Sodium in PDB 7smz: X-Ray Crystal Structure of CYP142A3 From Mycobacterium Marinum in Complex with 4-Cholesten-3-One

The structure of X-Ray Crystal Structure of CYP142A3 From Mycobacterium Marinum in Complex with 4-Cholesten-3-One, PDB code: 7smz was solved by A.Ghith, J.B.Bruning, S.G.Bell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.69 / 2.04
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.313, 50.395, 82.577, 82.32, 75.59, 72.05
R / Rfree (%)	18 / 22.5

The structure of X-Ray Crystal Structure of CYP142A3 From Mycobacterium Marinum in Complex with 4-Cholesten-3-One also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Sodium atom in the X-Ray Crystal Structure of CYP142A3 From Mycobacterium Marinum in Complex with 4-Cholesten-3-One (pdb code 7smz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the X-Ray Crystal Structure of CYP142A3 From Mycobacterium Marinum in Complex with 4-Cholesten-3-One, PDB code: 7smz:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the X-Ray Crystal Structure of CYP142A3 From Mycobacterium Marinum in Complex with 4-Cholesten-3-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of CYP142A3 From Mycobacterium Marinum in Complex with 4-Cholesten-3-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:29.1 occ:1.00 O A:HOH614 2.6 23.3 1.0 OD1 A:ASN64 2.6 19.9 1.0 O A:PHE62 2.9 19.9 1.0 O A:HOH784 3.2 26.4 1.0 O A:HOH701 3.4 21.0 1.0 N A:ASN64 3.5 21.7 1.0 CB A:PRO59 3.6 18.5 1.0 CG A:ASN64 3.6 24.4 1.0 CA A:PRO59 3.7 20.6 1.0 NE A:ARG285 3.7 20.7 1.0 C A:SER63 3.8 21.0 1.0 OD1 A:ASP82 3.9 24.3 1.0 CA A:SER63 3.9 22.7 1.0 CD A:ARG285 3.9 16.4 1.0 C A:PHE62 3.9 17.3 1.0 CD2 A:HIS341 4.0 20.8 1.0 NE2 A:HIS341 4.0 20.9 1.0 CB A:ASN64 4.1 21.8 1.0 O A:PRO59 4.2 25.0 1.0 CA A:ASN64 4.4 26.2 1.0 N A:SER63 4.4 18.6 1.0 C A:PRO59 4.5 25.2 1.0 CZ A:ARG285 4.5 23.3 1.0 O A:SER63 4.6 23.4 1.0 ND2 A:ASN64 4.7 20.1 1.0 O A:HOH735 4.8 19.4 1.0 N A:PRO59 4.9 24.5 1.0 NH2 A:ARG285 4.9 24.2 1.0 CG A:ASP82 4.9 27.0 1.0 CG A:PRO59 5.0 20.7 1.0

Sodium binding site 2 out of 4 in the X-Ray Crystal Structure of CYP142A3 From Mycobacterium Marinum in Complex with 4-Cholesten-3-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Crystal Structure of CYP142A3 From Mycobacterium Marinum in Complex with 4-Cholesten-3-One within 5.0Å range: probe atom residue distance (Å) B Occ B:Na507 b:33.7 occ:1.00 N B:GLY268 2.8 21.6 1.0 O A:GLN327 2.9 25.0 1.0 CD B:PRO267 3.2 29.6 1.0 O B:GLU264 3.3 47.0 1.0 O B:LEU265 3.4 23.8 1.0 C B:LEU265 3.4 31.8 1.0 N B:PRO267 3.5 24.4 1.0 CB B:PRO267 3.5 31.5 1.0 O B:HOH651 3.6 32.3 1.0 CA B:LEU265 3.6 31.7 1.0 O A:HOH762 3.7 29.5 1.0 CA B:GLY268 3.7 22.8 1.0 C B:PRO267 3.7 23.4 1.0 CG B:PRO267 3.7 29.6 1.0 CA B:PRO267 3.8 26.2 1.0 C A:GLN327 4.0 27.1 1.0 N B:LEU266 4.1 23.8 1.0 CB A:ASN329 4.1 22.4 1.0 C B:GLU264 4.2 39.6 1.0 C B:LEU266 4.2 23.3 1.0 CB A:GLN327 4.3 29.8 1.0 N B:LEU265 4.4 28.8 1.0 CA A:GLN327 4.6 29.1 1.0 O A:HOH781 4.7 23.7 1.0 N A:ASN329 4.7 20.0 1.0 CB B:LEU265 4.7 31.8 1.0 CA B:LEU266 4.8 22.4 1.0 O B:PRO267 4.9 22.9 1.0 C B:GLY268 4.9 20.1 1.0 O A:ASN329 4.9 26.9 1.0 CD2 B:LEU265 4.9 33.0 1.0 CA A:ASN329 5.0 21.8 1.0 O B:LEU266 5.0 21.0 1.0 N B:ALA269 5.0 18.2 1.0

Sodium binding site 3 out of 4 in the X-Ray Crystal Structure of CYP142A3 From Mycobacterium Marinum in Complex with 4-Cholesten-3-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Crystal Structure of CYP142A3 From Mycobacterium Marinum in Complex with 4-Cholesten-3-One within 5.0Å range: probe atom residue distance (Å) B Occ B:Na508 b:47.0 occ:1.00 N B:GLY215 2.8 40.0 1.0 N B:ASP214 3.4 40.6 1.0 CA B:GLY215 3.5 45.2 1.0 O B:GLU212 3.5 35.0 1.0 CB B:GLU212 3.6 43.7 1.0 C B:GLU212 3.7 40.6 1.0 C B:ASP214 3.8 44.7 1.0 CA B:ASP214 3.9 49.2 1.0 C B:VAL213 4.0 41.8 1.0 N B:VAL213 4.1 39.4 1.0 CA B:VAL213 4.2 41.0 1.0 CA B:GLU212 4.4 43.8 1.0 C B:GLY215 4.4 45.6 1.0 O B:HOH678 4.6 46.3 1.0 OE1 B:GLU212 4.7 54.4 1.0 O B:VAL213 4.8 38.6 1.0 CG B:GLU212 4.8 47.6 1.0 CD B:GLU212 4.9 50.1 1.0 N B:GLU216 4.9 41.5 1.0 O B:ASP214 4.9 46.8 1.0

Sodium binding site 4 out of 4 in the X-Ray Crystal Structure of CYP142A3 From Mycobacterium Marinum in Complex with 4-Cholesten-3-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Crystal Structure of CYP142A3 From Mycobacterium Marinum in Complex with 4-Cholesten-3-One within 5.0Å range: probe atom residue distance (Å) B Occ B:Na509 b:44.6 occ:1.00 NH2 B:ARG239 2.6 34.2 1.0 NE B:ARG379 2.7 30.6 0.5 O B:LEU387 2.9 21.0 1.0 CZ B:ARG379 3.0 31.5 0.5 NH2 B:ARG379 3.1 34.8 0.5 CG1 B:VAL129 3.4 26.5 1.0 CZ B:ARG239 3.5 35.4 1.0 CD B:ARG379 3.5 27.4 0.5 O B:HOH655 3.7 21.6 1.0 NE B:ARG239 3.7 27.1 1.0 CE1 B:HIS240 3.7 23.4 1.0 O B:GLU388 3.8 27.7 1.0 NH1 B:ARG379 3.8 33.8 0.5 O B:HOH769 3.9 31.5 1.0 C B:LEU387 4.1 28.7 1.0 CA B:GLU388 4.1 29.1 1.0 C B:GLU388 4.3 27.8 1.0 ND1 B:HIS240 4.3 22.6 1.0 O B:HOH613 4.5 40.3 1.0 N B:GLU388 4.6 30.0 1.0 NH1 B:ARG239 4.6 27.8 1.0 CB B:VAL129 4.7 27.3 1.0 NE2 B:HIS240 4.8 20.9 1.0 CG2 B:VAL129 4.8 27.8 1.0 CG B:ARG379 4.8 29.3 0.5

A.Ghith, D.Z.Doherty, J.B.Bruning, R.A.Russell, J.J.De Voss, S.G.Bell. The Structures of the Steroid Binding CYP142 Cytochrome P450 Enzymes From Mycobacterium Ulcerans and Mycobacterium Marinum. Acs Infect Dis. V. 8 1606 2022.
ISSN: ESSN 2373-8227
PubMed: 35881654
DOI: 10.1021/ACSINFECDIS.2C00215