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Iron in PDB 3r9b: Crystal Structure of Mycobacterium Smegmatis CYP164A2 in Ligand Free State

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Smegmatis CYP164A2 in Ligand Free State, PDB code: 3r9b was solved by C.R.J.Agnew, A.G.S.Warrilow, S.L.Kelly, R.L.Brady, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.45 / 1.89
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 178.396, 102.776, 92.412, 90.00, 90.06, 90.00
R / Rfree (%) 18.3 / 20.2

Other elements in 3r9b:

The structure of Crystal Structure of Mycobacterium Smegmatis CYP164A2 in Ligand Free State also contains other interesting chemical elements:

Potassium (K) 3 atoms
Sodium (Na) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Mycobacterium Smegmatis CYP164A2 in Ligand Free State (pdb code 3r9b). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Crystal Structure of Mycobacterium Smegmatis CYP164A2 in Ligand Free State, PDB code: 3r9b:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 3r9b

Go back to Iron Binding Sites List in 3r9b
Iron binding site 1 out of 3 in the Crystal Structure of Mycobacterium Smegmatis CYP164A2 in Ligand Free State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Mycobacterium Smegmatis CYP164A2 in Ligand Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:21.1
occ:1.00
FE A:HEM501 0.0 21.1 1.0
NB A:HEM501 2.0 19.5 1.0
ND A:HEM501 2.0 20.8 1.0
NC A:HEM501 2.1 19.9 1.0
NA A:HEM501 2.1 20.0 1.0
SG A:CYS366 2.3 7.7 1.0
C4B A:HEM501 3.0 20.5 1.0
C1B A:HEM501 3.1 21.4 1.0
C1D A:HEM501 3.1 21.9 1.0
C4D A:HEM501 3.1 22.0 1.0
C4A A:HEM501 3.1 19.1 1.0
C4C A:HEM501 3.1 20.1 1.0
C1C A:HEM501 3.1 20.5 1.0
C1A A:HEM501 3.1 19.9 1.0
CB A:CYS366 3.4 4.2 1.0
CHD A:HEM501 3.4 20.0 1.0
CHB A:HEM501 3.4 17.7 1.0
CHC A:HEM501 3.4 21.4 1.0
CHA A:HEM501 3.5 19.6 1.0
C6 A:D12509 3.7 40.9 1.0
CA A:CYS366 4.0 5.0 1.0
C5 A:D12509 4.2 40.6 1.0
C3B A:HEM501 4.2 20.8 1.0
C2B A:HEM501 4.3 20.6 1.0
C3D A:HEM501 4.3 20.6 1.0
C3A A:HEM501 4.3 18.6 1.0
C2D A:HEM501 4.3 20.1 1.0
C3C A:HEM501 4.3 21.3 1.0
C2A A:HEM501 4.3 19.1 1.0
C2C A:HEM501 4.3 19.1 1.0
N A:GLY368 4.4 7.0 1.0
C A:CYS366 4.7 5.4 1.0
N A:LEU367 4.7 6.4 1.0
CA A:GLY368 4.8 7.5 1.0
C7 A:D12509 4.8 42.5 1.0
C4 A:D12509 5.0 41.5 1.0

Iron binding site 2 out of 3 in 3r9b

Go back to Iron Binding Sites List in 3r9b
Iron binding site 2 out of 3 in the Crystal Structure of Mycobacterium Smegmatis CYP164A2 in Ligand Free State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Mycobacterium Smegmatis CYP164A2 in Ligand Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:20.5
occ:1.00
FE B:HEM501 0.0 20.5 1.0
NB B:HEM501 2.0 18.6 1.0
ND B:HEM501 2.0 20.3 1.0
NA B:HEM501 2.1 19.4 1.0
NC B:HEM501 2.1 18.5 1.0
SG B:CYS366 2.3 7.8 1.0
C4B B:HEM501 3.0 20.6 1.0
C1B B:HEM501 3.0 20.2 1.0
C4A B:HEM501 3.1 18.0 1.0
C1D B:HEM501 3.1 20.6 1.0
C4D B:HEM501 3.1 21.4 1.0
C1A B:HEM501 3.1 19.9 1.0
C4C B:HEM501 3.1 20.5 1.0
C1C B:HEM501 3.1 20.6 1.0
CB B:CYS366 3.4 4.1 1.0
CHB B:HEM501 3.4 18.0 1.0
CHC B:HEM501 3.4 21.4 1.0
CHA B:HEM501 3.5 19.7 1.0
CHD B:HEM501 3.5 20.2 1.0
CA B:CYS366 4.1 5.0 1.0
C8 B:D12509 4.1 47.7 1.0
C3B B:HEM501 4.2 19.6 1.0
C2B B:HEM501 4.2 20.0 1.0
C3A B:HEM501 4.3 17.5 1.0
C2A B:HEM501 4.3 18.1 1.0
C3D B:HEM501 4.3 20.6 1.0
C2D B:HEM501 4.3 19.0 1.0
C3C B:HEM501 4.3 22.1 1.0
C2C B:HEM501 4.3 20.5 1.0
C9 B:D12509 4.4 46.8 1.0
N B:GLY368 4.5 6.9 1.0
C7 B:D12509 4.6 48.3 1.0
C B:CYS366 4.7 5.2 1.0
N B:LEU367 4.7 6.5 1.0
CA B:GLY368 4.8 7.5 1.0

Iron binding site 3 out of 3 in 3r9b

Go back to Iron Binding Sites List in 3r9b
Iron binding site 3 out of 3 in the Crystal Structure of Mycobacterium Smegmatis CYP164A2 in Ligand Free State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Mycobacterium Smegmatis CYP164A2 in Ligand Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:21.2
occ:1.00
FE C:HEM501 0.0 21.2 1.0
NB C:HEM501 2.0 19.9 1.0
ND C:HEM501 2.0 19.2 1.0
NC C:HEM501 2.1 19.7 1.0
NA C:HEM501 2.1 20.0 1.0
SG C:CYS366 2.3 8.0 1.0
C1B C:HEM501 3.1 20.5 1.0
C4B C:HEM501 3.1 21.0 1.0
C1D C:HEM501 3.1 21.3 1.0
C4D C:HEM501 3.1 21.2 1.0
C4C C:HEM501 3.1 20.9 1.0
C4A C:HEM501 3.1 19.3 1.0
C1C C:HEM501 3.1 20.7 1.0
C1A C:HEM501 3.1 19.6 1.0
CB C:CYS366 3.4 4.2 1.0
CHD C:HEM501 3.4 21.0 1.0
CHB C:HEM501 3.4 18.8 1.0
CHC C:HEM501 3.5 21.3 1.0
CHA C:HEM501 3.5 18.4 1.0
C8 C:D12513 3.5 41.2 1.0
CA C:CYS366 4.0 5.2 1.0
C9 C:D12513 4.2 40.4 1.0
C3B C:HEM501 4.3 20.3 1.0
C2B C:HEM501 4.3 20.3 1.0
C3D C:HEM501 4.3 20.1 1.0
C2D C:HEM501 4.3 20.4 1.0
C3C C:HEM501 4.3 22.4 1.0
C3A C:HEM501 4.3 19.1 1.0
C2A C:HEM501 4.3 18.9 1.0
C2C C:HEM501 4.3 20.3 1.0
N C:GLY368 4.4 6.8 1.0
C7 C:D12513 4.5 42.0 1.0
C C:CYS366 4.7 5.5 1.0
N C:LEU367 4.7 6.5 1.0
CA C:GLY368 4.8 7.3 1.0

Reference:

C.R.Agnew, A.G.Warrilow, N.M.Burton, D.C.Lamb, S.L.Kelly, R.L.Brady. An Enlarged, Adaptable Active Site in CYP164 Family P450 Enzymes, the Sole P450 in Mycobacterium Leprae. Antimicrob.Agents Chemother. V. 56 391 2012.
ISSN: ISSN 0066-4804
PubMed: 22037849
DOI: 10.1128/AAC.05227-11
Page generated: Sun Dec 13 15:19:53 2020

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