Iron in PDB 8sm9: Air-Oxidized C. Fi Truffo Expressed From M9 Minimal Medium Supplemented with Fe

Protein crystallography data

The structure of Air-Oxidized C. Fi Truffo Expressed From M9 Minimal Medium Supplemented with Fe, PDB code: 8sm9 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) 60.04 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 112.818, 67.88, 138.508, 90, 111.74, 90
R / Rfree (%) 20.3 / 25.1

Iron Binding Sites:

The binding sites of Iron atom in the Air-Oxidized C. Fi Truffo Expressed From M9 Minimal Medium Supplemented with Fe (pdb code 8sm9). 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 C. Fi Truffo Expressed From M9 Minimal Medium Supplemented with Fe, PDB code: 8sm9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8sm9

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Iron binding site 1 out of 8 in the Air-Oxidized C. Fi 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 C. Fi Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe401

b:59.6
occ:1.00
 OE1 F:GLU264 1.9 49.8 1.0
NE2 F:HIS36 2.2 38.0 1.0
OD2 F:ASP34 2.3 43.9 1.0
OD1 F:ASP336 2.3 39.4 1.0
NE2 F:HIS212 2.4 37.8 1.0
O F:HOH531 2.8 50.5 1.0
CD2 F:HIS36 3.1 41.0 1.0
CD F:GLU264 3.1 46.3 1.0
CG F:ASP34 3.1 46.7 1.0
CE1 F:HIS212 3.1 43.0 1.0
CG F:ASP336 3.2 44.0 1.0
CE1 F:HIS36 3.2 45.2 1.0
OD1 F:ASP34 3.4 41.2 1.0
FE F:FE402 3.4 46.4 0.6
CD2 F:HIS212 3.5 44.2 1.0
OD2 F:ASP336 3.6 50.5 1.0
OE2 F:GLU264 3.7 44.5 1.0
ND1 F:HIS339 4.2 42.3 1.0
CG F:HIS36 4.2 46.4 1.0
CG F:GLU264 4.3 46.4 1.0
ND1 F:HIS36 4.3 46.2 1.0
ND1 F:HIS212 4.3 45.3 1.0
CE1 F:HIS339 4.4 47.1 1.0
CB F:ASP336 4.4 40.3 1.0
O F:HOH517 4.4 40.0 1.0
CB F:GLU264 4.4 38.9 1.0
CB F:ASP34 4.5 44.2 1.0
CG F:HIS212 4.5 40.2 1.0
CA F:ASP336 4.7 40.9 1.0

Iron binding site 2 out of 8 in 8sm9

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Iron binding site 2 out of 8 in the Air-Oxidized C. Fi 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 C. Fi Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe402

b:46.4
occ:0.56
 O F:HOH531 2.0 50.5 1.0
O F:HOH532 2.1 47.4 1.0
OE2 F:GLU264 2.2 44.5 1.0
OD2 F:ASP336 2.3 50.5 1.0
ND1 F:HIS339 2.5 42.3 1.0
CD F:GLU264 3.0 46.3 1.0
OE1 F:GLU264 3.0 49.8 1.0
CG F:ASP336 3.1 44.0 1.0
OD1 F:ASP336 3.2 39.4 1.0
CE1 F:HIS339 3.4 47.1 1.0
FE F:FE401 3.4 59.6 1.0
CG F:HIS339 3.5 48.6 1.0
CB F:HIS339 3.8 39.6 1.0
O F:HOH530 4.1 48.0 1.0
OD1 F:ASP341 4.2 48.5 1.0
O F:HOH502 4.2 52.5 1.0
CG F:GLU264 4.4 46.4 1.0
CB F:ASP336 4.5 40.3 1.0
NE2 F:HIS339 4.5 49.3 1.0
CD2 F:HIS339 4.6 47.9 1.0
NE2 F:HIS36 4.7 38.0 1.0
CD2 F:HIS36 4.8 41.0 1.0
OE1 F:GLN308 4.9 45.7 1.0
NE2 F:GLN308 4.9 46.8 1.0

Iron binding site 3 out of 8 in 8sm9

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Iron binding site 3 out of 8 in the Air-Oxidized C. Fi 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 C. Fi Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:44.5
occ:0.61
 OE1 B:GLU264 2.0 42.5 1.0
OD1 B:ASP336 2.0 46.0 1.0
NE2 B:HIS36 2.0 39.2 1.0
OD2 B:ASP34 2.2 40.7 1.0
NE2 B:HIS212 2.3 37.6 1.0
O B:HOH521 2.6 41.7 1.0
CD2 B:HIS36 2.9 39.3 1.0
CG B:ASP34 2.9 45.4 1.0
CG B:ASP336 3.0 45.4 1.0
CE1 B:HIS36 3.1 43.8 1.0
CD B:GLU264 3.1 41.5 1.0
CE1 B:HIS212 3.2 42.2 1.0
OD1 B:ASP34 3.2 42.1 1.0
CD2 B:HIS212 3.3 42.9 1.0
OD2 B:ASP336 3.5 49.6 1.0
OE2 B:GLU264 3.7 42.4 1.0
CG B:HIS36 4.1 41.4 1.0
ND1 B:HIS36 4.1 42.6 1.0
CB B:ASP336 4.2 38.0 1.0
CB B:ASP34 4.2 43.5 1.0
FE B:FE402 4.2 63.4 0.8
ND1 B:HIS212 4.3 42.2 1.0
CG B:GLU264 4.4 37.0 1.0
O B:HOH518 4.4 46.1 1.0
CG B:HIS212 4.4 36.6 1.0
ND1 B:HIS339 4.5 45.1 1.0
CB B:GLU264 4.5 37.7 1.0
CA B:ASP336 4.5 44.6 1.0
CE1 B:HIS339 4.7 47.3 1.0
O B:HOH573 4.9 44.6 1.0

Iron binding site 4 out of 8 in 8sm9

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Iron binding site 4 out of 8 in the Air-Oxidized C. Fi 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 C. Fi Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:63.4
occ:0.77
 O B:HOH521 2.2 41.7 1.0
OD2 B:ASP336 2.2 49.6 1.0
OE2 B:GLU264 2.3 42.4 1.0
ND1 B:HIS339 2.5 45.1 1.0
O B:HOH573 3.1 44.6 1.0
CD B:GLU264 3.3 41.5 1.0
CG B:HIS339 3.4 45.0 1.0
CG B:ASP336 3.4 45.4 1.0
O B:HOH541 3.4 49.3 1.0
CB B:HIS339 3.5 40.9 1.0
CE1 B:HIS339 3.5 47.3 1.0
OD1 B:ASP341 3.6 49.6 1.0
OE1 B:GLU264 3.7 42.5 1.0
OD1 B:ASP336 3.8 46.0 1.0
O B:HOH520 4.0 44.1 1.0
FE B:FE401 4.2 44.5 0.6
CG B:ASP341 4.4 52.4 1.0
OD2 B:ASP341 4.4 53.9 1.0
CD2 B:HIS339 4.6 45.3 1.0
NE2 B:HIS339 4.6 47.4 1.0
CB B:ASP336 4.6 38.0 1.0
CG B:GLU264 4.7 37.0 1.0
NE2 B:GLN308 4.7 48.4 1.0

Iron binding site 5 out of 8 in 8sm9

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Iron binding site 5 out of 8 in the Air-Oxidized C. Fi 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 C. Fi Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:63.9
occ:1.00
 NE2 D:HIS36 2.1 56.0 1.0
NE2 D:HIS212 2.1 47.4 1.0
OD2 D:ASP34 2.1 60.4 1.0
OE1 D:GLU264 2.2 50.7 1.0
OD1 D:ASP336 2.4 49.7 1.0
O D:HOH511 2.5 52.0 1.0
CG D:ASP34 2.7 55.0 1.0
OD1 D:ASP34 2.8 55.5 1.0
CE1 D:HIS36 2.9 52.0 1.0
CD2 D:HIS212 2.9 41.3 1.0
CE1 D:HIS212 3.2 45.0 1.0
CD2 D:HIS36 3.2 57.3 1.0
CG D:ASP336 3.3 55.9 1.0
CD D:GLU264 3.4 52.5 1.0
OD2 D:ASP336 3.8 56.8 1.0
OE2 D:GLU264 4.0 57.3 1.0
ND1 D:HIS36 4.0 51.6 1.0
CG D:HIS212 4.1 44.7 1.0
ND1 D:HIS212 4.2 42.4 1.0
CG D:HIS36 4.2 55.3 1.0
CB D:ASP34 4.2 55.7 1.0
FE D:FE402 4.3 63.5 0.6
CB D:GLU264 4.4 43.8 1.0
CB D:ASP336 4.4 60.2 1.0
CG D:GLU264 4.4 51.2 1.0
ND1 D:HIS339 4.6 64.1 1.0
CG2 D:ILE263 4.7 54.9 1.0
CA D:ASP336 4.8 61.5 1.0
CE1 D:HIS339 4.8 60.0 1.0
OE1 D:GLN308 4.9 55.2 1.0

Iron binding site 6 out of 8 in 8sm9

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Iron binding site 6 out of 8 in the Air-Oxidized C. Fi 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 C. Fi Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe402

b:63.5
occ:0.62
 O D:HOH501 2.0 60.5 1.0
O D:HOH511 2.1 52.0 1.0
OE2 D:GLU264 2.3 57.3 1.0
OD2 D:ASP336 2.4 56.8 1.0
ND1 D:HIS339 2.5 64.1 1.0
O D:HOH546 2.8 48.9 1.0
CD D:GLU264 3.3 52.5 1.0
CE1 D:HIS339 3.4 60.0 1.0
CG D:ASP336 3.4 55.9 1.0
CG D:HIS339 3.5 63.0 1.0
OE1 D:GLU264 3.6 50.7 1.0
O D:HOH524 3.7 56.3 1.0
CB D:HIS339 3.7 59.8 1.0
OD1 D:ASP336 3.8 49.7 1.0
O D:HOH519 3.9 55.5 1.0
OD1 D:ASP341 4.0 60.4 1.0
FE D:FE401 4.3 63.9 1.0
NE2 D:HIS339 4.5 61.4 1.0
CD2 D:HIS339 4.6 63.5 1.0
CG D:GLU264 4.6 51.2 1.0
OD2 D:ASP341 4.7 60.0 1.0
CB D:ASP336 4.8 60.2 1.0
CG D:ASP341 4.8 62.2 1.0
NE2 D:HIS36 4.9 56.0 1.0

Iron binding site 7 out of 8 in 8sm9

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Iron binding site 7 out of 8 in the Air-Oxidized C. Fi 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 C. Fi Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe401

b:72.6
occ:1.00
 OD2 H:ASP34 1.9 58.5 1.0
OE1 H:GLU264 2.1 54.8 1.0
NE2 H:HIS36 2.1 60.4 1.0
OD1 H:ASP336 2.2 50.5 1.0
NE2 H:HIS212 2.3 55.2 1.0
O H:HOH521 2.7 55.6 1.0
CG H:ASP34 2.8 55.7 1.0
CE1 H:HIS36 3.0 58.6 1.0
CD2 H:HIS212 3.1 48.7 1.0
CD2 H:HIS36 3.1 55.8 1.0
OD1 H:ASP34 3.2 58.3 1.0
CD H:GLU264 3.2 56.3 1.0
CG H:ASP336 3.3 58.0 1.0
CE1 H:HIS212 3.4 46.8 1.0
OE2 H:GLU264 3.8 59.4 1.0
OD2 H:ASP336 3.9 59.1 1.0
O H:HOH504 3.9 50.9 1.0
FE H:FE402 4.1 58.7 0.7
CB H:ASP34 4.1 59.8 1.0
ND1 H:HIS36 4.1 61.4 1.0
CG H:HIS36 4.2 61.3 1.0
CG H:HIS212 4.3 46.8 1.0
CB H:ASP336 4.4 58.5 1.0
CG H:GLU264 4.4 52.4 1.0
ND1 H:HIS212 4.4 44.1 1.0
ND1 H:HIS339 4.5 63.5 1.0
CB H:GLU264 4.5 50.1 1.0
CE1 H:HIS339 4.6 58.6 1.0
CA H:ASP336 4.7 61.0 1.0
CG2 H:ILE263 4.7 53.6 1.0
OE1 H:GLN308 4.7 53.3 1.0

Iron binding site 8 out of 8 in 8sm9

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Iron binding site 8 out of 8 in the Air-Oxidized C. Fi 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 C. Fi Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe402

b:58.7
occ:0.66
 O H:HOH515 1.9 57.2 1.0
O H:HOH521 1.9 55.6 1.0
OE2 H:GLU264 2.2 59.4 1.0
OD2 H:ASP336 2.4 59.1 1.0
ND1 H:HIS339 2.6 63.5 1.0
O H:HOH551 2.9 48.9 1.0
CD H:GLU264 3.2 56.3 1.0
CG H:ASP336 3.3 58.0 1.0
CE1 H:HIS339 3.4 58.6 1.0
OE1 H:GLU264 3.5 54.8 1.0
CG H:HIS339 3.5 65.8 1.0
OD1 H:ASP336 3.5 50.5 1.0
CB H:HIS339 3.8 62.7 1.0
O H:HOH508 3.9 57.6 1.0
FE H:FE401 4.1 72.6 1.0
OD1 H:ASP341 4.1 67.5 1.0
CG H:GLU264 4.5 52.4 1.0
NE2 H:HIS339 4.5 66.5 1.0
CD2 H:HIS339 4.6 68.7 1.0
CB H:ASP336 4.8 58.5 1.0
OD2 H:ASP341 4.8 65.1 1.0
NE2 H:HIS36 4.8 60.4 1.0
OE1 H:GLN308 4.9 53.3 1.0
CG H:ASP341 4.9 70.5 1.0
CD2 H:HIS36 4.9 55.8 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 17:49:49 2024

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