Iron in PDB 8sm8: Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe

Protein crystallography data

The structure of Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe, PDB code: 8sm8 was solved by C.Liu, J.Rittle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.41 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.93, 154.82, 74.95, 90, 104.93, 90
R / Rfree (%) 19.2 / 25.2

Other elements in 8sm8:

The structure of Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe (pdb code 8sm8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe, PDB code: 8sm8:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8sm8

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Iron binding site 1 out of 8 in the Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe401

b:29.8
occ:1.00
 NE2 G:HIS9 2.1 15.5 1.0
OE1 G:GLU236 2.1 18.2 1.0
OD1 G:ASP308 2.1 16.4 1.0
OD2 G:ASP7 2.2 17.3 1.0
NE2 G:HIS185 2.3 19.2 1.0
O G:HOH533 2.3 19.9 1.0
CG G:ASP7 2.9 16.2 1.0
CE1 G:HIS9 3.0 13.6 1.0
CG G:ASP308 3.1 11.9 1.0
OD1 G:ASP7 3.1 15.1 1.0
CD2 G:HIS9 3.2 17.3 1.0
CD G:GLU236 3.2 17.4 1.0
CE1 G:HIS185 3.2 13.9 1.0
CD2 G:HIS185 3.4 15.2 1.0
OD2 G:ASP308 3.5 13.3 1.0
FE G:FE402 3.6 24.6 1.0
OE2 G:GLU236 3.6 16.1 1.0
ND1 G:HIS9 4.2 12.5 1.0
O G:HOH538 4.2 13.8 1.0
CB G:ASP308 4.2 14.3 1.0
CG G:HIS9 4.3 17.4 1.0
CB G:ASP7 4.3 8.9 1.0
ND1 G:HIS185 4.3 16.2 1.0
CG G:GLU236 4.4 16.1 1.0
ND1 G:HIS311 4.4 15.1 1.0
CG G:HIS185 4.5 12.9 1.0
CB G:GLU236 4.5 10.1 1.0
CE1 G:HIS311 4.6 15.2 1.0
CA G:ASP308 4.7 10.8 1.0
OE1 G:GLN280 4.8 12.2 1.0
O G:HOH658 4.9 20.7 1.0

Iron binding site 2 out of 8 in 8sm8

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Iron binding site 2 out of 8 in the Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe402

b:24.6
occ:1.00
 O G:HOH533 2.0 19.9 1.0
O G:HOH511 2.1 13.3 1.0
OE2 G:GLU236 2.1 16.1 1.0
OD2 G:ASP308 2.2 13.3 1.0
ND1 G:HIS311 2.2 15.1 1.0
O2 G:SO4403 2.4 18.4 1.0
CD G:GLU236 3.0 17.4 1.0
CE1 G:HIS311 3.1 15.2 1.0
CG G:ASP308 3.1 11.9 1.0
CG G:HIS311 3.2 15.3 1.0
OE1 G:GLU236 3.3 18.2 1.0
OD1 G:ASP308 3.4 16.4 1.0
S G:SO4403 3.6 32.5 1.0
CB G:HIS311 3.6 14.1 1.0
FE G:FE401 3.6 29.8 1.0
O3 G:SO4403 3.9 14.9 1.0
O G:HOH658 4.0 20.7 1.0
O4 G:SO4403 4.1 27.2 1.0
O G:HOH581 4.1 11.2 1.0
NE2 G:HIS311 4.2 17.2 1.0
OD1 G:ASP313 4.2 14.0 1.0
CD2 G:HIS311 4.3 17.0 1.0
CG G:GLU236 4.4 16.1 1.0
NE2 G:HIS9 4.5 15.5 1.0
CB G:ASP308 4.5 14.3 1.0
CE1 G:HIS186 4.6 12.4 1.0
NE2 G:GLN280 4.6 13.6 1.0
O G:HOH556 4.7 20.0 1.0
CD2 G:HIS9 4.7 17.3 1.0
O1 G:SO4403 4.8 21.1 1.0
CE1 G:HIS185 5.0 13.9 1.0
NE2 G:HIS185 5.0 19.2 1.0

Iron binding site 3 out of 8 in 8sm8

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Iron binding site 3 out of 8 in the Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:26.9
occ:1.00
 OE2 A:GLU236 1.7 21.4 1.0
OD2 A:ASP7 2.1 13.0 1.0
OD1 A:ASP308 2.2 12.1 1.0
NE2 A:HIS9 2.2 13.4 1.0
NE2 A:HIS185 2.3 16.6 1.0
O A:HOH501 2.3 16.2 1.0
CD A:GLU236 2.9 12.3 1.0
CG A:ASP7 2.9 15.3 1.0
CG A:ASP308 3.0 9.5 1.0
CD2 A:HIS9 3.2 13.6 1.0
CE1 A:HIS9 3.2 13.8 1.0
CD2 A:HIS185 3.2 10.1 1.0
OD1 A:ASP7 3.2 13.9 1.0
CE1 A:HIS185 3.3 13.7 1.0
OD2 A:ASP308 3.5 11.8 1.0
FE A:FE402 3.6 25.7 1.0
CG A:GLU236 3.7 20.0 1.0
OE1 A:GLU236 3.8 13.3 1.0
CB A:ASP308 4.2 16.1 1.0
O A:HOH578 4.2 12.5 1.0
CB A:ASP7 4.2 11.5 1.0
ND1 A:HIS9 4.3 14.9 1.0
CG A:HIS9 4.3 12.8 1.0
CG A:HIS185 4.4 12.0 1.0
ND1 A:HIS185 4.4 11.4 1.0
CB A:GLU236 4.5 15.4 1.0
CA A:ASP308 4.7 12.4 1.0
ND1 A:HIS311 4.7 14.6 1.0
O A:HOH555 4.8 20.8 1.0
OE1 A:GLN280 4.8 11.4 1.0
CE1 A:HIS311 4.9 11.6 1.0

Iron binding site 4 out of 8 in 8sm8

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Iron binding site 4 out of 8 in the Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:25.7
occ:1.00
 O A:HOH501 2.0 16.2 1.0
OD2 A:ASP308 2.1 11.8 1.0
O A:HOH581 2.1 15.7 1.0
ND1 A:HIS311 2.2 14.6 1.0
OE1 A:GLU236 2.4 13.3 1.0
O2 A:SO4403 2.6 21.6 1.0
OE2 A:GLU236 2.8 21.4 1.0
CD A:GLU236 2.9 12.3 1.0
CG A:ASP308 3.1 9.5 1.0
CE1 A:HIS311 3.1 11.6 1.0
CG A:HIS311 3.3 11.2 1.0
OD1 A:ASP308 3.3 12.1 1.0
FE A:FE401 3.6 26.9 1.0
CB A:HIS311 3.7 11.1 1.0
O A:HOH555 3.8 20.8 1.0
S A:SO4403 3.8 30.4 1.0
O3 A:SO4403 3.9 23.9 1.0
O A:HOH516 4.2 16.1 1.0
NE2 A:HIS311 4.3 16.8 1.0
OD1 A:ASP313 4.3 15.3 1.0
CD2 A:HIS311 4.4 12.1 1.0
CG A:GLU236 4.4 20.0 1.0
NE2 A:HIS9 4.4 13.4 1.0
CB A:ASP308 4.4 16.1 1.0
O1 A:SO4403 4.5 30.5 1.0
CE1 A:HIS186 4.6 10.6 1.0
CD2 A:HIS9 4.6 13.6 1.0
NE2 A:GLN280 4.7 10.2 1.0
O A:HOH502 4.8 18.1 1.0
NE2 A:HIS185 4.8 16.6 1.0
CE1 A:HIS185 4.9 13.7 1.0
O A:ASP308 5.0 11.9 1.0

Iron binding site 5 out of 8 in 8sm8

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Iron binding site 5 out of 8 in the Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:35.4
occ:1.00
 O D:HOH501 2.1 21.4 1.0
OE1 D:GLU236 2.2 21.8 1.0
NE2 D:HIS9 2.2 18.4 1.0
OD1 D:ASP308 2.2 22.5 1.0
OD2 D:ASP7 2.2 21.4 1.0
NE2 D:HIS185 2.2 13.7 1.0
CE1 D:HIS9 3.1 16.6 1.0
CG D:ASP7 3.1 22.5 1.0
CE1 D:HIS185 3.1 12.0 1.0
CG D:ASP308 3.1 19.5 1.0
CD2 D:HIS9 3.2 16.8 1.0
CD2 D:HIS185 3.3 13.6 1.0
CD D:GLU236 3.3 24.8 1.0
OD1 D:ASP7 3.4 26.7 1.0
OD2 D:ASP308 3.6 21.2 1.0
FE D:FE402 3.6 28.1 1.0
OE2 D:GLU236 3.9 19.8 1.0
ND1 D:HIS9 4.2 15.4 1.0
CB D:ASP308 4.2 20.0 1.0
ND1 D:HIS185 4.2 11.9 1.0
CG D:HIS9 4.3 18.3 1.0
CG D:HIS185 4.4 14.5 1.0
ND1 D:HIS311 4.4 26.5 1.0
CB D:ASP7 4.4 17.3 1.0
CB D:GLU236 4.4 19.0 1.0
O D:HOH595 4.5 17.8 1.0
CG D:GLU236 4.5 19.3 1.0
CE1 D:HIS311 4.6 28.7 1.0
CA D:ASP308 4.7 21.2 1.0
O D:HOH507 4.7 28.5 1.0
OE1 D:GLN280 4.9 18.5 1.0

Iron binding site 6 out of 8 in 8sm8

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Iron binding site 6 out of 8 in the Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe402

b:28.1
occ:1.00
 O D:HOH501 2.1 21.4 1.0
O D:HOH534 2.1 21.8 1.0
ND1 D:HIS311 2.1 26.5 1.0
OD2 D:ASP308 2.2 21.2 1.0
OE2 D:GLU236 2.3 19.8 1.0
O1 D:SO4403 2.6 23.9 1.0
CE1 D:HIS311 3.0 28.7 1.0
CG D:ASP308 3.1 19.5 1.0
CD D:GLU236 3.1 24.8 1.0
CG D:HIS311 3.2 23.1 1.0
OE1 D:GLU236 3.2 21.8 1.0
OD1 D:ASP308 3.3 22.5 1.0
O D:HOH507 3.6 28.5 1.0
CB D:HIS311 3.6 21.1 1.0
FE D:FE401 3.6 35.4 1.0
S D:SO4403 3.8 36.4 1.0
O3 D:SO4403 4.0 28.6 1.0
NE2 D:HIS311 4.1 22.8 1.0
O D:HOH506 4.1 17.1 1.0
CD2 D:HIS311 4.2 24.1 1.0
OD1 D:ASP313 4.3 23.2 1.0
NE2 D:HIS9 4.4 18.4 1.0
CB D:ASP308 4.4 20.0 1.0
CE1 D:HIS186 4.5 15.2 1.0
O2 D:SO4403 4.5 36.7 1.0
CG D:GLU236 4.6 19.3 1.0
CD2 D:HIS9 4.6 16.8 1.0
NE2 D:GLN280 4.7 17.4 1.0
O D:HOH521 4.9 28.3 1.0
NE2 D:HIS186 5.0 18.8 1.0
O4 D:SO4403 5.0 23.9 1.0
CE1 D:HIS185 5.0 12.0 1.0
O D:ASP308 5.0 19.4 1.0

Iron binding site 7 out of 8 in 8sm8

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Iron binding site 7 out of 8 in the Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe401

b:31.0
occ:1.00
 OD2 J:ASP7 2.0 20.1 1.0
OE1 J:GLU236 2.1 19.6 1.0
NE2 J:HIS9 2.2 15.8 1.0
NE2 J:HIS185 2.2 16.0 1.0
O J:HOH512 2.2 22.3 1.0
OD1 J:ASP308 2.2 15.7 1.0
CG J:ASP7 2.9 17.1 1.0
CE1 J:HIS9 3.1 19.2 1.0
CE1 J:HIS185 3.1 16.0 1.0
CG J:ASP308 3.2 14.6 1.0
CD2 J:HIS9 3.2 17.2 1.0
CD2 J:HIS185 3.2 19.5 1.0
OD1 J:ASP7 3.2 14.4 1.0
CD J:GLU236 3.3 13.8 1.0
OD2 J:ASP308 3.7 11.9 1.0
FE J:FE402 3.9 30.2 1.0
OE2 J:GLU236 3.9 22.5 1.0
CB J:ASP7 4.2 12.0 1.0
ND1 J:HIS9 4.2 17.6 1.0
CB J:ASP308 4.2 15.1 1.0
ND1 J:HIS185 4.2 14.6 1.0
O J:HOH522 4.3 18.2 1.0
CG J:HIS9 4.3 18.9 1.0
CG J:HIS185 4.3 17.2 1.0
CG J:GLU236 4.4 20.0 1.0
CB J:GLU236 4.5 19.4 1.0
ND1 J:HIS311 4.6 26.1 1.0
CA J:ASP308 4.7 16.1 1.0
OE1 J:GLN280 4.8 14.3 1.0
O J:HOH616 4.8 17.2 1.0
CE1 J:HIS311 4.8 23.2 1.0

Iron binding site 8 out of 8 in 8sm8

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Iron binding site 8 out of 8 in the Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Air-Oxidized A. Ca Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe402

b:30.2
occ:1.00
 OE2 J:GLU236 2.1 22.5 1.0
ND1 J:HIS311 2.2 26.1 1.0
OD2 J:ASP308 2.2 11.9 1.0
O J:HOH531 2.2 18.2 1.0
O J:HOH512 2.3 22.3 1.0
O3 J:SO4403 2.5 22.1 1.0
CD J:GLU236 3.0 13.8 1.0
CG J:ASP308 3.1 14.6 1.0
CE1 J:HIS311 3.1 23.2 1.0
OE1 J:GLU236 3.2 19.6 1.0
CG J:HIS311 3.2 17.9 1.0
OD1 J:ASP308 3.4 15.7 1.0
CB J:HIS311 3.5 18.3 1.0
S J:SO4403 3.7 36.3 1.0
FE J:FE401 3.9 31.0 1.0
O1 J:SO4403 3.9 26.7 1.0
O J:HOH616 3.9 17.2 1.0
O J:HOH553 4.0 20.0 1.0
OD1 J:ASP313 4.1 24.6 1.0
NE2 J:HIS311 4.3 20.8 1.0
O4 J:SO4403 4.3 31.8 1.0
CD2 J:HIS311 4.3 19.6 1.0
O J:HOH536 4.4 23.4 1.0
CG J:GLU236 4.4 20.0 1.0
CB J:ASP308 4.5 15.1 1.0
NE2 J:HIS9 4.6 15.8 1.0
CE1 J:HIS186 4.6 19.6 1.0
CD2 J:HIS9 4.7 17.2 1.0
NE2 J:GLN280 4.8 16.7 1.0
O2 J:SO4403 4.9 20.8 1.0
CE1 J:HIS185 5.0 16.0 1.0
OE1 J:GLN280 5.0 14.3 1.0

Reference:

C.Liu, M.M.Powell, G.Rao, R.D.Britt, J.Rittle. Bioinformatic Discovery of A Cambialistic Monooxygenase. J.Am.Chem.Soc. V. 146 1783 2024.
ISSN: ESSN 1520-5126
PubMed: 38198693
DOI: 10.1021/JACS.3C12131
Page generated: Sat Aug 10 17:49:39 2024

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