Sodium in PDB 6zi3: Crystal Structure of Olep-6DEB Bound to L-Rhamnose

The structure of Crystal Structure of Olep-6DEB Bound to L-Rhamnose, PDB code: 6zi3 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)	48.09 / 2.08
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	247.379, 111.149, 159.144, 90.00, 129.40, 90.00
R / Rfree (%)	17.2 / 22.5

The structure of Crystal Structure of Olep-6DEB 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-6DEB Bound to L-Rhamnose (pdb code 6zi3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of Olep-6DEB Bound to L-Rhamnose, PDB code: 6zi3:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Crystal Structure of Olep-6DEB 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-6DEB Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na546 b:45.1 occ:1.00 O A:HOH730 2.8 34.3 1.0 O A:HOH723 2.8 33.0 1.0 N A:VAL297 3.0 35.8 1.0 CB A:VAL297 3.6 36.3 1.0 CG A:PHE296 3.6 35.0 1.0 CA A:PHE296 3.6 33.1 1.0 CD2 A:PHE296 3.6 34.5 1.0 CE2 A:PHE84 3.7 40.0 1.0 CZ A:PHE84 3.7 39.2 1.0 CD1 A:PHE296 3.8 34.2 1.0 CE2 A:PHE296 3.8 36.1 1.0 C A:PHE296 3.8 36.1 1.0 CG2 A:VAL297 3.8 35.6 1.0 CZ A:PHE296 3.9 37.2 1.0 CB A:ARG82 3.9 38.8 1.0 CE1 A:PHE296 3.9 37.2 1.0 CA A:VAL297 3.9 36.3 1.0 CG A:PRO88 4.2 47.8 1.0 CB A:PHE296 4.2 35.1 1.0 CA A:ARG82 4.3 37.4 1.0 O A:PRO81 4.5 39.5 1.0 O A:SER295 4.6 35.7 1.0 O A:VAL297 4.6 38.7 1.0 CB A:ALA75 4.7 48.5 1.0 N A:PHE296 4.8 34.9 1.0 C A:VAL297 4.8 37.1 1.0 CD2 A:PHE84 4.9 38.9 1.0 CE1 A:PHE84 4.9 41.4 1.0 CG1 A:VAL297 4.9 38.2 1.0

Sodium binding site 2 out of 7 in the Crystal Structure of Olep-6DEB 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-6DEB Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na547 b:66.9 occ:1.00 ND1 A:HIS258 2.8 54.8 1.0 NE2 A:GLN403 2.9 51.0 1.0 CB A:HIS258 3.5 52.9 1.0 CD1 A:LEU400 3.6 49.6 1.0 CG A:HIS258 3.6 54.8 1.0 CG A:LEU382 3.6 66.0 0.5 CA A:HIS258 3.6 51.6 1.0 CD1 A:LEU382 3.7 64.8 0.5 CG A:GLN403 3.7 52.8 1.0 CD A:GLN403 3.8 53.0 1.0 CD1 A:LEU389 3.8 52.3 1.0 CD1 A:LEU382 3.8 60.5 0.5 CD2 A:LEU382 3.8 65.1 0.5 CE1 A:HIS258 3.9 57.1 1.0 CD2 A:LEU382 3.9 60.6 0.5 CD2 A:LEU389 4.0 51.2 1.0 CG A:LEU382 4.4 62.0 0.5 N A:HIS258 4.4 51.6 1.0 CG A:LEU389 4.5 51.9 1.0 C A:HIS258 4.8 54.1 1.0 OG1 A:THR262 4.8 67.2 0.5 CD2 A:HIS258 4.8 53.4 1.0 O A:HIS258 4.8 53.8 1.0 OE1 A:GLN403 4.9 48.9 1.0 NE2 A:HIS258 4.9 55.4 1.0 CG A:LEU400 5.0 45.9 1.0

Sodium binding site 3 out of 7 in the Crystal Structure of Olep-6DEB 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-6DEB Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na570 b:53.0 occ:1.00 O B:HOH724 2.7 40.7 1.0 O B:HOH729 2.9 40.1 1.0 N B:VAL297 3.1 37.6 1.0 CD2 B:PHE296 3.6 34.8 1.0 CG B:PHE296 3.6 35.2 1.0 CB B:VAL297 3.7 37.2 1.0 CE2 B:PHE296 3.7 34.1 1.0 CE2 B:PHE84 3.7 40.7 1.0 CA B:PHE296 3.8 34.4 1.0 CD1 B:PHE296 3.8 34.6 1.0 CZ B:PHE84 3.8 42.2 1.0 CG2 B:VAL297 3.8 40.0 1.0 CE1 B:PHE296 3.8 34.8 1.0 CZ B:PHE296 3.9 33.9 1.0 C B:PHE296 3.9 38.0 1.0 CB B:ARG82 3.9 43.7 1.0 CA B:VAL297 4.0 38.8 1.0 CG B:PRO88 4.2 53.7 1.0 CB B:PHE296 4.3 34.0 1.0 CA B:ARG82 4.4 41.2 1.0 CB B:ALA75 4.5 46.2 1.0 O B:PRO81 4.6 41.6 1.0 O B:SER295 4.7 35.4 1.0 O B:ALA75 4.8 47.6 1.0 O B:VAL297 4.8 40.2 1.0 CD2 B:PHE84 4.8 42.4 1.0 CE1 B:PHE84 4.9 44.0 1.0 N B:PHE296 5.0 33.7 1.0 C B:VAL297 5.0 38.0 1.0 CG1 B:VAL297 5.0 40.3 1.0

Sodium binding site 4 out of 7 in the Crystal Structure of Olep-6DEB 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-6DEB Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ C:Na566 b:43.9 occ:1.00 O C:HOH752 2.8 32.7 1.0 O C:HOH753 2.9 36.1 1.0 N C:VAL297 3.0 37.3 1.0 CD2 C:PHE296 3.6 34.5 1.0 CB C:VAL297 3.6 36.9 1.0 CG C:PHE296 3.6 34.7 1.0 CA C:PHE296 3.6 33.9 1.0 CD1 C:PHE296 3.7 34.3 1.0 CE2 C:PHE84 3.7 37.5 1.0 CZ C:PHE84 3.7 38.9 1.0 CE2 C:PHE296 3.7 37.8 1.0 CZ C:PHE296 3.8 35.4 1.0 C C:PHE296 3.8 36.7 1.0 CE1 C:PHE296 3.8 36.6 1.0 CA C:VAL297 3.9 34.9 1.0 CG2 C:VAL297 3.9 38.0 1.0 CB C:ARG82 4.0 36.7 1.0 CB C:PHE296 4.3 34.8 1.0 CA C:ARG82 4.4 36.1 1.0 CG C:PRO88 4.5 47.2 1.0 O C:SER295 4.5 32.3 1.0 O C:PRO81 4.6 37.2 1.0 CB C:ALA75 4.6 40.0 1.0 O C:VAL297 4.7 34.8 1.0 N C:PHE296 4.8 33.5 1.0 C C:VAL297 4.8 36.5 1.0 CD2 C:PHE84 4.9 37.8 1.0 CE1 C:PHE84 4.9 39.2 1.0 CG1 C:VAL297 4.9 38.4 1.0

Sodium binding site 5 out of 7 in the Crystal Structure of Olep-6DEB 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-6DEB Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ D:Na520 b:62.4 occ:1.00 O D:HOH636 2.6 52.7 1.0 N D:VAL297 3.3 59.4 1.0 CE1 D:PHE84 3.5 56.0 1.0 CA D:PHE296 3.5 52.5 1.0 CB D:ARG82 3.6 64.2 1.0 CG2 D:VAL297 3.6 60.1 1.0 CB D:VAL297 3.7 59.0 1.0 CG D:PHE296 3.8 50.1 1.0 CZ D:PHE84 3.9 55.4 1.0 CD2 D:PHE296 3.9 51.9 1.0 C D:PHE296 3.9 57.6 1.0 CA D:ARG82 4.1 62.6 1.0 CA D:VAL297 4.1 56.5 1.0 CD1 D:PHE296 4.1 50.3 1.0 CB D:PHE296 4.2 50.9 1.0 CE2 D:PHE296 4.3 51.4 1.0 O D:SER295 4.4 52.4 1.0 CD1 D:PHE84 4.5 56.8 1.0 CE1 D:PHE296 4.5 50.5 1.0 O D:PRO81 4.5 62.6 1.0 CZ D:PHE296 4.5 50.5 1.0 CG D:PRO88 4.6 76.9 1.0 N D:PHE296 4.6 50.7 1.0 N D:MET83 4.8 55.9 1.0 C D:SER295 4.9 50.8 1.0 C D:ARG82 5.0 62.2 1.0 CG D:ARG82 5.0 65.8 1.0

Sodium binding site 6 out of 7 in the Crystal Structure of Olep-6DEB 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-6DEB Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ E:Na515 b:63.5 occ:1.00 O E:HOH667 2.7 50.8 1.0 O E:HOH635 2.8 54.0 1.0 N E:VAL297 3.1 56.1 1.0 CZ E:PHE84 3.6 52.6 1.0 CD2 E:PHE296 3.6 46.9 1.0 CG E:PHE296 3.6 48.0 1.0 CB E:VAL297 3.7 58.9 1.0 CA E:PHE296 3.7 50.7 1.0 CD1 E:PHE296 3.7 49.4 1.0 CE2 E:PHE296 3.8 48.4 1.0 CE1 E:PHE84 3.8 50.3 1.0 CG2 E:VAL297 3.8 59.5 1.0 CE1 E:PHE296 3.9 49.9 1.0 CB E:ARG82 3.9 59.9 1.0 CZ E:PHE296 3.9 50.4 1.0 C E:PHE296 3.9 53.5 1.0 CA E:VAL297 4.0 56.0 1.0 CG E:PRO88 4.2 60.2 1.0 CB E:PHE296 4.3 47.5 1.0 CA E:ARG82 4.3 56.9 1.0 O E:PRO81 4.5 56.2 1.0 CB E:ALA75 4.5 62.5 1.0 CE2 E:PHE84 4.7 55.0 1.0 O E:SER295 4.7 49.5 1.0 O E:VAL297 4.8 54.4 1.0 N E:PHE296 4.9 48.7 1.0 CD1 E:PHE84 5.0 50.7 1.0 C E:VAL297 5.0 58.9 1.0

Sodium binding site 7 out of 7 in the Crystal Structure of Olep-6DEB Bound to L-Rhamnose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Olep-6DEB Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ F:Na720 b:56.1 occ:1.00 O F:HOH861 2.6 50.0 1.0 O F:HOH858 2.8 51.2 1.0 N F:VAL297 3.1 52.9 1.0 CG F:PHE296 3.6 52.1 1.0 CD2 F:PHE296 3.6 54.5 1.0 CZ F:PHE84 3.6 52.8 1.0 CE2 F:PHE84 3.7 51.5 1.0 CA F:PHE296 3.7 50.1 1.0 CD1 F:PHE296 3.7 50.1 1.0 CB F:VAL297 3.8 55.0 1.0 CE2 F:PHE296 3.8 49.7 1.0 CB F:ARG82 3.9 57.0 1.0 C F:PHE296 3.9 51.2 1.0 CG2 F:VAL297 3.9 57.6 1.0 CZ F:PHE296 3.9 47.9 1.0 CE1 F:PHE296 3.9 49.1 1.0 CA F:VAL297 4.0 52.4 1.0 CG F:PRO88 4.2 58.9 1.0 CB F:PHE296 4.3 50.9 1.0 CA F:ARG82 4.4 52.8 1.0 O F:PRO81 4.5 54.1 1.0 CB F:ALA75 4.5 52.2 1.0 O F:SER295 4.7 48.2 1.0 CE1 F:PHE84 4.8 52.6 1.0 CD2 F:PHE84 4.8 54.2 1.0 O F:ALA75 4.8 56.2 1.0 O F:VAL297 4.8 50.4 1.0 N F:PHE296 4.9 52.6 1.0 C F:VAL297 5.0 51.9 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