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Iron in PDB 5l90: The Crystal Structure of Substrate-Free CYP109E1 From Bacillus Megaterium at 2.55 Angstrom Resolution

Protein crystallography data

The structure of The Crystal Structure of Substrate-Free CYP109E1 From Bacillus Megaterium at 2.55 Angstrom Resolution, PDB code: 5l90 was solved by I.K.Jozwik, A.M.W.H.Thunnissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.64 / 2.55
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 121.288, 121.288, 144.161, 90.00, 90.00, 120.00
R / Rfree (%) 21.4 / 25.9

Iron Binding Sites:

The binding sites of Iron atom in the The Crystal Structure of Substrate-Free CYP109E1 From Bacillus Megaterium at 2.55 Angstrom Resolution (pdb code 5l90). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the The Crystal Structure of Substrate-Free CYP109E1 From Bacillus Megaterium at 2.55 Angstrom Resolution, PDB code: 5l90:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 5l90

Go back to Iron Binding Sites List in 5l90
Iron binding site 1 out of 2 in the The Crystal Structure of Substrate-Free CYP109E1 From Bacillus Megaterium at 2.55 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of Substrate-Free CYP109E1 From Bacillus Megaterium at 2.55 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:35.8
occ:1.00
FE A:HEM501 0.0 35.8 1.0
NB A:HEM501 2.0 44.6 1.0
NC A:HEM501 2.1 49.5 1.0
NA A:HEM501 2.1 43.1 1.0
ND A:HEM501 2.1 48.5 1.0
SG A:CYS352 2.3 48.1 1.0
C4B A:HEM501 3.0 40.5 1.0
C1C A:HEM501 3.0 47.8 1.0
C4A A:HEM501 3.0 45.1 1.0
C1B A:HEM501 3.1 43.8 1.0
C4C A:HEM501 3.1 45.1 1.0
C1A A:HEM501 3.1 42.8 1.0
C4D A:HEM501 3.1 46.9 1.0
CB A:CYS352 3.1 40.0 1.0
C1D A:HEM501 3.1 46.4 1.0
CHC A:HEM501 3.4 43.1 1.0
CHB A:HEM501 3.4 41.3 1.0
CHA A:HEM501 3.5 45.3 1.0
CHD A:HEM501 3.5 45.9 1.0
CA A:CYS352 4.0 38.6 1.0
C3C A:HEM501 4.2 47.1 1.0
C3B A:HEM501 4.3 37.3 1.0
C3A A:HEM501 4.3 43.1 1.0
C2C A:HEM501 4.3 50.8 1.0
C2B A:HEM501 4.3 42.5 1.0
C2A A:HEM501 4.3 42.9 1.0
C2D A:HEM501 4.3 44.8 1.0
C3D A:HEM501 4.3 48.1 1.0
O A:ALA242 4.5 41.5 1.0
CB A:ALA242 4.5 42.9 1.0
C A:CYS352 4.7 44.8 1.0
N A:GLY354 4.8 41.5 1.0
C A:ALA242 4.9 46.2 1.0
CD1 A:PHE345 4.9 37.2 1.0
N A:LEU353 5.0 46.7 1.0

Iron binding site 2 out of 2 in 5l90

Go back to Iron Binding Sites List in 5l90
Iron binding site 2 out of 2 in the The Crystal Structure of Substrate-Free CYP109E1 From Bacillus Megaterium at 2.55 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of Substrate-Free CYP109E1 From Bacillus Megaterium at 2.55 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:47.8
occ:1.00
FE B:HEM501 0.0 47.8 1.0
NB B:HEM501 2.0 32.0 1.0
ND B:HEM501 2.0 32.4 1.0
NA B:HEM501 2.0 35.1 1.0
NC B:HEM501 2.1 31.0 1.0
SG B:CYS352 2.4 48.5 1.0
C1A B:HEM501 2.9 35.8 1.0
C4B B:HEM501 2.9 36.2 1.0
C4D B:HEM501 3.0 35.1 1.0
C1B B:HEM501 3.0 40.5 1.0
C4A B:HEM501 3.0 39.0 1.0
C1D B:HEM501 3.0 38.8 1.0
C4C B:HEM501 3.1 35.5 1.0
C1C B:HEM501 3.1 33.9 1.0
CHA B:HEM501 3.3 35.9 1.0
CB B:CYS352 3.3 51.8 1.0
CHC B:HEM501 3.4 35.1 1.0
CHB B:HEM501 3.4 45.4 1.0
CHD B:HEM501 3.4 44.0 1.0
CA B:CYS352 4.1 49.1 1.0
C3B B:HEM501 4.2 39.2 1.0
O B:ALA242 4.2 44.5 1.0
C2B B:HEM501 4.2 37.7 1.0
C3D B:HEM501 4.2 41.3 1.0
C2A B:HEM501 4.2 46.2 1.0
C3A B:HEM501 4.2 42.6 1.0
C2D B:HEM501 4.2 35.4 1.0
C3C B:HEM501 4.3 32.4 1.0
C2C B:HEM501 4.3 37.2 1.0
CB B:ALA242 4.6 49.5 1.0
C B:CYS352 4.8 51.6 1.0
C B:ALA242 4.8 44.1 1.0
N B:GLY354 4.8 52.3 1.0
CD1 B:PHE345 5.0 54.2 1.0
N B:LEU353 5.0 47.8 1.0

Reference:

I.K.Jozwik, F.M.Kiss, A.Abdulmughni, E.Brill, J.Zapp, J.Pleiss, R.Bernhardt, A.W.Thunnissen. Structural Basis of Steroid Binding and Oxidation By the Cytochrome P450 CYP109E1 From Bacillus Megaterium. Febs J. V. 283 4128 2016.
ISSN: ISSN 1742-464X
PubMed: 27686671
DOI: 10.1111/FEBS.13911
Page generated: Tue Aug 5 22:58:55 2025

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