Chlorine in PDB 8qmz: Soluble Epoxide Hydrolase in Complex with RK4

Enzymatic activity of Soluble Epoxide Hydrolase in Complex with RK4

All present enzymatic activity of Soluble Epoxide Hydrolase in Complex with RK4:
3.1.3.76; 3.3.2.10;

Protein crystallography data

The structure of Soluble Epoxide Hydrolase in Complex with RK4, PDB code: 8qmz was solved by A.Kumar, F.Zhu, J.M.H.Ehrler, F.Li, C.Empel, Y.Xu, I.Atodiresei, R.M.Koenigs, E.Proschak, S.Knapp, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.47 / 1.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.29, 90.642, 188.416, 90, 90, 90
R / Rfree (%) 18.8 / 21.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Soluble Epoxide Hydrolase in Complex with RK4 (pdb code 8qmz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Soluble Epoxide Hydrolase in Complex with RK4, PDB code: 8qmz:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 8qmz

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Chlorine binding site 1 out of 8 in the Soluble Epoxide Hydrolase in Complex with RK4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Soluble Epoxide Hydrolase in Complex with RK4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:27.0
occ:1.00
 CL1 A:W6O601 0.0 27.0 1.0
C17 A:W6O601 1.7 19.2 1.0
C18 A:W6O601 2.7 18.3 1.0
C16 A:W6O601 2.7 18.0 1.0
C15 A:W6O601 3.1 18.4 1.0
CD1 A:PHE267 3.9 14.8 1.0
C19 A:W6O601 3.9 20.1 1.0
O A:PHE267 4.0 14.2 1.0
CE A:MET419 4.0 24.5 1.0
C21 A:W6O601 4.0 18.4 1.0
CE1 A:PHE267 4.1 15.3 1.0
CH2 A:TRP525 4.2 14.4 1.0
CD2 A:LEU408 4.3 17.3 1.0
CD A:PRO268 4.5 13.5 1.0
C20 A:W6O601 4.5 18.6 1.0
CZ2 A:TRP525 4.5 14.0 1.0
N2 A:W6O601 4.5 17.9 1.0
SD A:MET419 4.6 28.2 1.0
C A:PHE267 4.8 14.2 1.0
OH A:TYR466 4.9 16.6 1.0
CD1 A:LEU408 4.9 18.1 1.0

Chlorine binding site 2 out of 8 in 8qmz

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Chlorine binding site 2 out of 8 in the Soluble Epoxide Hydrolase in Complex with RK4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Soluble Epoxide Hydrolase in Complex with RK4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:25.1
occ:1.00
 CL2 A:W6O601 0.0 25.1 1.0
C19 A:W6O601 1.7 20.1 1.0
C20 A:W6O601 2.7 18.6 1.0
C18 A:W6O601 2.7 18.3 1.0
O2 A:EDO605 3.6 34.6 1.0
O A:HOH816 3.7 27.6 1.0
CB A:HIS524 3.7 13.1 1.0
C2 A:EDO605 3.9 28.6 1.0
C1 A:EDO605 3.9 31.5 1.0
C21 A:W6O601 3.9 18.4 1.0
C17 A:W6O601 3.9 19.2 1.0
CG A:MET419 3.9 23.2 1.0
CG A:HIS524 4.0 13.6 1.0
CG2 A:VAL498 4.2 21.2 1.0
O A:HOH884 4.2 29.4 1.0
CD2 A:HIS524 4.3 12.8 1.0
O A:HOH735 4.4 24.2 1.0
O A:HOH748 4.4 21.6 1.0
C16 A:W6O601 4.5 18.0 1.0
O1 A:EDO605 4.5 31.0 1.0
CZ2 A:TRP525 4.7 14.0 1.0
ND1 A:HIS524 4.7 15.5 1.0
NE1 A:TRP525 4.7 16.3 1.0
SD A:MET419 4.8 28.2 1.0
CE2 A:TRP525 4.9 13.6 1.0
CB A:VAL498 4.9 19.9 1.0

Chlorine binding site 3 out of 8 in 8qmz

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Chlorine binding site 3 out of 8 in the Soluble Epoxide Hydrolase in Complex with RK4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Soluble Epoxide Hydrolase in Complex with RK4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:28.8
occ:1.00
 CL1 B:W6O601 0.0 28.8 1.0
C17 B:W6O601 1.8 22.5 1.0
C18 B:W6O601 2.7 19.9 1.0
C16 B:W6O601 2.8 20.1 1.0
C15 B:W6O601 3.2 20.0 1.0
CD2 B:PHE267 3.8 18.3 1.0
CE B:MET419 3.9 30.7 1.0
O B:PHE267 3.9 13.7 1.0
C19 B:W6O601 4.0 17.4 1.0
C21 B:W6O601 4.0 18.4 1.0
CE2 B:PHE267 4.1 17.2 1.0
CH2 B:TRP525 4.2 16.7 1.0
CD2 B:LEU408 4.3 20.3 1.0
CD B:PRO268 4.5 14.5 1.0
CZ2 B:TRP525 4.5 16.0 1.0
SD B:MET419 4.5 28.4 1.0
C20 B:W6O601 4.5 17.9 1.0
N2 B:W6O601 4.6 21.2 1.0
C B:PHE267 4.8 15.4 1.0
OH B:TYR466 4.9 19.7 1.0
CD1 B:LEU408 4.9 16.9 1.0

Chlorine binding site 4 out of 8 in 8qmz

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Chlorine binding site 4 out of 8 in the Soluble Epoxide Hydrolase in Complex with RK4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Soluble Epoxide Hydrolase in Complex with RK4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:25.6
occ:1.00
 CL2 B:W6O601 0.0 25.6 1.0
C19 B:W6O601 1.8 17.4 1.0
C20 B:W6O601 2.6 17.9 1.0
C18 B:W6O601 2.7 19.9 1.0
O B:HOH836 3.6 36.4 1.0
C1 B:EDO604 3.7 34.3 1.0
CB B:HIS524 3.7 14.4 1.0
O2 B:EDO604 3.7 38.5 1.0
C2 B:EDO604 3.8 35.7 1.0
CG2 B:VAL498 3.9 22.9 1.0
C21 B:W6O601 3.9 18.4 1.0
CG B:HIS524 3.9 12.9 1.0
CG B:MET419 4.0 26.4 1.0
C17 B:W6O601 4.0 22.5 1.0
O B:HOH876 4.1 30.2 1.0
CD2 B:HIS524 4.3 14.3 1.0
O B:HOH761 4.3 24.0 1.0
O B:HOH791 4.4 24.9 1.0
O1 B:EDO604 4.4 39.0 1.0
C16 B:W6O601 4.5 20.1 1.0
O B:HOH869 4.6 47.1 1.0
ND1 B:HIS524 4.6 13.6 1.0
CZ2 B:TRP525 4.7 16.0 1.0
NE1 B:TRP525 4.7 15.5 1.0
CB B:VAL498 4.8 20.2 1.0
SD B:MET419 4.9 28.4 1.0
CE2 B:TRP525 4.9 14.9 1.0

Chlorine binding site 5 out of 8 in 8qmz

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Chlorine binding site 5 out of 8 in the Soluble Epoxide Hydrolase in Complex with RK4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Soluble Epoxide Hydrolase in Complex with RK4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl601

b:26.3
occ:1.00
 CL1 C:W6O601 0.0 26.3 1.0
C17 C:W6O601 1.8 19.3 1.0
C18 C:W6O601 2.7 18.7 1.0
C16 C:W6O601 2.7 17.4 1.0
C15 C:W6O601 3.1 17.9 1.0
CE C:MET419 3.8 26.5 1.0
CD1 C:PHE267 3.9 14.8 1.0
O C:PHE267 3.9 13.2 1.0
C19 C:W6O601 4.0 18.1 1.0
C21 C:W6O601 4.0 17.7 1.0
CE1 C:PHE267 4.1 16.3 1.0
CH2 C:TRP525 4.1 14.9 1.0
CD2 C:LEU408 4.3 20.6 1.0
CD C:PRO268 4.4 12.6 1.0
C20 C:W6O601 4.5 20.1 1.0
CZ2 C:TRP525 4.5 15.2 1.0
SD C:MET419 4.6 25.4 1.0
N2 C:W6O601 4.6 17.8 1.0
C C:PHE267 4.8 13.8 1.0
OH C:TYR466 4.9 16.7 1.0
CD1 C:LEU408 4.9 17.3 1.0

Chlorine binding site 6 out of 8 in 8qmz

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Chlorine binding site 6 out of 8 in the Soluble Epoxide Hydrolase in Complex with RK4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Soluble Epoxide Hydrolase in Complex with RK4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl601

b:26.0
occ:1.00
 CL2 C:W6O601 0.0 26.0 1.0
C19 C:W6O601 1.7 18.1 1.0
C20 C:W6O601 2.6 20.1 1.0
C18 C:W6O601 2.7 18.7 1.0
O C:HOH831 3.6 29.4 1.0
O2 C:EDO602 3.6 35.1 1.0
CB C:HIS524 3.7 13.5 1.0
C2 C:EDO602 3.8 36.4 1.0
C1 C:EDO602 3.8 34.0 1.0
C21 C:W6O601 3.9 17.7 1.0
CG C:HIS524 4.0 13.5 1.0
CG C:MET419 4.0 24.4 1.0
C17 C:W6O601 4.0 19.3 1.0
O C:HOH857 4.1 24.1 1.0
CG2 C:VAL498 4.2 20.0 1.0
CD2 C:HIS524 4.2 13.4 1.0
O C:HOH761 4.4 21.7 1.0
C16 C:W6O601 4.5 17.4 1.0
O C:HOH758 4.5 27.0 1.0
O C:HOH868 4.5 50.6 1.0
O1 C:EDO602 4.6 34.0 1.0
CZ2 C:TRP525 4.6 15.2 1.0
NE1 C:TRP525 4.7 17.0 1.0
ND1 C:HIS524 4.7 14.2 1.0
SD C:MET419 4.8 25.4 1.0
CE2 C:TRP525 4.9 14.8 1.0
CB C:VAL498 4.9 19.2 1.0

Chlorine binding site 7 out of 8 in 8qmz

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Chlorine binding site 7 out of 8 in the Soluble Epoxide Hydrolase in Complex with RK4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Soluble Epoxide Hydrolase in Complex with RK4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl601

b:29.8
occ:1.00
 CL1 D:W6O601 0.0 29.8 1.0
C17 D:W6O601 1.8 21.6 1.0
C18 D:W6O601 2.7 20.4 1.0
C16 D:W6O601 2.8 20.2 1.0
C15 D:W6O601 3.1 18.6 1.0
CD1 D:PHE267 3.8 18.4 1.0
C19 D:W6O601 4.0 20.7 1.0
CE D:MET419 4.0 31.1 1.0
O D:PHE267 4.0 17.6 1.0
C21 D:W6O601 4.0 19.8 1.0
CE1 D:PHE267 4.0 18.2 1.0
CH2 D:TRP525 4.2 18.1 1.0
CD2 D:LEU408 4.3 22.1 1.0
SD D:MET419 4.5 31.7 1.0
CD D:PRO268 4.5 16.3 1.0
CZ2 D:TRP525 4.5 18.8 1.0
C20 D:W6O601 4.5 21.3 1.0
N2 D:W6O601 4.6 19.6 1.0
C D:PHE267 4.8 16.1 1.0
OH D:TYR466 4.9 22.3 1.0
CD1 D:LEU408 5.0 18.3 1.0

Chlorine binding site 8 out of 8 in 8qmz

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Chlorine binding site 8 out of 8 in the Soluble Epoxide Hydrolase in Complex with RK4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Soluble Epoxide Hydrolase in Complex with RK4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl601

b:27.1
occ:1.00
 CL2 D:W6O601 0.0 27.1 1.0
C19 D:W6O601 1.8 20.7 1.0
C20 D:W6O601 2.7 21.3 1.0
C18 D:W6O601 2.7 20.4 1.0
C2 D:EDO605 3.6 33.5 1.0
O1 D:EDO605 3.6 35.8 1.0
O D:HOH860 3.6 29.6 1.0
CB D:HIS524 3.8 13.5 1.0
C1 D:EDO605 3.8 31.2 1.0
CG D:MET419 3.9 25.9 1.0
C21 D:W6O601 4.0 19.8 1.0
C17 D:W6O601 4.0 21.6 1.0
CG D:HIS524 4.0 12.9 1.0
CG2 D:VAL498 4.0 23.8 1.0
O D:HOH883 4.1 29.5 1.0
CD2 D:HIS524 4.3 13.4 1.0
O D:HOH805 4.4 22.4 1.0
O D:HOH760 4.4 28.0 1.0
O2 D:EDO605 4.5 31.6 1.0
C16 D:W6O601 4.5 20.2 1.0
CZ2 D:TRP525 4.6 18.8 1.0
NE1 D:TRP525 4.6 16.5 1.0
ND1 D:HIS524 4.7 13.8 1.0
SD D:MET419 4.8 31.7 1.0
CE2 D:TRP525 4.8 16.9 1.0
CB D:VAL498 4.9 22.8 1.0

Reference:

F.Li, W.F.Zhu, C.Empel, O.Datsenko, A.Kumar, Y.Xu, J.H.M.Ehrler, I.Atodiresei, S.Knapp, P.K.Mykhailiuk, E.Proschak, R.M.Koenigs. Photosensitization Enables Pauson-Khand-Type Reactions with Nitrenes. Science V. 383 498 2024.
ISSN: ESSN 1095-9203
PubMed: 38301027
DOI: 10.1126/SCIENCE.ADM8095
Page generated: Tue Jul 30 12:01:42 2024

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