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Iron in PDB 6q2c: Domain-Swapped Dimer of Acanthamoeba Castellanii CYP51

Protein crystallography data

The structure of Domain-Swapped Dimer of Acanthamoeba Castellanii CYP51, PDB code: 6q2c was solved by V.Sharma, L.M.Podust, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.51 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.350, 101.570, 123.740, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.7

Other elements in 6q2c:

The structure of Domain-Swapped Dimer of Acanthamoeba Castellanii CYP51 also contains other interesting chemical elements:

Potassium (K) 2 atoms
Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Domain-Swapped Dimer of Acanthamoeba Castellanii CYP51 (pdb code 6q2c). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Domain-Swapped Dimer of Acanthamoeba Castellanii CYP51, PDB code: 6q2c:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6q2c

Go back to Iron Binding Sites List in 6q2c
Iron binding site 1 out of 4 in the Domain-Swapped Dimer of Acanthamoeba Castellanii CYP51


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Domain-Swapped Dimer of Acanthamoeba Castellanii CYP51 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:35.7
occ:0.50
 FE A:HEM501 0.0 35.7 0.5
FE A:HEM501 0.1 34.3 0.5
ND A:HEM501 1.9 34.7 0.5
NB A:HEM501 2.0 33.5 0.5
NA A:HEM501 2.0 34.6 0.5
NA A:HEM501 2.0 33.5 0.5
ND A:HEM501 2.0 36.1 0.5
NB A:HEM501 2.1 35.3 0.5
NC A:HEM501 2.1 34.2 0.5
NC A:HEM501 2.1 33.4 0.5
SG A:CYS434 2.4 36.2 1.0
O A:HOH691 2.5 50.3 1.0
C1B A:HEM501 2.9 33.2 0.5
C4B A:HEM501 2.9 33.4 0.5
C4D A:HEM501 3.0 35.2 0.5
C1D A:HEM501 3.0 33.4 0.5
C4A A:HEM501 3.0 33.6 0.5
C1A A:HEM501 3.0 32.5 0.5
C4A A:HEM501 3.0 34.5 0.5
C4B A:HEM501 3.0 34.1 0.5
C4D A:HEM501 3.0 32.1 0.5
C1D A:HEM501 3.0 30.4 0.5
C1B A:HEM501 3.1 33.3 0.5
C4C A:HEM501 3.1 34.9 0.5
C1A A:HEM501 3.1 32.4 0.5
C1C A:HEM501 3.1 34.3 0.5
C4C A:HEM501 3.1 33.6 0.5
C1C A:HEM501 3.1 35.2 0.5
CHB A:HEM501 3.3 31.3 0.5
CHC A:HEM501 3.4 33.8 0.5
CHA A:HEM501 3.4 34.6 0.5
CHB A:HEM501 3.4 33.1 0.5
CHD A:HEM501 3.4 32.2 0.5
CHC A:HEM501 3.4 34.9 0.5
CHD A:HEM501 3.5 30.3 0.5
CHA A:HEM501 3.5 35.3 0.5
CB A:CYS434 3.5 35.8 1.0
O A:ALA294 4.1 36.2 1.0
C2B A:HEM501 4.1 31.3 0.5
CA A:CYS434 4.1 37.8 1.0
C3B A:HEM501 4.2 34.0 0.5
C2A A:HEM501 4.2 36.1 0.5
C3A A:HEM501 4.2 37.1 0.5
C3A A:HEM501 4.2 34.6 0.5
C2D A:HEM501 4.2 38.7 0.5
C3D A:HEM501 4.3 40.8 0.5
C3C A:HEM501 4.3 34.7 0.5
C2A A:HEM501 4.3 32.6 0.5
C2B A:HEM501 4.3 33.0 0.5
C3B A:HEM501 4.3 32.6 0.5
C3C A:HEM501 4.3 33.6 0.5
C2C A:HEM501 4.3 35.6 0.5
C3D A:HEM501 4.3 35.2 0.5
C2C A:HEM501 4.3 34.5 0.5
C2D A:HEM501 4.3 33.1 0.5
O A:HOH863 4.5 60.1 1.0
CB A:ALA294 4.7 35.3 1.0
N A:GLY436 4.8 35.7 1.0
C A:ALA294 4.8 35.8 1.0
C A:CYS434 4.9 38.6 1.0
N A:MET435 4.9 34.7 1.0

Iron binding site 2 out of 4 in 6q2c

Go back to Iron Binding Sites List in 6q2c
Iron binding site 2 out of 4 in the Domain-Swapped Dimer of Acanthamoeba Castellanii CYP51


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Domain-Swapped Dimer of Acanthamoeba Castellanii CYP51 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:34.3
occ:0.50
 FE A:HEM501 0.0 34.3 0.5
FE A:HEM501 0.1 35.7 0.5
ND A:HEM501 1.8 34.7 0.5
ND A:HEM501 1.9 36.1 0.5
NA A:HEM501 2.0 33.5 0.5
NA A:HEM501 2.0 34.6 0.5
NB A:HEM501 2.1 33.5 0.5
NC A:HEM501 2.1 34.2 0.5
NC A:HEM501 2.1 33.4 0.5
NB A:HEM501 2.2 35.3 0.5
SG A:CYS434 2.3 36.2 1.0
O A:HOH691 2.6 50.3 1.0
C1D A:HEM501 2.9 33.4 0.5
C4D A:HEM501 2.9 35.2 0.5
C4D A:HEM501 2.9 32.1 0.5
C1D A:HEM501 2.9 30.4 0.5
C1A A:HEM501 3.0 32.5 0.5
C1B A:HEM501 3.0 33.2 0.5
C4C A:HEM501 3.0 34.9 0.5
C4B A:HEM501 3.0 33.4 0.5
C4A A:HEM501 3.0 33.6 0.5
C4C A:HEM501 3.1 33.6 0.5
C1A A:HEM501 3.1 32.4 0.5
C4A A:HEM501 3.1 34.5 0.5
C1C A:HEM501 3.1 34.3 0.5
C4B A:HEM501 3.1 34.1 0.5
C1C A:HEM501 3.1 35.2 0.5
C1B A:HEM501 3.2 33.3 0.5
CHD A:HEM501 3.3 32.2 0.5
CHA A:HEM501 3.4 34.6 0.5
CHB A:HEM501 3.4 31.3 0.5
CHD A:HEM501 3.4 30.3 0.5
CHA A:HEM501 3.4 35.3 0.5
CHC A:HEM501 3.4 33.8 0.5
CB A:CYS434 3.5 35.8 1.0
CHB A:HEM501 3.5 33.1 0.5
CHC A:HEM501 3.5 34.9 0.5
CA A:CYS434 4.0 37.8 1.0
O A:ALA294 4.2 36.2 1.0
C2D A:HEM501 4.2 38.7 0.5
C3D A:HEM501 4.2 40.8 0.5
C2B A:HEM501 4.2 31.3 0.5
C2D A:HEM501 4.2 33.1 0.5
C3D A:HEM501 4.2 35.2 0.5
C3C A:HEM501 4.2 34.7 0.5
C2A A:HEM501 4.2 36.1 0.5
C3B A:HEM501 4.3 34.0 0.5
C3C A:HEM501 4.3 33.6 0.5
C3A A:HEM501 4.3 34.6 0.5
C3A A:HEM501 4.3 37.1 0.5
C2A A:HEM501 4.3 32.6 0.5
C2C A:HEM501 4.3 35.6 0.5
C2C A:HEM501 4.3 34.5 0.5
C2B A:HEM501 4.4 33.0 0.5
C3B A:HEM501 4.4 32.6 0.5
O A:HOH863 4.6 60.1 1.0
CB A:ALA294 4.7 35.3 1.0
N A:GLY436 4.7 35.7 1.0
C A:CYS434 4.8 38.6 1.0
N A:MET435 4.8 34.7 1.0
C A:ALA294 4.9 35.8 1.0

Iron binding site 3 out of 4 in 6q2c

Go back to Iron Binding Sites List in 6q2c
Iron binding site 3 out of 4 in the Domain-Swapped Dimer of Acanthamoeba Castellanii CYP51


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Domain-Swapped Dimer of Acanthamoeba Castellanii CYP51 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:35.0
occ:0.50
 FE B:HEM501 0.0 35.0 0.5
FE B:HEM501 0.2 35.8 0.5
NB B:HEM501 1.9 35.9 0.5
ND B:HEM501 1.9 35.2 0.5
NA B:HEM501 2.0 34.3 0.5
NA B:HEM501 2.0 32.8 0.5
ND B:HEM501 2.1 37.5 0.5
NC B:HEM501 2.1 34.2 0.5
NC B:HEM501 2.1 36.4 0.5
NB B:HEM501 2.1 34.2 0.5
SG B:CYS434 2.3 36.1 1.0
O B:HOH728 2.6 50.7 1.0
C1B B:HEM501 2.9 37.4 0.5
C4B B:HEM501 2.9 35.4 0.5
C1D B:HEM501 3.0 34.4 0.5
C4A B:HEM501 3.0 35.5 0.5
C4D B:HEM501 3.0 34.0 0.5
C4C B:HEM501 3.0 32.9 0.5
C4A B:HEM501 3.0 31.7 0.5
C1B B:HEM501 3.0 32.9 0.5
C1C B:HEM501 3.1 35.0 0.5
C1D B:HEM501 3.1 36.1 0.5
C4B B:HEM501 3.1 31.8 0.5
C4C B:HEM501 3.1 34.4 0.5
C1A B:HEM501 3.1 31.9 0.5
C1A B:HEM501 3.1 35.3 0.5
C1C B:HEM501 3.1 33.5 0.5
C4D B:HEM501 3.1 36.3 0.5
CHB B:HEM501 3.3 35.4 0.5
CHD B:HEM501 3.4 31.5 0.5
CHB B:HEM501 3.4 31.8 0.5
CHC B:HEM501 3.4 33.9 0.5
CB B:CYS434 3.4 38.4 1.0
CHD B:HEM501 3.5 34.2 0.5
CHA B:HEM501 3.5 34.9 0.5
CHC B:HEM501 3.5 31.5 0.5
CHA B:HEM501 3.6 36.0 0.5
CA B:CYS434 4.1 36.9 1.0
C2B B:HEM501 4.1 37.3 0.5
C3B B:HEM501 4.1 36.0 0.5
O B:ALA294 4.2 38.8 1.0
C3A B:HEM501 4.2 36.5 0.5
C2D B:HEM501 4.2 35.4 0.5
C3A B:HEM501 4.2 32.6 0.5
C2A B:HEM501 4.3 37.6 0.5
C3C B:HEM501 4.3 34.7 0.5
C3D B:HEM501 4.3 36.8 0.5
C2B B:HEM501 4.3 34.7 0.5
C2C B:HEM501 4.3 34.1 0.5
C2A B:HEM501 4.3 33.1 0.5
C3C B:HEM501 4.3 36.6 0.5
C2C B:HEM501 4.3 32.8 0.5
C3B B:HEM501 4.3 32.5 0.5
C2D B:HEM501 4.3 39.0 0.5
C3D B:HEM501 4.4 40.6 0.5
O B:HOH816 4.4 63.0 1.0
CB B:ALA294 4.7 38.6 1.0
N B:GLY436 4.7 35.8 1.0
C B:ALA294 4.8 36.9 1.0
C B:CYS434 4.8 36.1 1.0
N B:MET435 4.9 35.1 1.0

Iron binding site 4 out of 4 in 6q2c

Go back to Iron Binding Sites List in 6q2c
Iron binding site 4 out of 4 in the Domain-Swapped Dimer of Acanthamoeba Castellanii CYP51


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Domain-Swapped Dimer of Acanthamoeba Castellanii CYP51 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:35.8
occ:0.50
 FE B:HEM501 0.0 35.8 0.5
FE B:HEM501 0.2 35.0 0.5
ND B:HEM501 1.8 35.2 0.5
ND B:HEM501 1.9 37.5 0.5
NA B:HEM501 2.0 34.3 0.5
NA B:HEM501 2.0 32.8 0.5
NB B:HEM501 2.1 35.9 0.5
NC B:HEM501 2.1 36.4 0.5
NC B:HEM501 2.1 34.2 0.5
NB B:HEM501 2.2 34.2 0.5
SG B:CYS434 2.4 36.1 1.0
O B:HOH728 2.6 50.7 1.0
C1D B:HEM501 2.8 34.4 0.5
C4D B:HEM501 2.9 34.0 0.5
C1D B:HEM501 2.9 36.1 0.5
C4C B:HEM501 3.0 32.9 0.5
C4D B:HEM501 3.0 36.3 0.5
C1B B:HEM501 3.0 37.4 0.5
C4A B:HEM501 3.0 35.5 0.5
C1A B:HEM501 3.0 31.9 0.5
C4C B:HEM501 3.0 34.4 0.5
C1A B:HEM501 3.0 35.3 0.5
C4B B:HEM501 3.1 35.4 0.5
C4A B:HEM501 3.1 31.7 0.5
C1C B:HEM501 3.1 35.0 0.5
C1C B:HEM501 3.2 33.5 0.5
C1B B:HEM501 3.2 32.9 0.5
C4B B:HEM501 3.2 31.8 0.5
CHD B:HEM501 3.3 31.5 0.5
CHD B:HEM501 3.4 34.2 0.5
CHA B:HEM501 3.4 34.9 0.5
CHB B:HEM501 3.4 35.4 0.5
CB B:CYS434 3.4 38.4 1.0
CHA B:HEM501 3.5 36.0 0.5
CHB B:HEM501 3.5 31.8 0.5
CHC B:HEM501 3.5 33.9 0.5
CHC B:HEM501 3.6 31.5 0.5
CA B:CYS434 4.0 36.9 1.0
C2D B:HEM501 4.1 35.4 0.5
C3D B:HEM501 4.1 36.8 0.5
C2D B:HEM501 4.2 39.0 0.5
O B:ALA294 4.2 38.8 1.0
C2A B:HEM501 4.2 37.6 0.5
C3A B:HEM501 4.2 36.5 0.5
C2B B:HEM501 4.2 37.3 0.5
C3D B:HEM501 4.2 40.6 0.5
C3C B:HEM501 4.3 34.7 0.5
C2A B:HEM501 4.3 33.1 0.5
C3A B:HEM501 4.3 32.6 0.5
C3C B:HEM501 4.3 36.6 0.5
C3B B:HEM501 4.3 36.0 0.5
C2C B:HEM501 4.3 34.1 0.5
C2C B:HEM501 4.3 32.8 0.5
O B:HOH816 4.4 63.0 1.0
C2B B:HEM501 4.4 34.7 0.5
C3B B:HEM501 4.5 32.5 0.5
CB B:ALA294 4.6 38.6 1.0
N B:GLY436 4.7 35.8 1.0
C B:CYS434 4.8 36.1 1.0
N B:MET435 4.8 35.1 1.0
C B:ALA294 4.8 36.9 1.0

Reference:

V.Sharma, B.Shing, L.Hernandez-Alvarez, A.Debnath, L.M.Podust. Domain-Swap Dimerization of Acanthamoeba Castellanii CYP51 and A Unique Mechanism of Inactivation By Isavuconazole. Mol.Pharmacol. V. 98 770 2020.
ISSN: ESSN 1521-0111
PubMed: 33008918
DOI: 10.1124/MOLPHARM.120.000092
Page generated: Wed Aug 7 06:49:24 2024

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