Iron in PDB 8sm7: Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe

Protein crystallography data

The structure of Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe, PDB code: 8sm7 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) 82.78 / 2.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 127.369, 127.369, 217.84, 90, 90, 90
R / Rfree (%) 19.9 / 24.2

Other elements in 8sm7:

The structure of Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe (pdb code 8sm7). 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 G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe, PDB code: 8sm7:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8sm7

Go back to Iron Binding Sites List in 8sm7
Iron binding site 1 out of 8 in the Air-Oxidized G. Y4 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 G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:45.7
occ:0.55
 NE2 A:HIS12 1.9 51.2 1.0
OE1 A:GLU242 2.0 46.2 1.0
OD2 A:ASP10 2.1 49.6 1.0
NE2 A:HIS185 2.2 47.4 1.0
OD1 A:ASP315 2.4 56.5 1.0
CE1 A:HIS12 2.7 46.5 1.0
CG A:ASP10 2.9 44.8 1.0
OD1 A:ASP10 3.0 44.9 1.0
CD2 A:HIS12 3.0 51.0 1.0
CE1 A:HIS185 3.1 46.1 1.0
CD A:GLU242 3.2 49.3 1.0
CD2 A:HIS185 3.3 40.2 1.0
CG A:ASP315 3.4 57.9 1.0
ND1 A:HIS12 3.8 47.4 1.0
OE2 A:GLU242 3.9 52.1 1.0
FE A:FE402 3.9 57.7 0.6
CG A:HIS12 4.0 50.7 1.0
OD2 A:ASP315 4.1 59.5 1.0
CB A:GLU242 4.3 39.9 1.0
ND1 A:HIS185 4.3 45.4 1.0
CB A:ASP10 4.3 43.3 1.0
CG A:GLU242 4.3 49.6 1.0
CG A:HIS185 4.4 41.3 1.0
CB A:ASP315 4.4 56.1 1.0
CG1 A:VAL241 4.6 40.0 1.0
CA A:ASP315 4.8 57.5 1.0
NE2 A:GLN286 4.9 53.4 1.0
OH A:TYR90 4.9 44.0 1.0
O A:ASP10 5.0 49.8 1.0

Iron binding site 2 out of 8 in 8sm7

Go back to Iron Binding Sites List in 8sm7
Iron binding site 2 out of 8 in the Air-Oxidized G. Y4 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 G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:57.7
occ:0.55
 OE2 A:GLU242 2.1 52.1 1.0
ND1 A:HIS318 2.2 71.7 1.0
O A:HOH540 2.4 65.1 1.0
OD2 A:ASP315 2.4 59.5 1.0
CE1 A:HIS318 2.7 68.1 1.0
CD A:GLU242 3.0 49.3 1.0
CG A:HIS318 3.2 68.8 1.0
CG A:ASP315 3.2 57.9 1.0
OE1 A:GLU242 3.2 46.2 1.0
OD1 A:ASP315 3.3 56.5 1.0
NE2 A:HIS318 3.8 67.2 1.0
CB A:HIS318 3.8 67.7 1.0
FE A:FE401 3.9 45.7 0.6
CD2 A:HIS318 4.1 68.2 1.0
NE2 A:HIS12 4.2 51.2 1.0
O A:HOH535 4.2 48.9 1.0
OD1 A:ASP320 4.3 64.2 1.0
CD2 A:HIS12 4.4 51.0 1.0
CG A:GLU242 4.4 49.6 1.0
CB A:ASP315 4.7 56.1 1.0
CE1 A:HIS185 4.8 46.1 1.0
OE1 A:GLN286 4.9 61.2 1.0

Iron binding site 3 out of 8 in 8sm7

Go back to Iron Binding Sites List in 8sm7
Iron binding site 3 out of 8 in the Air-Oxidized G. Y4 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 G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:47.2
occ:0.61
 OE1 B:GLU242 2.0 46.6 1.0
NE2 B:HIS12 2.0 49.1 1.0
OD2 B:ASP10 2.0 45.1 1.0
NE2 B:HIS185 2.2 46.6 1.0
OD1 B:ASP315 2.3 55.2 1.0
O B:HOH517 2.7 55.1 1.0
CE1 B:HIS12 2.8 48.1 1.0
CG B:ASP10 2.9 44.0 1.0
CE1 B:HIS185 3.0 47.3 1.0
OD1 B:ASP10 3.1 44.8 1.0
CD2 B:HIS12 3.1 49.9 1.0
CD B:GLU242 3.2 49.9 1.0
CD2 B:HIS185 3.2 44.0 1.0
CG B:ASP315 3.3 54.8 1.0
OE2 B:GLU242 3.8 52.6 1.0
OD2 B:ASP315 3.9 55.8 1.0
ND1 B:HIS12 4.0 49.2 1.0
CG B:HIS12 4.1 49.5 1.0
ND1 B:HIS185 4.2 45.4 1.0
FE B:FE402 4.2 64.5 0.6
CB B:GLU242 4.2 43.5 1.0
CB B:ASP10 4.3 42.0 1.0
CG B:GLU242 4.3 44.8 1.0
CG B:HIS185 4.3 42.8 1.0
CB B:ASP315 4.4 55.7 1.0
O B:HOH513 4.4 44.8 1.0
CG1 B:VAL241 4.5 40.6 1.0
ND1 B:HIS318 4.7 60.1 1.0
CA B:ASP315 4.8 54.4 1.0
CE1 B:HIS318 4.9 61.4 1.0
OE1 B:GLN286 4.9 51.4 1.0

Iron binding site 4 out of 8 in 8sm7

Go back to Iron Binding Sites List in 8sm7
Iron binding site 4 out of 8 in the Air-Oxidized G. Y4 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 G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:64.5
occ:0.60
 O B:HOH517 1.9 55.1 1.0
OE2 B:GLU242 2.1 52.6 1.0
O B:HOH599 2.3 59.0 1.0
ND1 B:HIS318 2.5 60.1 1.0
OD2 B:ASP315 2.5 55.8 1.0
CD B:GLU242 3.1 49.9 1.0
CE1 B:HIS318 3.3 61.4 1.0
CG B:HIS318 3.4 69.9 1.0
CG B:ASP315 3.4 54.8 1.0
OE1 B:GLU242 3.5 46.6 1.0
OD1 B:ASP315 3.6 55.2 1.0
CB B:HIS318 3.7 66.9 1.0
OD1 B:ASP320 4.0 65.3 1.0
FE B:FE401 4.2 47.2 0.6
O B:HOH520 4.2 53.7 1.0
NE2 B:HIS318 4.4 67.8 1.0
CG B:GLU242 4.5 44.8 1.0
CD2 B:HIS318 4.5 69.7 1.0
O B:HOH598 4.6 60.1 1.0
NE2 B:HIS12 4.6 49.1 1.0
NE2 B:GLN286 4.7 53.8 1.0
CD2 B:HIS12 4.8 49.9 1.0
CB B:ASP315 4.8 55.7 1.0
CE1 B:HIS185 4.8 47.3 1.0
CG B:ASP320 5.0 62.6 1.0

Iron binding site 5 out of 8 in 8sm7

Go back to Iron Binding Sites List in 8sm7
Iron binding site 5 out of 8 in the Air-Oxidized G. Y4 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 G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:44.0
occ:0.63
 OD2 D:ASP10 1.9 46.3 1.0
O D:HOH501 1.9 53.4 1.0
NE2 D:HIS12 2.0 53.5 1.0
OD1 D:ASP315 2.1 55.7 1.0
NE2 D:HIS185 2.2 44.6 1.0
OE1 D:GLU242 2.3 51.0 1.0
CG D:ASP10 2.7 47.6 1.0
CE1 D:HIS12 2.8 48.8 1.0
OD1 D:ASP10 2.9 46.8 1.0
CD2 D:HIS12 3.1 51.3 1.0
CE1 D:HIS185 3.2 40.4 1.0
CD2 D:HIS185 3.2 38.8 1.0
CG D:ASP315 3.3 61.4 1.0
CD D:GLU242 3.4 49.2 1.0
OD2 D:ASP315 4.0 62.2 1.0
ND1 D:HIS12 4.0 51.7 1.0
OE2 D:GLU242 4.1 55.4 1.0
CB D:ASP10 4.1 41.5 1.0
CG D:HIS12 4.2 53.5 1.0
FE D:FE402 4.2 60.6 0.5
O D:HOH517 4.3 47.7 1.0
ND1 D:HIS185 4.3 40.1 1.0
CG D:HIS185 4.3 42.6 1.0
CG1 D:VAL241 4.3 39.1 1.0
CB D:ASP315 4.4 56.2 1.0
CB D:GLU242 4.4 45.0 1.0
CG D:GLU242 4.5 48.0 1.0
CA D:ASP315 4.7 52.7 1.0
O D:ASP10 4.8 48.2 1.0
ND1 D:HIS318 4.9 66.7 1.0
OG1 D:THR86 4.9 45.1 1.0
OH D:TYR90 4.9 47.5 1.0
CE1 D:HIS318 5.0 64.6 1.0
OE1 D:GLN286 5.0 52.6 1.0

Iron binding site 6 out of 8 in 8sm7

Go back to Iron Binding Sites List in 8sm7
Iron binding site 6 out of 8 in the Air-Oxidized G. Y4 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 G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe402

b:60.6
occ:0.48
 OE2 D:GLU242 2.1 55.4 1.0
ND1 D:HIS318 2.2 66.7 1.0
OD2 D:ASP315 2.4 62.2 1.0
O D:HOH501 2.4 53.4 1.0
O D:HOH575 2.5 56.7 1.0
CE1 D:HIS318 3.0 64.6 1.0
CD D:GLU242 3.0 49.2 1.0
OE1 D:GLU242 3.3 51.0 1.0
CG D:ASP315 3.3 61.4 1.0
CG D:HIS318 3.4 67.3 1.0
OD1 D:ASP315 3.5 55.7 1.0
CB D:HIS318 3.9 68.0 1.0
NE2 D:HIS318 4.2 72.1 1.0
FE D:FE401 4.2 44.0 0.6
O D:HOH558 4.2 42.6 1.0
CD2 D:HIS318 4.4 69.5 1.0
CG D:GLU242 4.4 48.0 1.0
OD1 D:ASP320 4.5 68.2 1.0
NE2 D:HIS12 4.5 53.5 1.0
CB D:ASP315 4.7 56.2 1.0
CE1 D:HIS185 4.7 40.4 1.0
CD2 D:HIS12 4.8 51.3 1.0
NE2 D:HIS185 5.0 44.6 1.0

Iron binding site 7 out of 8 in 8sm7

Go back to Iron Binding Sites List in 8sm7
Iron binding site 7 out of 8 in the Air-Oxidized G. Y4 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 G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe401

b:43.7
occ:0.67
 OD2 G:ASP10 1.9 42.4 1.0
NE2 G:HIS185 2.0 42.5 1.0
NE2 G:HIS12 2.1 48.9 1.0
OE1 G:GLU242 2.2 49.5 1.0
OD1 G:ASP315 2.2 60.3 1.0
CE1 G:HIS12 2.8 45.8 1.0
CG G:ASP10 2.8 43.8 1.0
CD2 G:HIS185 3.0 37.1 1.0
CE1 G:HIS185 3.0 43.6 1.0
OD1 G:ASP10 3.2 42.0 1.0
CD2 G:HIS12 3.2 49.4 1.0
CG G:ASP315 3.3 59.5 1.0
CD G:GLU242 3.4 52.3 1.0
OD2 G:ASP315 3.9 63.0 1.0
FE G:FE402 3.9 77.1 0.6
ND1 G:HIS12 4.0 43.8 1.0
ND1 G:HIS185 4.1 42.1 1.0
CG G:HIS185 4.1 40.8 1.0
OE2 G:GLU242 4.2 56.5 1.0
O G:HOH536 4.2 51.5 1.0
CB G:ASP10 4.2 40.4 1.0
CB G:GLU242 4.2 45.9 1.0
CG G:HIS12 4.2 45.1 1.0
CG1 G:VAL241 4.4 33.0 1.0
CG G:GLU242 4.4 51.8 1.0
CB G:ASP315 4.4 59.9 1.0
OH G:TYR90 4.7 46.9 1.0
CA G:ASP315 4.8 53.4 1.0
OG1 G:THR86 5.0 42.5 1.0

Iron binding site 8 out of 8 in 8sm7

Go back to Iron Binding Sites List in 8sm7
Iron binding site 8 out of 8 in the Air-Oxidized G. Y4 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 G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe402

b:77.1
occ:0.63
 ND1 G:HIS318 2.1 66.7 1.0
OD2 G:ASP315 2.2 63.0 1.0
OE2 G:GLU242 2.4 56.5 1.0
O G:HOH600 2.6 58.1 1.0
CE1 G:HIS318 2.8 66.2 1.0
CD G:GLU242 3.1 52.3 1.0
OE1 G:GLU242 3.1 49.5 1.0
CG G:ASP315 3.1 59.5 1.0
OD1 G:ASP315 3.3 60.3 1.0
CG G:HIS318 3.4 70.9 1.0
FE G:FE401 3.9 43.7 0.7
CB G:HIS318 3.9 69.8 1.0
NE2 G:HIS318 4.0 70.0 1.0
NE2 G:HIS12 4.2 48.9 1.0
CD2 G:HIS318 4.3 71.3 1.0
O G:HOH635 4.3 56.3 1.0
CD2 G:HIS12 4.5 49.4 1.0
CG G:GLU242 4.5 51.8 1.0
OD1 G:ASP320 4.5 69.8 1.0
CB G:ASP315 4.6 59.9 1.0
CE1 G:HIS185 4.6 43.6 1.0
NE2 G:HIS185 4.7 42.5 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 17:49:36 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy