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Chlorine in PDB 4ubs: The Crystal Structure of Cytochrome P450 105D7 From Streptomyces Avermitilis in Complex with Diclofenac

Enzymatic activity of The Crystal Structure of Cytochrome P450 105D7 From Streptomyces Avermitilis in Complex with Diclofenac

All present enzymatic activity of The Crystal Structure of Cytochrome P450 105D7 From Streptomyces Avermitilis in Complex with Diclofenac:
1.14.15.11;

Protein crystallography data

The structure of The Crystal Structure of Cytochrome P450 105D7 From Streptomyces Avermitilis in Complex with Diclofenac, PDB code: 4ubs was solved by L.H.Xu, H.Ikeda, T.Arakawa, T.Wakagi, H.Shoun, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.40 / 2.20
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 139.897, 139.897, 65.268, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 22.8

Other elements in 4ubs:

The structure of The Crystal Structure of Cytochrome P450 105D7 From Streptomyces Avermitilis in Complex with Diclofenac also contains other interesting chemical elements:

Iron (Fe) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Crystal Structure of Cytochrome P450 105D7 From Streptomyces Avermitilis in Complex with Diclofenac (pdb code 4ubs). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the The Crystal Structure of Cytochrome P450 105D7 From Streptomyces Avermitilis in Complex with Diclofenac, PDB code: 4ubs:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4ubs

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Chlorine binding site 1 out of 4 in the The Crystal Structure of Cytochrome P450 105D7 From Streptomyces Avermitilis in Complex with Diclofenac


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Crystal Structure of Cytochrome P450 105D7 From Streptomyces Avermitilis in Complex with Diclofenac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:56.8
occ:1.00
 CL2 A:DIF502 0.0 56.8 1.0
C2 A:DIF502 1.8 46.2 1.0
C1 A:DIF502 2.7 50.0 1.0
C3 A:DIF502 2.8 41.2 1.0
N1 A:DIF502 3.2 39.0 1.0
C4 A:PGE504 3.4 49.2 1.0
O1 A:PO4523 3.6 70.3 1.0
O1 A:DIF502 3.7 46.2 1.0
NH1 A:ARG70 3.8 41.6 1.0
O3 A:PO4523 3.9 60.7 1.0
C3 A:PGE504 3.9 53.4 1.0
C8 A:DIF502 4.0 36.3 1.0
C6 A:DIF502 4.0 45.1 1.0
C4 A:DIF502 4.1 39.6 1.0
CG1 A:VAL90 4.1 39.9 1.0
P A:PO4523 4.5 81.8 1.0
O3 A:PGE504 4.5 54.2 1.0
C9 A:DIF502 4.5 39.8 1.0
C5 A:DIF502 4.6 46.5 1.0
CE1 A:PHE82 4.6 44.5 1.0
CG2 A:VAL90 4.6 62.2 1.0
CZ A:ARG70 4.6 38.9 1.0
C14 A:DIF502 4.7 43.6 1.0
CB A:VAL90 4.8 44.9 1.0

Chlorine binding site 2 out of 4 in 4ubs

Go back to Chlorine Binding Sites List in 4ubs
Chlorine binding site 2 out of 4 in the The Crystal Structure of Cytochrome P450 105D7 From Streptomyces Avermitilis in Complex with Diclofenac


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Crystal Structure of Cytochrome P450 105D7 From Streptomyces Avermitilis in Complex with Diclofenac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:39.8
occ:1.00
 CL4 A:DIF502 0.0 39.8 1.0
C4 A:DIF502 1.7 39.6 1.0
C3 A:DIF502 2.7 41.2 1.0
C5 A:DIF502 2.7 46.5 1.0
N1 A:DIF502 2.9 39.0 1.0
C8 A:DIF502 3.2 36.3 1.0
C9 A:DIF502 3.4 39.8 1.0
CB A:ILE240 3.6 30.7 1.0
CD1 A:ILE240 3.6 35.2 1.0
CG2 A:ILE240 3.7 33.0 1.0
C6 A:DIF502 4.0 45.1 1.0
C2 A:DIF502 4.0 46.2 1.0
C7 A:DIF502 4.1 40.2 1.0
CG1 A:ILE240 4.1 33.6 1.0
O A:THR236 4.1 26.3 1.0
CG2 A:THR236 4.2 29.1 1.0
C10 A:DIF502 4.3 36.0 1.0
CA A:LEU237 4.3 27.3 1.0
CD2 A:LEU178 4.4 42.2 1.0
C1 A:DIF502 4.5 50.0 1.0
C A:THR236 4.6 26.8 1.0
CD2 A:LEU177 4.7 39.7 1.0
C13 A:DIF502 4.7 44.9 1.0
N A:LEU237 4.7 27.9 1.0
CD1 A:LEU237 4.9 37.6 1.0
C12 A:DIF502 4.9 38.0 1.0
C11 A:DIF502 5.0 37.8 1.0
CA A:ILE240 5.0 29.1 1.0
O A:LEU237 5.0 26.5 1.0

Chlorine binding site 3 out of 4 in 4ubs

Go back to Chlorine Binding Sites List in 4ubs
Chlorine binding site 3 out of 4 in the The Crystal Structure of Cytochrome P450 105D7 From Streptomyces Avermitilis in Complex with Diclofenac


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Crystal Structure of Cytochrome P450 105D7 From Streptomyces Avermitilis in Complex with Diclofenac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:41.8
occ:1.00
 CL2 A:DIF503 0.0 41.8 1.0
C2 A:DIF503 1.7 41.7 1.0
C3 A:DIF503 2.6 36.0 1.0
C1 A:DIF503 2.8 41.4 1.0
N1 A:DIF503 2.8 41.3 1.0
C1A A:HEM501 3.4 25.4 1.0
C2A A:HEM501 3.5 27.9 1.0
CBA A:HEM501 3.5 28.5 1.0
C3A A:HEM501 3.6 28.2 1.0
C4A A:HEM501 3.7 27.9 1.0
NA A:HEM501 3.8 29.1 1.0
C8 A:DIF503 3.9 41.0 1.0
CHA A:HEM501 4.0 25.1 1.0
C4 A:DIF503 4.0 42.9 1.0
C6 A:DIF503 4.0 40.7 1.0
O2 A:DIF503 4.1 39.5 1.0
CAA A:HEM501 4.1 28.5 1.0
CMA A:HEM501 4.4 31.9 1.0
C9 A:DIF503 4.4 38.9 1.0
CHB A:HEM501 4.5 28.7 1.0
C4D A:HEM501 4.5 29.2 1.0
CD2 A:LEU93 4.5 39.2 1.0
C5 A:DIF503 4.5 43.8 1.0
C6 A:DIF502 4.8 45.1 1.0
FE A:HEM501 4.8 28.7 1.0
CGA A:HEM501 4.9 33.8 1.0
CB A:ALA288 4.9 26.2 1.0
ND A:HEM501 4.9 26.5 1.0
C7 A:DIF503 5.0 44.3 1.0

Chlorine binding site 4 out of 4 in 4ubs

Go back to Chlorine Binding Sites List in 4ubs
Chlorine binding site 4 out of 4 in the The Crystal Structure of Cytochrome P450 105D7 From Streptomyces Avermitilis in Complex with Diclofenac


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Crystal Structure of Cytochrome P450 105D7 From Streptomyces Avermitilis in Complex with Diclofenac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:47.1
occ:1.00
 CL4 A:DIF503 0.0 47.1 1.0
C4 A:DIF503 1.8 42.9 1.0
C5 A:DIF503 2.8 43.8 1.0
C3 A:DIF503 2.8 36.0 1.0
N1 A:DIF503 3.2 41.3 1.0
C8 A:DIF503 3.3 41.0 1.0
C9 A:DIF503 3.5 38.9 1.0
O3 A:PGE504 3.6 54.2 1.0
C6 A:DIF502 3.9 45.1 1.0
C7 A:DIF503 4.0 44.3 1.0
C1 A:DIF502 4.0 50.0 1.0
C6 A:DIF503 4.1 40.7 1.0
C2 A:DIF503 4.1 41.7 1.0
C4 A:PGE504 4.2 49.2 1.0
C10 A:DIF503 4.3 40.0 1.0
O A:HOH712 4.3 42.4 1.0
CD2 A:LEU178 4.4 42.2 1.0
C5 A:PGE504 4.5 63.7 1.0
C5 A:DIF502 4.5 46.5 1.0
C3 A:PGE504 4.6 53.4 1.0
C2 A:DIF502 4.6 46.2 1.0
C13 A:DIF503 4.7 40.2 1.0
CB A:ILE392 4.7 40.5 1.0
C1 A:DIF503 4.7 41.4 1.0
CG2 A:ILE392 4.7 46.4 1.0
C12 A:DIF503 4.7 41.4 1.0
C6 A:PGE504 4.8 71.1 1.0
C11 A:DIF503 4.8 42.7 1.0

Reference:

L.H.Xu, H.Ikeda, L.Liu, T.Arakawa, T.Wakagi, H.Shoun, S.Fushinobu. Structural Basis For the 4'-Hydroxylation of Diclofenac By A Microbial Cytochrome P450 Monooxygenase. Appl.Microbiol.Biotechnol. 2014.
ISSN: ESSN 1432-0614
PubMed: 25341403
DOI: 10.1007/S00253-014-6148-Y
Page generated: Fri Jul 26 02:10:12 2024

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