Sodium in PDB 6zi7: Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose

The structure of Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose, PDB code: 6zi7 was solved by L.C.Montemiglio, C.Savino, B.Vallone, G.Parisi, I.Freda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.92 / 2.28
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	247.531, 110.683, 159.285, 90.00, 129.46, 90.00
R / Rfree (%)	18.4 / 24.7

The structure of Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose also contains other interesting chemical elements:

Iron

(Fe)

6 atoms

The binding sites of Sodium atom in the Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose (pdb code 6zi7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose, PDB code: 6zi7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose


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 Olep-Oleandolide(Deo) Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na526 b:41.3 occ:1.00 O A:HOH726 2.7 28.9 1.0 O A:HOH706 2.9 33.0 1.0 N A:VAL297 3.0 33.5 1.0 CG A:PHE296 3.6 30.4 1.0 CA A:PHE296 3.6 30.8 1.0 CD2 A:PHE296 3.6 31.1 1.0 CB A:VAL297 3.7 33.1 1.0 CZ A:PHE84 3.8 36.1 1.0 CD1 A:PHE296 3.8 32.0 1.0 C A:PHE296 3.8 32.0 1.0 CE2 A:PHE296 3.9 32.4 1.0 CB A:ARG82 3.9 35.9 1.0 CE2 A:PHE84 3.9 35.4 1.0 CG2 A:VAL297 4.0 32.9 1.0 CA A:VAL297 4.0 35.2 1.0 CE1 A:PHE296 4.1 32.2 1.0 CZ A:PHE296 4.1 32.3 1.0 CB A:PHE296 4.1 29.9 1.0 CG A:PRO88 4.3 43.7 1.0 CA A:ARG82 4.3 35.2 1.0 O A:PRO81 4.5 37.1 1.0 O A:SER295 4.5 30.3 1.0 O A:VAL297 4.6 35.3 1.0 N A:PHE296 4.7 31.5 1.0 CB A:ALA75 4.8 41.8 1.0 CE1 A:PHE84 4.8 38.3 1.0 C A:VAL297 4.8 35.6 1.0 O A:ALA75 5.0 45.9 1.0

Sodium binding site 2 out of 6 in the Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na515 b:57.9 occ:1.00 O B:HOH697 2.7 38.7 1.0 O B:HOH692 2.8 38.8 1.0 N B:VAL297 3.3 37.5 1.0 CZ B:PHE84 3.6 44.5 1.0 CD2 B:PHE296 3.7 35.3 1.0 CG B:PHE296 3.8 36.4 1.0 CE2 B:PHE296 3.8 35.2 1.0 CB B:ARG82 3.8 44.5 1.0 CA B:PHE296 3.8 34.4 1.0 CE2 B:PHE84 3.9 43.4 1.0 CB B:VAL297 3.9 38.4 1.0 CG B:PRO88 3.9 51.8 1.0 CD1 B:PHE296 4.0 34.1 1.0 CG2 B:VAL297 4.0 38.9 1.0 CZ B:PHE296 4.1 36.4 1.0 C B:PHE296 4.1 38.2 1.0 CE1 B:PHE296 4.1 35.4 1.0 CA B:ARG82 4.2 42.8 1.0 CA B:VAL297 4.2 38.6 1.0 CB B:PHE296 4.4 34.7 1.0 O B:PRO81 4.4 40.4 1.0 CB B:ALA75 4.6 45.2 1.0 CE1 B:PHE84 4.6 44.7 1.0 O B:SER295 4.7 36.1 1.0 O B:ALA75 4.7 44.6 1.0 O B:VAL297 4.9 39.0 1.0 CB B:PRO88 4.9 51.4 1.0 N B:MET83 4.9 43.0 1.0 CD2 B:PHE84 4.9 43.4 1.0 CD B:PRO88 5.0 51.2 1.0 N B:PHE296 5.0 33.4 1.0

Sodium binding site 3 out of 6 in the Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ C:Na527 b:42.4 occ:1.00 O C:HOH788 2.9 33.1 1.0 O C:HOH737 2.9 28.1 1.0 N C:VAL297 3.0 33.3 1.0 CD2 C:PHE296 3.5 29.9 1.0 CG C:PHE296 3.5 30.4 1.0 CE2 C:PHE296 3.6 30.7 1.0 CD1 C:PHE296 3.6 31.3 1.0 CA C:PHE296 3.6 30.3 1.0 CE1 C:PHE296 3.7 31.7 1.0 CZ C:PHE84 3.7 31.0 1.0 CZ C:PHE296 3.7 31.7 1.0 CB C:VAL297 3.7 35.4 1.0 C C:PHE296 3.8 32.2 1.0 CA C:VAL297 3.9 34.5 1.0 CE2 C:PHE84 4.0 31.7 1.0 CB C:ARG82 4.1 34.8 1.0 CG2 C:VAL297 4.1 36.2 1.0 CB C:PHE296 4.2 29.9 1.0 CG C:PRO88 4.2 39.8 1.0 O C:VAL297 4.5 33.4 1.0 CA C:ARG82 4.5 32.7 1.0 CB C:ALA75 4.6 39.2 1.0 O C:PRO81 4.6 32.6 1.0 O C:SER295 4.7 29.7 1.0 CE1 C:PHE84 4.7 32.5 1.0 C C:VAL297 4.8 33.9 1.0 N C:PHE296 4.8 30.3 1.0 O C:ALA75 4.8 37.6 1.0 O C:PHE296 5.0 29.5 1.0

Sodium binding site 4 out of 6 in the Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ D:Na513 b:54.4 occ:1.00 O D:HOH694 2.4 41.6 1.0 O D:HOH642 3.0 55.6 1.0 N D:VAL297 3.2 50.8 1.0 CD2 D:PHE296 3.5 44.1 1.0 CG D:PHE296 3.6 42.5 1.0 CB D:VAL297 3.6 47.3 1.0 CZ D:PHE84 3.7 47.7 1.0 CA D:PHE296 3.7 45.4 1.0 CE2 D:PHE296 3.8 45.2 1.0 CG2 D:VAL297 3.8 46.5 1.0 CB D:ARG82 3.9 56.0 1.0 CE2 D:PHE84 3.9 46.5 1.0 CD1 D:PHE296 3.9 42.2 1.0 C D:PHE296 4.0 49.3 1.0 CA D:VAL297 4.1 47.8 1.0 CZ D:PHE296 4.1 45.0 1.0 CE1 D:PHE296 4.1 43.6 1.0 CG D:PRO88 4.2 60.2 1.0 CA D:ARG82 4.3 55.5 1.0 CB D:PHE296 4.3 43.2 1.0 O D:SER295 4.6 50.0 1.0 O D:PRO81 4.6 58.0 1.0 CE1 D:PHE84 4.7 46.4 1.0 N D:PHE296 4.8 44.7 1.0 O D:VAL297 4.8 50.3 1.0 CG1 D:VAL297 4.9 50.5 1.0 CD2 D:PHE84 5.0 47.4 1.0

Sodium binding site 5 out of 6 in the Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ E:Na507 b:81.2 occ:1.00 O E:HOH641 2.8 65.8 1.0 O E:HOH630 2.8 52.9 1.0 N E:VAL297 3.2 59.6 1.0 CZ E:PHE84 3.6 56.7 1.0 CG E:PHE296 3.7 57.2 1.0 CD1 E:PHE296 3.7 55.9 1.0 CD2 E:PHE296 3.7 53.5 1.0 CB E:VAL297 3.8 65.0 1.0 CE1 E:PHE296 3.8 59.1 1.0 CE2 E:PHE296 3.8 56.5 1.0 CA E:PHE296 3.8 57.4 1.0 CB E:ARG82 3.8 68.0 1.0 CZ E:PHE296 3.9 59.0 1.0 CE2 E:PHE84 3.9 54.6 1.0 CG E:PRO88 4.0 62.7 1.0 C E:PHE296 4.0 59.5 1.0 CA E:VAL297 4.1 64.2 1.0 CG2 E:VAL297 4.1 66.0 1.0 CA E:ARG82 4.3 66.4 1.0 O E:PRO81 4.3 64.3 1.0 CB E:PHE296 4.4 58.4 1.0 CE1 E:PHE84 4.5 57.5 1.0 CB E:ALA75 4.5 66.3 1.0 O E:SER295 4.8 53.5 1.0 O E:VAL297 4.8 62.9 1.0 CD E:PRO88 5.0 61.9 1.0 C E:VAL297 5.0 67.6 1.0 N E:PHE296 5.0 57.7 1.0 CD2 E:PHE84 5.0 57.0 1.0 CG1 E:VAL297 5.0 64.8 1.0

Sodium binding site 6 out of 6 in the Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ F:Na508 b:59.5 occ:1.00 O F:HOH644 2.4 49.5 1.0 N F:VAL297 3.2 59.6 1.0 O F:HOH646 3.2 54.5 1.0 CZ F:PHE84 3.6 60.6 1.0 CB F:ARG82 3.7 59.2 1.0 CB F:VAL297 3.7 64.1 1.0 CD2 F:PHE296 3.7 57.4 1.0 CG F:PHE296 3.8 57.0 1.0 CE2 F:PHE296 3.9 54.3 1.0 CA F:PHE296 3.9 55.3 1.0 CG F:PRO88 3.9 70.4 1.0 CE2 F:PHE84 3.9 60.1 1.0 CA F:VAL297 4.0 59.8 1.0 C F:PHE296 4.0 55.7 1.0 CG2 F:VAL297 4.0 64.6 1.0 CD1 F:PHE296 4.0 54.2 1.0 CZ F:PHE296 4.1 53.6 1.0 CE1 F:PHE296 4.1 54.4 1.0 O F:PRO81 4.2 53.8 1.0 CA F:ARG82 4.3 58.4 1.0 CB F:ALA75 4.5 55.6 1.0 CB F:PHE296 4.5 53.9 1.0 CE1 F:PHE84 4.6 64.2 1.0 O F:ALA75 4.6 59.5 1.0 O F:VAL297 4.7 60.1 1.0 O F:SER295 4.7 51.5 1.0 CB F:PRO88 4.8 65.3 1.0 C F:VAL297 4.9 61.5 1.0 CG F:ARG82 4.9 60.5 1.0 CG1 F:VAL297 5.0 62.7 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