34.9 1.0 CB B:ALA357 3.2 36.3 1.0 N B:PHE358 3.3 35.0 1.0 N B:THR356 3.5 35.3 1.0 CA B:ALA357 3.6 35.6 1.0 O B:GLY355 3.6 34.1 1.0 CG2 B:ILE97 3.7 50.1 1.0 C B:VAL354 3.8 37.7 1.0 N B:GLY355 3.8 36.7 1.0 C B:ALA357 3.9 35.4 1.0 C B:THR356 4.1 34.8 1.0 CB B:PHE358 4.2 35.4 1.0 CA B:PHE358 4.3 34.7 1.0 CA B:THR356 4.4 35.0 1.0 CB B:ILE97 4.4 53.0 1.0 O B:ARG94 4.8 60.0 1.0 CD2 B:LEU101 4.9 58.4 1.0

M.J.Cryle, S.G.Bell, I.Schlichting. Structural and Biochemical Characterization of the Cytochrome P450 Cypx (CYP134A1) From Bacillus Subtilis: A Cyclo-L-Leucyl-L-Leucyl Dipeptide Oxidase. Biochemistry V. 49 7282 2010.
ISSN: ISSN 0006-2960
PubMed: 20690619
DOI: 10.1021/BI100910Y