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Iron in PDB 5ofq: Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium

Protein crystallography data

The structure of Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium, PDB code: 5ofq 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) 49.93 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.125, 155.534, 158.151, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 27.5

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium (pdb code 5ofq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium, PDB code: 5ofq:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5ofq

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Iron binding site 1 out of 4 in the Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium


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 Substrate-Free CYP109A2 From Bacillus Megaterium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:40.4
occ:1.00
FE A:HEM501 0.0 40.4 1.0
NB A:HEM501 1.9 42.7 1.0
NA A:HEM501 1.9 44.5 1.0
ND A:HEM501 2.0 44.1 1.0
NC A:HEM501 2.1 42.7 1.0
SG A:CYS351 2.3 41.7 1.0
C1B A:HEM501 2.8 42.4 1.0
C4A A:HEM501 2.9 44.0 1.0
C1A A:HEM501 2.9 45.6 1.0
C4B A:HEM501 3.0 42.0 1.0
C4D A:HEM501 3.0 44.6 1.0
C1D A:HEM501 3.1 43.7 1.0
C4C A:HEM501 3.1 42.8 1.0
C1C A:HEM501 3.1 41.9 1.0
CHB A:HEM501 3.2 42.7 1.0
CHA A:HEM501 3.3 44.9 1.0
CHD A:HEM501 3.4 43.1 1.0
CHC A:HEM501 3.5 41.8 1.0
CB A:CYS351 3.5 42.1 1.0
O A:ALA241 3.9 41.2 1.0
C2B A:HEM501 4.1 41.1 1.0
C3A A:HEM501 4.1 44.3 1.0
C3B A:HEM501 4.1 41.0 1.0
C2A A:HEM501 4.2 44.9 1.0
CA A:CYS351 4.2 42.6 1.0
C3D A:HEM501 4.2 44.4 1.0
C2D A:HEM501 4.3 44.2 1.0
CB A:ALA241 4.3 41.2 1.0
C2C A:HEM501 4.4 41.7 1.0
C3C A:HEM501 4.4 42.1 1.0
C A:ALA241 4.6 41.0 1.0
N A:GLY353 4.9 41.5 1.0
CA A:ALA241 4.9 40.7 1.0
C A:CYS351 5.0 42.1 1.0

Iron binding site 2 out of 4 in 5ofq

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Iron binding site 2 out of 4 in the Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium


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 Substrate-Free CYP109A2 From Bacillus Megaterium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:49.5
occ:1.00
FE B:HEM501 0.0 49.5 1.0
NA B:HEM501 1.9 45.3 1.0
NB B:HEM501 2.0 44.4 1.0
ND B:HEM501 2.0 45.3 1.0
NC B:HEM501 2.1 44.2 1.0
SG B:CYS351 2.2 42.8 1.0
C4A B:HEM501 2.8 44.9 1.0
C1B B:HEM501 2.9 44.0 1.0
C1A B:HEM501 3.0 45.4 1.0
C4C B:HEM501 3.0 44.5 1.0
C1D B:HEM501 3.0 45.1 1.0
C4B B:HEM501 3.1 43.7 1.0
C4D B:HEM501 3.1 45.4 1.0
C1C B:HEM501 3.1 43.8 1.0
CHB B:HEM501 3.2 44.1 1.0
CHD B:HEM501 3.4 44.8 1.0
CHA B:HEM501 3.4 45.3 1.0
CB B:CYS351 3.5 43.1 1.0
CHC B:HEM501 3.5 43.4 1.0
O B:ALA241 3.8 43.7 1.0
C3A B:HEM501 4.1 44.9 1.0
C2A B:HEM501 4.2 45.3 1.0
C2B B:HEM501 4.2 43.3 1.0
CA B:CYS351 4.2 43.1 1.0
C3B B:HEM501 4.2 42.9 1.0
C2D B:HEM501 4.2 45.3 1.0
C3D B:HEM501 4.3 45.0 1.0
C3C B:HEM501 4.3 44.2 1.0
C2C B:HEM501 4.3 43.8 1.0
CB B:ALA241 4.3 44.0 1.0
C B:ALA241 4.6 43.6 1.0
N B:GLY353 5.0 41.2 1.0
CA B:ALA241 5.0 43.8 1.0

Iron binding site 3 out of 4 in 5ofq

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Iron binding site 3 out of 4 in the Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium


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 Substrate-Free CYP109A2 From Bacillus Megaterium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe503

b:49.8
occ:1.00
FE C:HEM503 0.0 49.8 1.0
NA C:HEM503 1.9 51.7 1.0
ND C:HEM503 2.0 50.6 1.0
NB C:HEM503 2.1 49.6 1.0
SG C:CYS351 2.1 47.3 1.0
NC C:HEM503 2.1 49.1 1.0
C1A C:HEM503 3.0 51.1 1.0
C4A C:HEM503 3.0 51.0 1.0
C4D C:HEM503 3.0 50.5 1.0
C1B C:HEM503 3.0 49.5 1.0
C1D C:HEM503 3.1 50.0 1.0
C4C C:HEM503 3.1 49.1 1.0
C4B C:HEM503 3.1 48.6 1.0
C1C C:HEM503 3.2 48.4 1.0
CHA C:HEM503 3.3 51.0 1.0
CHB C:HEM503 3.3 49.9 1.0
CHD C:HEM503 3.4 49.0 1.0
CB C:CYS351 3.5 47.6 1.0
CHC C:HEM503 3.5 47.9 1.0
CB C:ALA241 4.1 46.7 1.0
CA C:CYS351 4.1 47.1 1.0
C3A C:HEM503 4.2 50.7 1.0
C2A C:HEM503 4.2 50.9 1.0
O C:ALA241 4.2 46.0 1.0
C3D C:HEM503 4.2 49.5 1.0
C2D C:HEM503 4.3 49.9 1.0
C2B C:HEM503 4.3 48.6 1.0
C3B C:HEM503 4.3 47.9 1.0
C3C C:HEM503 4.3 48.9 1.0
C2C C:HEM503 4.4 48.1 1.0
C C:ALA241 4.7 45.5 1.0
N C:GLY353 4.9 46.2 1.0
C C:CYS351 4.9 46.3 1.0
N C:LEU352 4.9 46.4 1.0
OG1 C:THR245 5.0 45.9 1.0
CA C:ALA241 5.0 44.9 1.0

Iron binding site 4 out of 4 in 5ofq

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Iron binding site 4 out of 4 in the Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Substrate-Free CYP109A2 From Bacillus Megaterium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:47.1
occ:1.00
FE D:HEM501 0.0 47.1 1.0
NA D:HEM501 1.9 51.4 1.0
NB D:HEM501 1.9 48.5 1.0
ND D:HEM501 2.1 51.8 1.0
SG D:CYS351 2.2 49.3 1.0
NC D:HEM501 2.2 49.5 1.0
C4A D:HEM501 2.8 50.3 1.0
C1B D:HEM501 2.9 48.3 1.0
C1A D:HEM501 2.9 52.2 1.0
C4D D:HEM501 3.0 52.7 1.0
C4B D:HEM501 3.0 47.6 1.0
C1D D:HEM501 3.1 52.1 1.0
CHB D:HEM501 3.2 48.9 1.0
C1C D:HEM501 3.2 48.4 1.0
C4C D:HEM501 3.2 49.9 1.0
CHA D:HEM501 3.4 52.9 1.0
CB D:CYS351 3.4 49.7 1.0
CHC D:HEM501 3.5 47.4 1.0
CHD D:HEM501 3.6 51.0 1.0
O D:ALA241 4.0 46.9 1.0
C3A D:HEM501 4.0 50.9 1.0
CA D:CYS351 4.1 50.6 1.0
C2A D:HEM501 4.1 51.7 1.0
C2B D:HEM501 4.1 46.8 1.0
C3B D:HEM501 4.2 46.4 1.0
CB D:ALA241 4.3 48.8 1.0
C3D D:HEM501 4.3 53.3 1.0
C2D D:HEM501 4.3 53.4 1.0
C3C D:HEM501 4.4 49.1 1.0
C2C D:HEM501 4.4 48.4 1.0
C D:ALA241 4.7 46.7 1.0
C D:CYS351 4.9 51.0 1.0
N D:GLY353 4.9 50.5 1.0
N D:LEU352 4.9 51.9 1.0
CA D:ALA241 5.0 46.9 1.0

Reference:

A.Abdulmughni, I.K.Jozwik, E.Brill, F.Hannemann, A.W.H.Thunnissen, R.Bernhardt. Biochemical and Structural Characterization of CYP109A2, A Vitamin D3 25-Hydroxylase From Bacillus Megaterium. Febs J. V. 284 3881 2017.
ISSN: ISSN 1742-4658
PubMed: 28940959
DOI: 10.1111/FEBS.14276
Page generated: Sun Dec 13 16:10:36 2020

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