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Chlorine in PDB 5ohf: Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide, Partially Reduced

Enzymatic activity of Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide, Partially Reduced

All present enzymatic activity of Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide, Partially Reduced:
2.7.13.3;

Protein crystallography data

The structure of Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide, Partially Reduced, PDB code: 5ohf was solved by T.Skalova, P.Kolenko, J.Dohnalek, M.Stranava, M.Martinkova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.17 / 1.80
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.685, 77.685, 441.238, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23.9

Other elements in 5ohf:

The structure of Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide, Partially Reduced also contains other interesting chemical elements:

Iron (Fe) 9 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide, Partially Reduced (pdb code 5ohf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide, Partially Reduced, PDB code: 5ohf:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5ohf

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Chlorine binding site 1 out of 5 in the Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide, Partially Reduced


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide, Partially Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:27.4
occ:1.00
 O B:HOH377 3.3 27.3 1.0
O A:HOH364 3.5 23.1 1.0
NH1 A:ARG139 3.5 29.2 1.0
NH1 B:ARG139 3.5 26.1 1.0
CD A:ARG139 3.6 26.5 1.0
CD B:ARG139 3.7 26.0 1.0
CD2 A:LEU135 4.0 25.8 1.0
CD2 B:LEU135 4.0 23.2 1.0
CD2 B:TYR125 4.2 26.7 1.0
CD2 A:TYR125 4.3 24.0 1.0
CZ A:ARG139 4.3 27.4 1.0
NE A:ARG139 4.3 26.8 1.0
CZ B:ARG139 4.4 25.9 1.0
NE B:ARG139 4.4 25.3 1.0
CD1 B:LEU135 4.5 22.5 1.0
CG A:LEU135 4.5 24.6 1.0
CG B:LEU135 4.5 22.5 1.0
CD1 A:LEU135 4.6 25.2 1.0
CG A:ARG139 4.7 25.1 1.0
CB A:TYR125 4.8 23.7 1.0
CB B:TYR125 4.8 26.2 1.0
CG B:ARG139 4.8 26.0 1.0
CG B:TYR125 5.0 26.5 1.0
CG A:TYR125 5.0 23.7 1.0

Chlorine binding site 2 out of 5 in 5ohf

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Chlorine binding site 2 out of 5 in the Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide, Partially Reduced


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide, Partially Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl202

b:32.2
occ:1.00
 O C:HOH363 3.3 30.0 1.0
NH1 C:ARG139 3.3 26.4 1.0
O D:HOH375 3.4 24.4 1.0
NH1 D:ARG139 3.4 28.0 1.0
CD D:ARG139 3.7 26.4 1.0
CD C:ARG139 3.8 26.5 1.0
CD2 D:LEU135 4.0 23.9 1.0
CD2 C:LEU135 4.2 24.1 1.0
CD1 D:TYR125 4.2 24.6 1.0
CD1 C:TYR125 4.3 26.7 1.0
CZ C:ARG139 4.3 27.7 1.0
CZ D:ARG139 4.3 28.4 1.0
NE D:ARG139 4.4 26.6 1.0
NE C:ARG139 4.4 25.1 1.0
CD1 C:LEU135 4.5 24.5 1.0
CG C:LEU135 4.5 23.9 1.0
CG D:LEU135 4.5 24.4 1.0
CD1 D:LEU135 4.6 24.4 1.0
CG D:ARG139 4.7 26.8 1.0
CB D:TYR125 4.8 23.2 1.0
CB C:TYR125 4.8 26.0 1.0
CG C:ARG139 4.8 25.5 1.0
CG C:TYR125 5.0 27.3 1.0
CG D:TYR125 5.0 24.1 1.0

Chlorine binding site 3 out of 5 in 5ohf

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Chlorine binding site 3 out of 5 in the Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide, Partially Reduced


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide, Partially Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl202

b:47.1
occ:1.00
 O F:HOH411 2.9 32.2 1.0
NE D:ARG55 3.0 29.9 1.0
NH2 D:ARG55 3.0 33.3 1.0
O F:HOH430 3.2 38.6 1.0
O F:HOH347 3.2 24.1 1.0
CZ D:ARG55 3.4 29.3 1.0
NH1 F:ARG39 3.8 23.3 1.0
O F:HOH348 3.9 46.0 1.0
O D:GLU52 3.9 41.2 1.0
NH1 F:ARG122 4.1 36.1 1.0
CD D:ARG55 4.1 28.5 1.0
CG F:ARG122 4.1 26.8 1.0
NH2 F:ARG39 4.2 22.5 1.0
CZ F:ARG39 4.2 23.4 1.0
CG D:ARG55 4.3 27.6 1.0
CG D:GLU52 4.6 42.2 1.0
O F:HOH397 4.6 28.5 1.0
CZ F:ARG122 4.7 35.8 1.0
CG2 D:THR56 4.7 32.5 1.0
NH1 D:ARG55 4.8 32.6 1.0
C D:GLU52 4.8 35.4 1.0
O F:HOH336 4.8 43.8 1.0
CA D:GLU52 4.8 34.1 1.0
CB F:ARG122 4.9 23.3 1.0

Chlorine binding site 4 out of 5 in 5ohf

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Chlorine binding site 4 out of 5 in the Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide, Partially Reduced


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide, Partially Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl203

b:23.5
occ:1.00
 O F:HOH378 3.3 24.2 1.0
O E:HOH378 3.3 21.9 1.0
NH1 E:ARG139 3.3 22.1 1.0
NH1 F:ARG139 3.5 23.9 1.0
CD F:ARG139 3.6 23.0 1.0
CD E:ARG139 3.7 21.1 1.0
CD2 F:LEU135 4.1 24.1 1.0
CD1 F:TYR125 4.2 25.9 1.0
CZ E:ARG139 4.2 22.1 1.0
CD1 E:TYR125 4.3 26.8 1.0
CD2 E:LEU135 4.3 23.5 1.0
CZ F:ARG139 4.3 24.1 1.0
NE F:ARG139 4.3 23.6 1.0
NE E:ARG139 4.4 21.2 1.0
CB F:TYR125 4.4 23.4 1.0
CG F:LEU135 4.6 23.9 1.0
CD1 F:LEU135 4.6 23.8 1.0
CB E:TYR125 4.6 24.4 1.0
CG F:ARG139 4.7 23.8 1.0
CG E:LEU135 4.7 22.4 1.0
CD1 E:LEU135 4.8 22.9 1.0
CG F:TYR125 4.8 24.8 1.0
CG E:ARG139 4.8 20.7 1.0
CG E:TYR125 4.9 25.8 1.0
O F:HOH440 4.9 28.7 1.0

Chlorine binding site 5 out of 5 in 5ohf

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Chlorine binding site 5 out of 5 in the Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide, Partially Reduced


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide, Partially Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl202

b:33.5
occ:1.00
 NH1 G:ARG139 3.3 30.9 1.0
O H:HOH370 3.4 23.7 1.0
O G:HOH340 3.4 38.1 1.0
NH1 H:ARG139 3.4 33.1 1.0
CD G:ARG139 3.7 30.6 1.0
CD H:ARG139 3.8 32.2 1.0
CD2 G:LEU135 4.1 29.4 1.0
CD2 H:LEU135 4.2 32.5 1.0
CD1 G:TYR125 4.2 33.2 1.0
CD1 H:TYR125 4.2 28.7 1.0
CZ G:ARG139 4.2 30.9 1.0
NE G:ARG139 4.3 31.1 1.0
CZ H:ARG139 4.4 32.3 1.0
NE H:ARG139 4.5 32.5 1.0
CD1 H:LEU135 4.5 32.5 1.0
CD1 G:LEU135 4.5 31.6 1.0
CG H:LEU135 4.6 32.9 1.0
CG G:LEU135 4.6 29.5 1.0
CB H:TYR125 4.7 26.4 1.0
CB G:TYR125 4.8 35.4 1.0
CG G:ARG139 4.8 30.9 1.0
CG H:ARG139 4.8 31.3 1.0
CG H:TYR125 4.9 26.9 1.0
CG G:TYR125 4.9 33.3 1.0
CE1 G:TYR125 5.0 32.4 1.0

Reference:

M.Stranava, P.Man, T.Skalova, P.Kolenko, J.Blaha, V.Fojtikova, V.Martinek, J.Dohnalek, A.Lengalova, M.Rosulek, T.Shimizu, M.Martinkova. Coordination and Redox State-Dependent Structural Changes of the Heme-Based Oxygen Sensor Afgchk Associated with Intraprotein Signal Transduction. J. Biol. Chem. V. 292 20921 2017.
ISSN: ESSN 1083-351X
PubMed: 29092908
DOI: 10.1074/JBC.M117.817023
Page generated: Fri Jul 26 14:28:38 2024

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