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Sodium in PDB 7q89: Olep Mutant G92W in Complex with 6DEB

Protein crystallography data

The structure of Olep Mutant G92W in Complex with 6DEB, PDB code: 7q89 was solved by C.Savino, L.C.Montemiglio, B.Vallone, C.Exertier, I.Freda, E.Gugole, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.03 / 2.08
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 247.758, 110.489, 159.818, 90, 129.66, 90
R / Rfree (%) 17 / 22.8

Other elements in 7q89:

The structure of Olep Mutant G92W in Complex with 6DEB also contains other interesting chemical elements:

Iron (Fe) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Olep Mutant G92W in Complex with 6DEB (pdb code 7q89). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Olep Mutant G92W in Complex with 6DEB, PDB code: 7q89:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 7q89

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Sodium binding site 1 out of 8 in the Olep Mutant G92W in Complex with 6DEB


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na540

b:56.5
occ:1.00
 OH A:TYR31 2.5 43.0 1.0
O A:SER292 2.8 37.8 1.0
O2 A:FMT510 2.8 46.9 1.0
O A:HOH751 3.3 45.6 1.0
O A:HOH605 3.3 57.8 1.0
CE2 A:TYR31 3.3 44.7 1.0
CZ A:TYR31 3.3 37.4 1.0
NE2 A:HIS320 3.3 33.7 1.0
CE1 A:HIS320 3.5 36.0 1.0
C A:FMT510 3.6 67.8 1.0
O1 A:FMT510 3.7 70.8 1.0
NH2 A:ARG398 3.7 44.8 1.0
CB A:ALA293 3.8 38.5 1.0
C A:SER292 3.9 38.3 1.0
CA A:ALA293 3.9 35.3 1.0
CD2 A:HIS320 4.1 36.7 1.0
OH A:TYR17 4.3 40.8 1.0
ND1 A:HIS320 4.3 34.6 1.0
N A:ALA293 4.4 37.0 1.0
O A:HOH700 4.5 48.3 1.0
CD2 A:TYR31 4.6 36.4 1.0
CE1 A:TYR31 4.6 42.6 1.0
CG A:HIS320 4.6 36.1 1.0
CZ A:ARG398 5.0 42.4 1.0

Sodium binding site 2 out of 8 in 7q89

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Sodium binding site 2 out of 8 in the Olep Mutant G92W in Complex with 6DEB


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na541

b:47.8
occ:1.00
 O A:HOH693 2.7 33.6 1.0
NE A:ARG298 3.0 32.5 1.0
O A:HOH660 3.1 36.9 1.0
O A:HOH781 3.1 37.9 1.0
NH2 A:ARG298 3.5 35.3 1.0
O A:LEU65 3.6 37.1 1.0
CD2 A:HIS354 3.7 36.8 1.0
CZ A:ARG298 3.7 35.1 1.0
CG A:ARG298 3.7 31.3 1.0
CD A:ARG298 3.9 34.2 1.0
O A:HOH690 3.9 38.8 1.0
CG2 A:THR72 3.9 35.1 1.0
O A:HOH716 4.1 47.1 1.0
O A:VAL64 4.2 35.6 1.0
C A:LEU65 4.2 38.4 1.0
O A:PHE70 4.2 50.2 1.0
NE2 A:HIS354 4.3 30.4 1.0
O A:HOH827 4.4 57.5 1.0
CA A:LEU65 4.4 34.9 1.0
CG A:HIS354 4.8 32.3 1.0
OG1 A:THR72 5.0 38.6 1.0

Sodium binding site 3 out of 8 in 7q89

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Sodium binding site 3 out of 8 in the Olep Mutant G92W in Complex with 6DEB


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na540

b:52.3
occ:1.00
 O B:THR80 2.8 45.0 1.0
O B:HOH715 3.0 39.1 1.0
O B:ALA75 3.0 43.1 1.0
NH1 B:ARG82 3.1 53.5 1.0
O B:ASP77 3.2 46.3 1.0
CD B:PRO88 3.5 47.4 1.0
C B:THR80 3.6 41.7 1.0
CD B:ARG82 3.6 47.5 1.0
CB B:THR80 3.6 39.0 1.0
CA B:THR80 3.9 40.9 1.0
CB B:ARG82 3.9 42.7 1.0
CG B:ARG82 3.9 41.5 1.0
N B:THR80 3.9 42.5 1.0
O B:PRO81 4.1 44.9 1.0
CZ B:ARG82 4.1 52.7 1.0
C B:ALA75 4.2 45.8 1.0
C B:ASP77 4.3 44.3 1.0
NE B:ARG82 4.3 44.8 1.0
O B:PRO78 4.3 43.3 1.0
CA B:PRO78 4.3 44.9 1.0
CG B:PRO88 4.3 46.6 1.0
C B:PRO78 4.4 46.4 1.0
OG1 B:THR80 4.4 44.0 1.0
C B:PRO81 4.4 43.1 1.0
CA B:PRO87 4.5 49.4 1.0
CG2 B:THR80 4.6 43.0 1.0
N B:PRO88 4.7 42.8 1.0
N B:PRO81 4.7 37.6 1.0
N B:PRO78 4.8 50.0 1.0
N B:ARG82 4.9 43.8 1.0
CB B:PRO87 4.9 46.2 1.0
CA B:ALA75 4.9 47.0 1.0
C B:ALA79 4.9 51.1 1.0
CA B:ARG82 5.0 39.0 1.0

Sodium binding site 4 out of 8 in 7q89

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Sodium binding site 4 out of 8 in the Olep Mutant G92W in Complex with 6DEB


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na541

b:50.0
occ:1.00
 O B:HOH746 2.7 34.2 1.0
O B:HOH715 2.8 39.1 1.0
N B:VAL297 3.0 39.5 1.0
CD2 B:PHE296 3.6 35.5 1.0
CB B:VAL297 3.6 36.8 1.0
CA B:PHE296 3.7 30.4 1.0
CG B:PHE296 3.7 34.6 1.0
CZ B:PHE84 3.7 38.4 1.0
CE2 B:PHE296 3.8 33.8 1.0
CG2 B:VAL297 3.8 36.7 1.0
C B:PHE296 3.8 35.5 1.0
CD1 B:PHE296 3.8 31.1 1.0
CE2 B:PHE84 3.9 36.4 1.0
CA B:VAL297 3.9 38.4 1.0
CB B:ARG82 3.9 42.7 1.0
CE1 B:PHE296 3.9 31.4 1.0
CZ B:PHE296 3.9 32.6 1.0
CB B:PHE296 4.3 35.6 1.0
CA B:ARG82 4.3 39.0 1.0
CG B:PRO88 4.3 46.6 1.0
O B:PRO81 4.4 44.9 1.0
CB B:ALA75 4.5 47.4 1.0
O B:SER295 4.6 37.5 1.0
O B:VAL297 4.6 39.5 1.0
CE1 B:PHE84 4.8 37.9 1.0
C B:VAL297 4.8 34.9 1.0
N B:PHE296 4.8 29.1 1.0
CG1 B:VAL297 4.9 44.8 1.0
CD2 B:PHE84 5.0 39.0 1.0

Sodium binding site 5 out of 8 in 7q89

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Sodium binding site 5 out of 8 in the Olep Mutant G92W in Complex with 6DEB


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na530

b:47.6
occ:1.00
 O C:HOH779 2.8 35.2 1.0
O C:HOH785 2.9 38.7 1.0
N C:VAL297 2.9 38.8 1.0
CD2 C:PHE296 3.5 35.6 1.0
CG C:PHE296 3.6 34.4 1.0
CB C:VAL297 3.6 39.3 1.0
CE2 C:PHE296 3.7 33.2 1.0
CZ C:PHE84 3.7 41.5 1.0
CE2 C:PHE84 3.7 40.8 1.0
CD1 C:PHE296 3.7 33.6 1.0
CA C:PHE296 3.7 33.6 1.0
CG2 C:VAL297 3.7 43.1 1.0
C C:PHE296 3.8 35.8 1.0
CZ C:PHE296 3.8 35.3 1.0
CE1 C:PHE296 3.8 33.3 1.0
CA C:VAL297 3.9 35.4 1.0
CB C:ARG82 4.1 37.8 1.0
CB C:PHE296 4.3 35.8 1.0
CA C:ARG82 4.5 36.9 1.0
CG C:PRO88 4.5 52.9 1.0
O C:SER295 4.5 40.8 1.0
O C:PRO81 4.6 39.4 1.0
O C:VAL297 4.7 33.4 1.0
CB C:ALA75 4.7 46.6 1.0
CE1 C:PHE84 4.8 39.8 1.0
C C:VAL297 4.8 38.5 1.0
CD2 C:PHE84 4.9 42.3 1.0
N C:PHE296 4.9 39.7 1.0
CG1 C:VAL297 5.0 40.6 1.0
O C:PHE296 5.0 38.6 1.0

Sodium binding site 6 out of 8 in 7q89

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Sodium binding site 6 out of 8 in the Olep Mutant G92W in Complex with 6DEB


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na519

b:56.2
occ:1.00
 O D:HOH712 2.4 39.8 1.0
N D:VAL297 2.9 50.7 1.0
CG2 D:VAL297 3.2 51.9 1.0
O D:HOH697 3.3 54.3 1.0
CB D:VAL297 3.5 53.9 1.0
CA D:PHE296 3.5 44.6 1.0
CG D:PHE296 3.6 36.2 1.0
CD2 D:PHE296 3.6 44.2 1.0
C D:PHE296 3.6 53.0 1.0
CA D:VAL297 3.8 49.9 1.0
CB D:ARG82 3.8 64.6 1.0
CZ D:PHE84 3.8 48.9 1.0
CD1 D:PHE296 3.8 37.1 1.0
CE2 D:PHE84 3.9 45.8 1.0
CE2 D:PHE296 3.9 36.2 1.0
CB D:PHE296 4.1 36.2 1.0
CE1 D:PHE296 4.1 36.1 1.0
CA D:ARG82 4.2 56.1 1.0
CZ D:PHE296 4.2 35.4 1.0
O D:SER295 4.4 45.0 1.0
CG D:PRO88 4.5 72.4 1.0
O D:PRO81 4.5 59.7 1.0
O D:VAL297 4.7 46.2 1.0
N D:PHE296 4.7 40.3 1.0
C D:VAL297 4.8 45.4 1.0
O D:PHE296 4.8 42.9 1.0
CB D:ALA75 4.9 59.4 1.0
CG1 D:VAL297 4.9 61.2 1.0
N D:MET83 4.9 48.7 1.0
CE1 D:PHE84 4.9 49.8 1.0
CD2 D:PHE84 5.0 51.6 1.0
C D:SER295 5.0 44.6 1.0

Sodium binding site 7 out of 8 in 7q89

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Sodium binding site 7 out of 8 in the Olep Mutant G92W in Complex with 6DEB


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na514

b:63.4
occ:1.00
 O E:HOH652 2.9 56.7 1.0
O E:HOH671 2.9 50.5 1.0
N E:VAL297 3.0 47.5 1.0
CB E:VAL297 3.5 54.8 1.0
CD2 E:PHE296 3.5 44.0 1.0
CG E:PHE296 3.6 45.4 1.0
CZ E:PHE84 3.7 49.6 1.0
CA E:PHE296 3.7 44.7 1.0
CE2 E:PHE296 3.7 48.4 1.0
CD1 E:PHE296 3.7 50.8 1.0
CE1 E:PHE296 3.8 52.0 1.0
C E:PHE296 3.8 51.8 1.0
CA E:VAL297 3.8 49.3 1.0
CB E:ARG82 3.9 56.4 1.0
CZ E:PHE296 3.9 50.1 1.0
CG2 E:VAL297 3.9 52.2 1.0
CE2 E:PHE84 3.9 47.5 1.0
CG E:PRO88 4.1 54.5 1.0
CB E:PHE296 4.2 47.6 1.0
CB E:ALA75 4.4 56.1 1.0
CA E:ARG82 4.4 55.9 1.0
O E:PRO81 4.4 55.4 1.0
O E:VAL297 4.6 54.5 1.0
CE1 E:PHE84 4.7 49.0 1.0
CG1 E:VAL297 4.7 63.1 1.0
O E:SER295 4.7 47.2 1.0
C E:VAL297 4.8 60.5 1.0
N E:PHE296 4.9 47.4 1.0

Sodium binding site 8 out of 8 in 7q89

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Sodium binding site 8 out of 8 in the Olep Mutant G92W in Complex with 6DEB


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na513

b:63.4
occ:1.00
 O F:HOH679 2.5 61.1 1.0
O F:HOH671 3.1 60.2 1.0
N F:VAL297 3.1 57.5 1.0
CB F:VAL297 3.5 55.8 1.0
CZ F:PHE84 3.7 58.9 1.0
CG2 F:VAL297 3.7 59.0 1.0
CE2 F:PHE84 3.7 54.8 1.0
CG F:PHE296 3.8 52.7 1.0
CD2 F:PHE296 3.8 57.5 1.0
CD1 F:PHE296 3.8 45.0 1.0
CB F:ARG82 3.9 58.1 1.0
CA F:VAL297 3.9 57.5 1.0
CE2 F:PHE296 3.9 51.2 1.0
CA F:PHE296 3.9 50.5 1.0
C F:PHE296 3.9 51.2 1.0
CZ F:PHE296 3.9 49.7 1.0
CE1 F:PHE296 4.0 49.6 1.0
CG F:PRO88 4.2 77.8 1.0
CA F:ARG82 4.3 52.1 1.0
O F:PRO81 4.3 54.1 1.0
CB F:ALA75 4.5 59.4 1.0
CB F:PHE296 4.5 48.3 1.0
O F:SER295 4.7 49.8 1.0
CE1 F:PHE84 4.8 65.3 1.0
O F:VAL297 4.8 55.7 1.0
CG1 F:VAL297 4.8 64.7 1.0
C F:VAL297 4.9 63.5 1.0
CD2 F:PHE84 4.9 59.8 1.0
O F:ALA75 4.9 62.1 1.0

Reference:

L.C.Montemiglio, E.Gugole, I.Freda, C.Exertier, L.D'auria, C.G.Chen, A.N.Nardi, G.Cerutti, G.Parisi, M.D'abramo, C.Savino, B.Vallone. Point Mutations at A Key Site Alter the Cytochrome P450 Olep Structural Dynamics. Biomolecules V. 12 2021.
ISSN: ESSN 2218-273X
PubMed: 35053203
DOI: 10.3390/BIOM12010055
Page generated: Fri Apr 7 15:44:23 2023

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