Atomistry » Sodium » PDB 6z72-6zl3 » 6zhz
Atomistry »
  Sodium »
    PDB 6z72-6zl3 »
      6zhz »

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

Protein crystallography data

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

Other elements in 6zhz:

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

Iron (Fe) 6 atoms

Sodium Binding Sites:

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 6zhz

Go back to Sodium Binding Sites List in 6zhz
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 6zhz

Go back to Sodium Binding Sites List in 6zhz
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 6zhz

Go back to Sodium Binding Sites List in 6zhz
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 6zhz

Go back to Sodium Binding Sites List in 6zhz
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 6zhz

Go back to Sodium Binding Sites List in 6zhz
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

Reference:

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
Page generated: Tue Oct 8 15:29:19 2024

Last articles

Mg in 5DGD
Mg in 5DGB
Mg in 5DGA
Mg in 5DG9
Mg in 5DG8
Mg in 5DDR
Mg in 5DED
Mg in 5DFH
Mg in 5DFF
Mg in 5DDY
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy