Sodium in PDB 6zhz: Olep-Oleandolide(Deo) in High Salt Crystallization Conditions

The structure of Olep-Oleandolide(Deo) in High Salt Crystallization Conditions, PDB code: 6zhz was solved by L.C.Montemiglio, C.Savino, B.Vallone, G.Parisi, C.Cecchetti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.73 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	247.469, 111.215, 159.203, 90.00, 129.39, 90.00
R / Rfree (%)	18.7 / 24.3

The structure of Olep-Oleandolide(Deo) in High Salt Crystallization Conditions also contains other interesting chemical elements:

Iron

(Fe)

6 atoms

The binding sites of Sodium atom in the Olep-Oleandolide(Deo) in High Salt Crystallization Conditions (pdb code 6zhz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Olep-Oleandolide(Deo) in High Salt Crystallization Conditions, PDB code: 6zhz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Olep-Oleandolide(Deo) in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Olep-Oleandolide(Deo) in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na519 b:55.4 occ:1.00 O A:HOH656 2.6 39.4 1.0 O A:HOH663 2.9 37.2 1.0 N A:VAL297 3.2 38.4 1.0 CB A:VAL297 3.6 39.3 1.0 CD2 A:PHE296 3.6 35.6 1.0 CG A:PHE296 3.6 36.0 1.0 CD1 A:PHE296 3.7 37.3 1.0 CE2 A:PHE296 3.7 37.5 1.0 CE1 A:PHE296 3.8 38.8 1.0 CZ A:PHE296 3.8 38.2 1.0 CZ A:PHE84 3.8 43.7 1.0 CA A:PHE296 3.8 35.4 1.0 CB A:ARG82 3.8 43.8 1.0 CG2 A:VAL297 3.9 40.4 1.0 CE2 A:PHE84 3.9 43.5 1.0 CA A:VAL297 4.0 39.4 1.0 C A:PHE296 4.0 36.5 1.0 CG A:PRO88 4.0 52.8 1.0 CA A:ARG82 4.3 42.0 1.0 CB A:PHE296 4.3 35.7 1.0 O A:PRO81 4.4 46.9 1.0 CB A:ALA75 4.5 52.2 1.0 O A:VAL297 4.5 41.6 1.0 O A:SER295 4.8 36.3 1.0 O A:ALA75 4.8 50.8 1.0 C A:VAL297 4.8 40.2 1.0 CE1 A:PHE84 4.8 47.2 1.0 CG1 A:VAL297 4.9 39.3 1.0 N A:PHE296 5.0 36.3 1.0

Sodium binding site 2 out of 5 in the Olep-Oleandolide(Deo) in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Olep-Oleandolide(Deo) in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ B:Na533 b:52.9 occ:1.00 O B:HOH671 2.7 36.3 1.0 O B:HOH673 2.8 42.7 1.0 N B:VAL297 3.0 38.8 1.0 CB B:VAL297 3.6 39.5 1.0 CA B:PHE296 3.8 33.4 1.0 CD2 B:PHE296 3.8 34.1 1.0 CG B:PHE296 3.8 35.6 1.0 CZ B:PHE84 3.8 39.7 1.0 CB B:ARG82 3.8 41.5 1.0 CG2 B:VAL297 3.9 40.6 1.0 CD1 B:PHE296 3.9 33.5 1.0 C B:PHE296 3.9 36.4 1.0 CA B:VAL297 3.9 39.6 1.0 CE2 B:PHE84 3.9 40.1 1.0 CE2 B:PHE296 4.0 34.8 1.0 CE1 B:PHE296 4.1 34.3 1.0 CZ B:PHE296 4.1 36.5 1.0 CA B:ARG82 4.3 41.6 1.0 O B:PRO81 4.3 46.9 1.0 CG B:PRO88 4.4 54.3 1.0 CB B:PHE296 4.4 33.5 1.0 CB B:ALA75 4.6 44.5 1.0 O B:SER295 4.7 31.4 1.0 O B:VAL297 4.7 39.5 1.0 CE1 B:PHE84 4.8 42.0 1.0 C B:VAL297 4.9 39.6 1.0 O B:ALA75 4.9 47.6 1.0 CG1 B:VAL297 5.0 43.0 1.0 N B:PHE296 5.0 31.3 1.0

Sodium binding site 3 out of 5 in the Olep-Oleandolide(Deo) in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Olep-Oleandolide(Deo) in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ C:Na530 b:51.6 occ:1.00 O C:HOH644 2.9 38.5 1.0 O C:HOH680 2.9 35.1 1.0 N C:VAL297 3.0 35.8 1.0 CD2 C:PHE296 3.5 33.7 1.0 CB C:VAL297 3.6 33.8 1.0 CG C:PHE296 3.6 34.4 1.0 CA C:PHE296 3.6 35.5 1.0 CE2 C:PHE296 3.7 34.1 1.0 CZ C:PHE84 3.7 38.5 1.0 C C:PHE296 3.8 36.2 1.0 CD1 C:PHE296 3.8 33.4 1.0 CE2 C:PHE84 3.8 37.5 1.0 CG2 C:VAL297 3.8 37.2 1.0 CA C:VAL297 3.9 35.4 1.0 CZ C:PHE296 3.9 34.9 1.0 CB C:ARG82 3.9 36.0 1.0 CE1 C:PHE296 3.9 35.4 1.0 CB C:PHE296 4.2 34.0 1.0 CA C:ARG82 4.3 35.1 1.0 CG C:PRO88 4.4 47.6 1.0 O C:PRO81 4.4 37.1 1.0 O C:SER295 4.6 30.2 1.0 O C:VAL297 4.6 35.8 1.0 CB C:ALA75 4.7 46.6 1.0 C C:VAL297 4.8 35.7 1.0 N C:PHE296 4.8 34.5 1.0 CE1 C:PHE84 4.8 40.6 1.0 O C:ALA75 4.8 41.5 1.0 CG1 C:VAL297 4.9 34.1 1.0 CD2 C:PHE84 4.9 38.0 1.0 O C:PHE296 5.0 36.4 1.0

Sodium binding site 4 out of 5 in the Olep-Oleandolide(Deo) in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Olep-Oleandolide(Deo) in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ D:Na513 b:67.9 occ:1.00 O D:HOH649 2.5 50.4 1.0 N D:VAL297 3.5 63.8 1.0 CD2 D:PHE296 3.6 56.2 1.0 CE2 D:PHE84 3.7 62.5 1.0 CG D:PHE296 3.7 55.0 1.0 CE2 D:PHE296 3.7 57.3 1.0 CB D:VAL297 3.7 63.6 1.0 CZ D:PHE84 3.8 62.0 1.0 CB D:ARG82 3.8 67.0 1.0 CA D:PHE296 3.8 53.4 1.0 CD1 D:PHE296 4.0 56.2 1.0 CG D:PRO88 4.0 77.8 1.0 CZ D:PHE296 4.0 59.4 1.0 CE1 D:PHE296 4.1 57.5 1.0 C D:PHE296 4.2 59.9 1.0 CA D:VAL297 4.2 63.7 1.0 CG2 D:VAL297 4.3 64.9 1.0 CA D:ARG82 4.3 68.4 1.0 CB D:PHE296 4.3 53.1 1.0 O D:PRO81 4.4 70.9 1.0 CB D:ALA75 4.6 72.9 1.0 O D:ALA75 4.7 65.1 1.0 CG1 D:VAL297 4.7 67.5 1.0 CD2 D:PHE84 4.8 63.8 1.0 O D:VAL297 4.8 66.7 1.0 CB D:PRO88 4.8 79.4 1.0 CE1 D:PHE84 4.9 64.0 1.0 O D:SER295 4.9 51.5 1.0

Sodium binding site 5 out of 5 in the Olep-Oleandolide(Deo) in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Olep-Oleandolide(Deo) in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ F:Na513 b:64.8 occ:1.00 O F:HOH633 2.5 58.0 1.0 O F:HOH632 2.8 50.8 1.0 N F:VAL297 3.1 57.0 1.0 CD2 F:PHE296 3.6 60.8 1.0 CZ F:PHE84 3.6 55.9 1.0 CB F:VAL297 3.7 61.7 1.0 CG F:PHE296 3.7 59.9 1.0 CE2 F:PHE84 3.7 53.4 1.0 CA F:PHE296 3.7 56.1 1.0 CE2 F:PHE296 3.8 58.1 1.0 CB F:ARG82 3.8 58.2 1.0 CD1 F:PHE296 3.8 56.0 1.0 CG2 F:VAL297 3.8 65.5 1.0 C F:PHE296 3.9 56.5 1.0 CZ F:PHE296 3.9 58.6 1.0 CA F:VAL297 3.9 56.8 1.0 CE1 F:PHE296 4.0 57.9 1.0 CB F:PHE296 4.3 56.9 1.0 CG F:PRO88 4.3 70.4 1.0 CA F:ARG82 4.4 59.8 1.0 O F:PRO81 4.4 57.3 1.0 CB F:ALA75 4.5 60.6 1.0 O F:SER295 4.6 49.6 1.0 O F:ALA75 4.6 59.4 1.0 O F:VAL297 4.7 54.0 1.0 CE1 F:PHE84 4.7 60.5 1.0 CD2 F:PHE84 4.8 58.8 1.0 C F:VAL297 4.9 57.1 1.0 N F:PHE296 4.9 55.4 1.0 CG1 F:VAL297 5.0 60.4 1.0

G.Parisi, I.Freda, C.Exertier, C.Cecchetti, E.Gugole, G.Cerutti, L.D'auria, A.Macone, B.Vallone, C.Savino, L.C.Montemiglio. Dissecting the Cytochrome P450 Olep Substrate Specificity: Evidence For A Preferential Substrate. Biomolecules V. 10 2020.
ISSN: ESSN 2218-273X
PubMed: 33036250
DOI: 10.3390/BIOM10101411