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Iron in PDB 6wk3: Engineered Carbene Transferase Rmanod Q52V, Putative Nitric Oxide Dioxygenase From Rhodothermus Marinus

Enzymatic activity of Engineered Carbene Transferase Rmanod Q52V, Putative Nitric Oxide Dioxygenase From Rhodothermus Marinus

All present enzymatic activity of Engineered Carbene Transferase Rmanod Q52V, Putative Nitric Oxide Dioxygenase From Rhodothermus Marinus:
1.14.12.17;

Protein crystallography data

The structure of Engineered Carbene Transferase Rmanod Q52V, Putative Nitric Oxide Dioxygenase From Rhodothermus Marinus, PDB code: 6wk3 was solved by A.M.Knight, F.H.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.67 / 2.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 124.269, 102.472, 84.273, 90.00, 98.53, 90.00
R / Rfree (%) 20.8 / 24.7

Other elements in 6wk3:

The structure of Engineered Carbene Transferase Rmanod Q52V, Putative Nitric Oxide Dioxygenase From Rhodothermus Marinus also contains other interesting chemical elements:

Copper (Cu) 6 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Engineered Carbene Transferase Rmanod Q52V, Putative Nitric Oxide Dioxygenase From Rhodothermus Marinus (pdb code 6wk3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Engineered Carbene Transferase Rmanod Q52V, Putative Nitric Oxide Dioxygenase From Rhodothermus Marinus, PDB code: 6wk3:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6wk3

Go back to Iron Binding Sites List in 6wk3
Iron binding site 1 out of 4 in the Engineered Carbene Transferase Rmanod Q52V, Putative Nitric Oxide Dioxygenase From Rhodothermus Marinus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Engineered Carbene Transferase Rmanod Q52V, Putative Nitric Oxide Dioxygenase From Rhodothermus Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:62.9
occ:1.00
 FE A:HEM201 0.0 62.9 1.0
NC A:HEM201 2.0 53.8 1.0
NA A:HEM201 2.0 51.5 1.0
ND A:HEM201 2.0 52.4 1.0
NB A:HEM201 2.1 54.0 1.0
NE2 A:HIS84 2.4 50.7 1.0
OXT A:ACT202 2.7 53.5 1.0
C1C A:HEM201 3.0 54.3 1.0
C1A A:HEM201 3.0 52.3 1.0
C4D A:HEM201 3.1 48.4 1.0
C4C A:HEM201 3.1 50.7 1.0
C4B A:HEM201 3.1 50.6 1.0
C4A A:HEM201 3.1 51.9 1.0
C1D A:HEM201 3.1 49.9 1.0
C1B A:HEM201 3.1 51.0 1.0
CD2 A:HIS84 3.4 48.8 1.0
CE1 A:HIS84 3.4 55.1 1.0
CHD A:HEM201 3.4 52.5 1.0
CHC A:HEM201 3.4 49.8 1.0
CHA A:HEM201 3.4 50.9 1.0
CHB A:HEM201 3.4 49.1 1.0
C A:ACT202 3.6 55.8 1.0
O A:ACT202 3.8 57.5 1.0
C2C A:HEM201 4.2 52.8 1.0
C2A A:HEM201 4.3 49.9 1.0
C3C A:HEM201 4.3 54.2 1.0
C3A A:HEM201 4.3 52.0 1.0
C3D A:HEM201 4.3 51.1 1.0
C2D A:HEM201 4.3 55.1 1.0
C3B A:HEM201 4.3 56.6 1.0
C2B A:HEM201 4.3 53.6 1.0
ND1 A:HIS84 4.5 53.6 1.0
CG A:HIS84 4.5 47.5 1.0
CD1 A:LEU56 5.0 56.5 1.0

Iron binding site 2 out of 4 in 6wk3

Go back to Iron Binding Sites List in 6wk3
Iron binding site 2 out of 4 in the Engineered Carbene Transferase Rmanod Q52V, Putative Nitric Oxide Dioxygenase From Rhodothermus Marinus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Engineered Carbene Transferase Rmanod Q52V, Putative Nitric Oxide Dioxygenase From Rhodothermus Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:62.4
occ:1.00
 FE B:HEM201 0.0 62.4 1.0
NB B:HEM201 2.0 54.7 1.0
NC B:HEM201 2.0 55.3 1.0
ND B:HEM201 2.1 52.8 1.0
NA B:HEM201 2.1 53.6 1.0
NE2 B:HIS84 2.4 50.7 1.0
OXT B:ACT202 2.7 55.6 1.0
C4B B:HEM201 3.0 54.9 1.0
C1C B:HEM201 3.0 56.1 1.0
C1B B:HEM201 3.0 51.7 1.0
C1A B:HEM201 3.1 52.6 1.0
C4D B:HEM201 3.1 50.7 1.0
C1D B:HEM201 3.1 53.2 1.0
C4C B:HEM201 3.1 50.5 1.0
C4A B:HEM201 3.1 49.6 1.0
CH3 B:ACT202 3.1 54.6 1.0
C B:ACT202 3.3 51.4 1.0
CD2 B:HIS84 3.3 51.3 1.0
CHC B:HEM201 3.4 52.7 1.0
CHA B:HEM201 3.4 51.4 1.0
CHB B:HEM201 3.4 52.3 1.0
CE1 B:HIS84 3.4 51.1 1.0
CHD B:HEM201 3.4 52.5 1.0
C3B B:HEM201 4.2 52.8 1.0
C2B B:HEM201 4.2 51.7 1.0
C2C B:HEM201 4.3 53.1 1.0
C2A B:HEM201 4.3 52.0 1.0
C3C B:HEM201 4.3 54.4 1.0
C3D B:HEM201 4.3 52.4 1.0
C2D B:HEM201 4.3 54.8 1.0
C3A B:HEM201 4.3 49.1 1.0
O B:ACT202 4.4 55.5 1.0
CG B:HIS84 4.5 52.8 1.0
ND1 B:HIS84 4.5 51.1 1.0

Iron binding site 3 out of 4 in 6wk3

Go back to Iron Binding Sites List in 6wk3
Iron binding site 3 out of 4 in the Engineered Carbene Transferase Rmanod Q52V, Putative Nitric Oxide Dioxygenase From Rhodothermus Marinus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Engineered Carbene Transferase Rmanod Q52V, Putative Nitric Oxide Dioxygenase From Rhodothermus Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:61.9
occ:1.00
 FE C:HEM201 0.0 61.9 1.0
ND C:HEM201 2.0 53.8 1.0
NA C:HEM201 2.0 51.5 1.0
NB C:HEM201 2.0 52.6 1.0
NC C:HEM201 2.0 54.5 1.0
NE2 C:HIS84 2.5 48.8 1.0
O C:ACT203 2.8 56.7 1.0
OXT C:ACT203 2.9 51.5 1.0
C1D C:HEM201 3.0 53.7 1.0
C4A C:HEM201 3.0 53.6 1.0
C1B C:HEM201 3.0 54.0 1.0
C4C C:HEM201 3.1 52.6 1.0
C4D C:HEM201 3.1 48.6 1.0
C1A C:HEM201 3.1 53.4 1.0
C1C C:HEM201 3.1 53.4 1.0
C4B C:HEM201 3.1 52.9 1.0
C C:ACT203 3.1 53.1 1.0
CD2 C:HIS84 3.4 50.9 1.0
CHB C:HEM201 3.4 52.5 1.0
CHD C:HEM201 3.4 53.7 1.0
CHA C:HEM201 3.4 52.2 1.0
CHC C:HEM201 3.4 50.8 1.0
CE1 C:HIS84 3.5 51.9 1.0
C2D C:HEM201 4.3 51.9 1.0
C3A C:HEM201 4.3 52.5 1.0
C3D C:HEM201 4.3 58.8 1.0
C2A C:HEM201 4.3 52.5 1.0
C2C C:HEM201 4.3 53.9 1.0
C3C C:HEM201 4.3 50.8 1.0
C2B C:HEM201 4.3 50.9 1.0
C3B C:HEM201 4.3 49.5 1.0
CG C:HIS84 4.5 50.6 1.0
ND1 C:HIS84 4.6 50.9 1.0
CH3 C:ACT203 4.7 54.4 1.0

Iron binding site 4 out of 4 in 6wk3

Go back to Iron Binding Sites List in 6wk3
Iron binding site 4 out of 4 in the Engineered Carbene Transferase Rmanod Q52V, Putative Nitric Oxide Dioxygenase From Rhodothermus Marinus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Engineered Carbene Transferase Rmanod Q52V, Putative Nitric Oxide Dioxygenase From Rhodothermus Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:68.1
occ:1.00
 FE D:HEM201 0.0 68.1 1.0
NB D:HEM201 2.0 57.0 1.0
NC D:HEM201 2.0 52.2 1.0
NA D:HEM201 2.1 53.9 1.0
ND D:HEM201 2.1 52.0 1.0
NE2 D:HIS84 2.5 51.1 1.0
O D:ACT204 3.0 67.1 1.0
C4B D:HEM201 3.0 53.6 1.0
C1C D:HEM201 3.0 51.1 1.0
C1B D:HEM201 3.1 55.1 1.0
C4A D:HEM201 3.1 53.7 1.0
C4C D:HEM201 3.1 48.7 1.0
C1A D:HEM201 3.1 55.1 1.0
C1D D:HEM201 3.1 51.2 1.0
C4D D:HEM201 3.1 52.1 1.0
OXT D:ACT204 3.2 56.9 1.0
CE1 D:HIS84 3.4 52.2 1.0
CHC D:HEM201 3.4 54.2 1.0
CD2 D:HIS84 3.4 51.0 1.0
CHB D:HEM201 3.4 53.3 1.0
C D:ACT204 3.4 58.8 1.0
CHD D:HEM201 3.4 49.6 1.0
CHA D:HEM201 3.5 50.2 1.0
C2C D:HEM201 4.3 51.7 1.0
C3B D:HEM201 4.3 55.6 1.0
C2B D:HEM201 4.3 55.2 1.0
C3A D:HEM201 4.3 54.8 1.0
C3C D:HEM201 4.3 50.7 1.0
C2A D:HEM201 4.3 54.1 1.0
C2D D:HEM201 4.3 51.4 1.0
C3D D:HEM201 4.3 52.2 1.0
ND1 D:HIS84 4.5 49.7 1.0
CG D:HIS84 4.5 49.3 1.0
CH3 D:ACT204 4.9 62.3 1.0

Reference:

B.J.Wittmann, A.M.Knight, J.L.Hofstra, S.E.Reisman, S.B.J.Kan, F.H.Arnold. Diversity-Oriented Enzymatic Synthesis of Cyclopropane Building Blocks Acs Catalysis 2020.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.0C01888
Page generated: Wed Aug 7 14:00:55 2024

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