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Chlorine in PDB 5mog: Oryza Sativa Phytoene Desaturase Inhibited By Norflurazon

Protein crystallography data

The structure of Oryza Sativa Phytoene Desaturase Inhibited By Norflurazon, PDB code: 5mog was solved by A.Brausemann, S.Gemmecker, J.Koschmieder, P.Beyer, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.25 / 2.77
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 230.210, 230.210, 179.230, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 22.4

Other elements in 5mog:

The structure of Oryza Sativa Phytoene Desaturase Inhibited By Norflurazon also contains other interesting chemical elements:

Fluorine (F) 15 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Oryza Sativa Phytoene Desaturase Inhibited By Norflurazon (pdb code 5mog). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Oryza Sativa Phytoene Desaturase Inhibited By Norflurazon, PDB code: 5mog:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5mog

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Chlorine binding site 1 out of 5 in the Oryza Sativa Phytoene Desaturase Inhibited By Norflurazon


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Oryza Sativa Phytoene Desaturase Inhibited By Norflurazon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:52.8
occ:1.00
 CL A:NRF601 0.0 52.8 1.0
C2 A:NRF601 1.7 49.0 1.0
C3 A:NRF601 2.7 47.7 1.0
C1 A:NRF601 2.7 48.3 1.0
O A:NRF601 2.9 48.3 1.0
N A:NRF601 3.0 45.5 1.0
CB A:SER540 3.4 42.8 1.0
NH2 A:ARG300 3.8 45.4 1.0
O A:ALA539 3.8 44.4 1.0
N1 A:NRF601 4.0 47.9 1.0
CD2 A:LEU281 4.0 47.0 1.0
OH A:TYR165 4.0 45.1 1.0
C4 A:NRF601 4.0 49.6 1.0
CD1 A:LEU538 4.0 44.3 1.0
O A:LEU281 4.1 44.3 1.0
CA A:SER540 4.2 41.0 1.0
CB A:LEU538 4.3 40.6 1.0
C A:ALA539 4.4 44.4 1.0
OG A:SER540 4.4 46.4 1.0
C A:NRF601 4.5 42.6 1.0
N2 A:NRF601 4.5 49.6 1.0
N A:SER540 4.6 40.9 1.0
CA A:LEU281 4.7 41.4 1.0
O2 A:FAD600 4.7 35.1 1.0
C2 A:FAD600 4.8 35.3 1.0
CG A:LEU538 4.8 45.0 1.0
CB A:LEU281 4.8 41.3 1.0
C A:LEU281 4.9 44.1 1.0
O A:HOH766 4.9 40.9 1.0
CZ A:ARG300 4.9 57.7 1.0

Chlorine binding site 2 out of 5 in 5mog

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Chlorine binding site 2 out of 5 in the Oryza Sativa Phytoene Desaturase Inhibited By Norflurazon


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Oryza Sativa Phytoene Desaturase Inhibited By Norflurazon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:53.3
occ:1.00
 CL B:NRF601 0.0 53.3 1.0
C2 B:NRF601 1.7 48.1 1.0
C3 B:NRF601 2.7 47.0 1.0
C1 B:NRF601 2.7 46.5 1.0
O B:NRF601 2.9 47.4 1.0
N B:NRF601 3.0 43.2 1.0
CB B:SER540 3.4 41.7 1.0
NH2 B:ARG300 3.7 49.9 1.0
O B:ALA539 3.8 46.2 1.0
N1 B:NRF601 4.0 47.5 1.0
CD1 B:LEU538 4.0 45.1 1.0
CD2 B:LEU281 4.0 51.5 1.0
OH B:TYR165 4.0 47.6 1.0
C4 B:NRF601 4.0 48.1 1.0
O B:LEU281 4.2 49.6 1.0
CA B:SER540 4.2 41.0 1.0
CB B:LEU538 4.3 42.0 1.0
O B:HOH708 4.4 38.2 1.0
C B:ALA539 4.4 46.4 1.0
OG B:SER540 4.5 42.6 1.0
C B:NRF601 4.5 39.7 1.0
N2 B:NRF601 4.5 47.9 1.0
N B:SER540 4.6 42.1 1.0
CA B:LEU281 4.7 45.7 1.0
O2 B:FAD600 4.7 41.4 1.0
C2 B:FAD600 4.8 42.6 1.0
CG B:LEU538 4.8 46.2 1.0
CB B:LEU281 4.8 45.9 1.0
CZ B:ARG300 4.9 61.3 1.0
C B:LEU281 4.9 49.1 1.0

Chlorine binding site 3 out of 5 in 5mog

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Chlorine binding site 3 out of 5 in the Oryza Sativa Phytoene Desaturase Inhibited By Norflurazon


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Oryza Sativa Phytoene Desaturase Inhibited By Norflurazon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl601

b:68.5
occ:1.00
 CL C:NRF601 0.0 68.5 1.0
C2 C:NRF601 1.7 65.7 1.0
C3 C:NRF601 2.7 63.6 1.0
C1 C:NRF601 2.7 64.6 1.0
O C:NRF601 2.9 64.1 1.0
N C:NRF601 3.0 61.8 1.0
CB C:SER540 3.4 54.5 1.0
NH2 C:ARG300 3.8 65.5 1.0
O C:ALA539 3.8 55.2 1.0
N1 C:NRF601 4.0 62.8 1.0
OH C:TYR165 4.0 67.5 1.0
CD2 C:LEU281 4.0 61.4 1.0
C4 C:NRF601 4.0 64.3 1.0
CD1 C:LEU538 4.0 63.9 1.0
CA C:SER540 4.2 52.5 1.0
O C:LEU281 4.2 55.4 1.0
CB C:LEU538 4.3 59.4 1.0
C C:ALA539 4.4 56.6 1.0
OG C:SER540 4.4 60.3 1.0
C C:NRF601 4.5 59.6 1.0
N2 C:NRF601 4.5 62.8 1.0
N C:SER540 4.6 52.4 1.0
O C:HOH709 4.6 60.0 1.0
CA C:LEU281 4.7 53.3 1.0
O2 C:FAD600 4.7 49.9 1.0
C2 C:FAD600 4.8 49.8 1.0
CG C:LEU538 4.8 63.9 1.0
CB C:LEU281 4.9 53.6 1.0
CZ C:ARG300 4.9 81.7 1.0
C C:LEU281 4.9 55.8 1.0

Chlorine binding site 4 out of 5 in 5mog

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Chlorine binding site 4 out of 5 in the Oryza Sativa Phytoene Desaturase Inhibited By Norflurazon


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Oryza Sativa Phytoene Desaturase Inhibited By Norflurazon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl601

b:62.2
occ:1.00
 CL D:NRF601 0.0 62.2 1.0
C2 D:NRF601 1.7 62.9 1.0
C3 D:NRF601 2.7 62.8 1.0
C1 D:NRF601 2.7 62.2 1.0
O D:NRF601 2.9 63.1 1.0
N D:NRF601 3.0 59.9 1.0
CB D:SER540 3.4 55.4 1.0
NH2 D:ARG300 3.8 53.9 1.0
O D:ALA539 3.8 54.8 1.0
N1 D:NRF601 4.0 63.6 1.0
OH D:TYR165 4.0 72.7 1.0
CD1 D:LEU538 4.0 60.2 1.0
C4 D:NRF601 4.0 62.7 1.0
CD2 D:LEU281 4.0 55.0 1.0
CA D:SER540 4.2 51.4 1.0
O D:LEU281 4.2 51.8 1.0
CB D:LEU538 4.3 56.3 1.0
C D:ALA539 4.4 55.8 1.0
O D:HOH706 4.4 45.8 1.0
OG D:SER540 4.4 62.3 1.0
C D:NRF601 4.5 57.3 1.0
N2 D:NRF601 4.5 63.3 1.0
N D:SER540 4.6 51.2 1.0
O2 D:FAD600 4.7 56.0 1.0
CA D:LEU281 4.7 50.4 1.0
C2 D:FAD600 4.7 54.0 1.0
CG D:LEU538 4.8 60.5 1.0
O D:HOH722 4.8 48.7 1.0
CB D:LEU281 4.9 50.5 1.0
C D:LEU281 4.9 52.9 1.0
CZ D:ARG300 4.9 75.7 1.0

Chlorine binding site 5 out of 5 in 5mog

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Chlorine binding site 5 out of 5 in the Oryza Sativa Phytoene Desaturase Inhibited By Norflurazon


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Oryza Sativa Phytoene Desaturase Inhibited By Norflurazon within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl601

b:1.0
occ:1.00
 CL E:NRF601 0.0 1.0 1.0
C2 E:NRF601 1.7 0.2 1.0
C3 E:NRF601 2.7 1.0 1.0
C1 E:NRF601 2.7 0.1 1.0
O E:NRF601 2.9 0.8 1.0
N E:NRF601 3.0 0.8 1.0
CB E:SER540 3.4 0.8 1.0
NH2 E:ARG300 3.8 91.0 1.0
O E:ALA539 3.8 0.5 1.0
N1 E:NRF601 4.0 0.7 1.0
OH E:TYR165 4.0 0.4 1.0
C4 E:NRF601 4.0 0.0 1.0
CD1 E:LEU538 4.0 0.8 1.0
CD2 E:LEU281 4.1 92.2 1.0
O E:LEU281 4.2 89.9 1.0
CA E:SER540 4.2 98.5 1.0
CB E:LEU538 4.3 0.9 1.0
C E:ALA539 4.4 0.6 1.0
OG E:SER540 4.4 0.4 1.0
C E:NRF601 4.5 0.8 1.0
N2 E:NRF601 4.5 0.0 1.0
N E:SER540 4.6 99.0 1.0
O2 E:FAD600 4.7 93.8 1.0
CA E:LEU281 4.7 86.2 1.0
C2 E:FAD600 4.7 94.5 1.0
CG E:LEU538 4.8 0.8 1.0
CB E:LEU281 4.9 86.1 1.0
C E:LEU281 4.9 90.9 1.0
CZ E:ARG300 4.9 0.4 1.0

Reference:

A.Brausemann, S.Gemmecker, J.Koschmieder, S.Ghisla, P.Beyer, O.Einsle. Structure of Phytoene Desaturase Provides Insights Into Herbicide Binding and Reaction Mechanisms Involved in Carotene Desaturation. Structure V. 25 1222 2017.
ISSN: ISSN 1878-4186
PubMed: 28669634
DOI: 10.1016/J.STR.2017.06.002
Page generated: Fri Jul 26 12:50:37 2024

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