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Iron in PDB 7szg: Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon

Protein crystallography data

The structure of Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon, PDB code: 7szg was solved by J.Bridwell-Rabb, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.47 / 2.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.73, 96.932, 80.809, 90, 106.97, 90
R / Rfree (%) 20.5 / 24.4

Other elements in 7szg:

The structure of Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon also contains other interesting chemical elements:

Xenon (Xe) 3 atoms
Chlorine (Cl) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon (pdb code 7szg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon, PDB code: 7szg:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 7szg

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Iron binding site 1 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:44.1
occ:1.00
 FE1 A:FES501 0.0 44.1 1.0
S1 A:FES501 2.2 36.1 1.0
S2 A:FES501 2.2 40.4 1.0
ND1 A:HIS57 2.5 42.2 1.0
ND1 A:HIS77 2.5 30.9 1.0
FE2 A:FES501 2.9 39.7 1.0
CG A:HIS77 3.2 42.1 1.0
CB A:HIS77 3.3 40.1 1.0
CG A:HIS57 3.3 43.7 1.0
CB A:HIS57 3.3 40.5 1.0
CE1 A:HIS77 3.6 35.2 1.0
CE1 A:HIS57 3.6 47.9 1.0
N A:HIS77 3.8 39.3 1.0
CB A:TYR76 4.1 44.2 1.0
CA A:HIS77 4.1 43.9 1.0
CD2 A:TYR76 4.3 41.3 1.0
N A:ARG58 4.4 39.5 1.0
CD2 A:HIS77 4.4 47.6 1.0
CG A:TYR76 4.5 41.1 1.0
CG A:ARG58 4.5 38.0 1.0
CD2 A:HIS57 4.5 49.1 1.0
CB A:ARG58 4.5 39.8 1.0
C A:TYR76 4.6 36.7 1.0
NE2 A:HIS77 4.6 45.9 1.0
NE2 A:HIS57 4.6 52.5 1.0
CA A:HIS57 4.6 47.4 1.0
SG A:CYS55 4.6 39.2 1.0
NE1 A:TRP79 4.7 42.7 1.0
CE2 A:TRP79 4.7 42.1 1.0
C A:HIS57 4.8 44.2 1.0
SG A:CYS74 4.8 38.4 1.0
CA A:TYR76 4.9 42.5 1.0
CD1 A:TRP79 4.9 44.8 1.0
CD2 A:TRP79 5.0 42.1 1.0

Iron binding site 2 out of 9 in 7szg

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Iron binding site 2 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:39.7
occ:1.00
 FE2 A:FES501 0.0 39.7 1.0
S2 A:FES501 2.2 40.4 1.0
S1 A:FES501 2.2 36.1 1.0
SG A:CYS74 2.3 38.4 1.0
SG A:CYS55 2.4 39.2 1.0
FE1 A:FES501 2.9 44.1 1.0
CB A:CYS55 3.1 33.7 1.0
CB A:CYS74 3.2 33.3 1.0
CB A:HIS57 4.2 40.5 1.0
CB A:TYR76 4.4 44.2 1.0
CA A:CYS55 4.6 39.4 1.0
CA A:CYS74 4.6 40.5 1.0
N A:HIS77 4.6 39.3 1.0
CB A:VAL60 4.8 45.8 1.0
N A:ARG58 4.8 39.5 1.0
N A:TYR76 4.8 41.9 1.0
C A:CYS55 4.9 41.3 1.0
ND1 A:HIS57 5.0 42.2 1.0

Iron binding site 3 out of 9 in 7szg

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Iron binding site 3 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe504

b:39.2
occ:1.00
 NE2 A:HIS164 2.1 47.0 1.0
NE2 A:HIS169 2.1 39.3 1.0
OD1 A:ASP280 2.1 35.2 1.0
O A:HOH637 2.1 41.9 1.0
O A:HOH622 2.4 39.8 1.0
OD2 A:ASP280 2.4 41.0 1.0
CG A:ASP280 2.6 36.8 1.0
CD2 A:HIS169 2.9 41.7 1.0
CD2 A:HIS164 3.0 35.7 1.0
CE1 A:HIS164 3.0 47.6 1.0
CE1 A:HIS169 3.2 38.6 1.0
O A:HOH604 4.0 57.5 1.0
CB A:ASP280 4.1 30.7 1.0
CG A:HIS164 4.1 37.4 1.0
ND1 A:HIS164 4.1 43.9 1.0
ND2 A:ASN158 4.1 40.2 1.0
CG A:HIS169 4.1 43.6 1.0
ND1 A:HIS169 4.2 41.9 1.0
CD1 A:ILE168 4.2 48.0 1.0
OD1 A:ASN158 4.3 37.3 1.0
CG1 A:VAL276 4.4 34.7 1.0
CE1 A:PHE165 4.5 48.8 1.0
CG A:ASN158 4.6 39.4 1.0
CD1 A:PHE165 4.6 50.2 1.0
O A:ASN158 4.7 33.7 1.0
O A:VAL276 4.8 32.4 1.0
CA A:ASP280 4.9 33.4 1.0
CG1 A:ILE168 5.0 45.7 1.0

Iron binding site 4 out of 9 in 7szg

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Iron binding site 4 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:53.1
occ:1.00
 FE1 B:FES501 0.0 53.1 1.0
SG B:CYS55 2.1 47.1 1.0
S2 B:FES501 2.2 46.7 1.0
S1 B:FES501 2.2 42.8 1.0
SG B:CYS74 2.3 40.5 1.0
FE2 B:FES501 3.0 52.0 1.0
CB B:CYS55 3.2 42.1 1.0
CB B:CYS74 3.2 44.5 1.0
CB B:HIS57 4.0 43.8 1.0
CB B:TYR76 4.4 42.1 1.0
ND1 B:HIS57 4.5 45.6 1.0
CA B:CYS55 4.5 39.1 1.0
ND1 B:HIS77 4.6 44.6 1.0
CA B:CYS74 4.7 44.4 1.0
N B:ARG58 4.7 45.4 1.0
CB B:VAL60 4.7 43.3 1.0
N B:HIS77 4.8 49.7 1.0
CG B:HIS57 4.8 44.4 1.0
N B:TYR76 4.9 47.3 1.0
OH B:TYR81 4.9 39.4 1.0
C B:CYS55 4.9 42.8 1.0
N B:HIS57 4.9 41.8 1.0

Iron binding site 5 out of 9 in 7szg

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Iron binding site 5 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:52.0
occ:1.00
 FE2 B:FES501 0.0 52.0 1.0
ND1 B:HIS77 1.9 44.6 1.0
ND1 B:HIS57 2.1 45.6 1.0
S2 B:FES501 2.2 46.7 1.0
S1 B:FES501 2.2 42.8 1.0
CE1 B:HIS77 2.8 44.3 1.0
CG B:HIS77 2.9 45.5 1.0
FE1 B:FES501 3.0 53.1 1.0
CE1 B:HIS57 3.1 42.0 1.0
CG B:HIS57 3.1 44.4 1.0
CB B:HIS77 3.4 42.8 1.0
CB B:HIS57 3.4 43.8 1.0
N B:HIS77 3.8 49.7 1.0
NE2 B:HIS77 3.9 43.4 1.0
CD2 B:HIS77 4.0 42.4 1.0
CB B:TYR76 4.0 42.1 1.0
NE2 B:HIS57 4.2 41.9 1.0
CD2 B:HIS57 4.2 44.3 1.0
CA B:HIS77 4.2 52.3 1.0
N B:ARG58 4.3 45.4 1.0
CD2 B:TYR76 4.4 43.1 1.0
CG B:TYR76 4.4 41.8 1.0
CG B:ARG58 4.4 43.6 1.0
CB B:ARG58 4.4 41.5 1.0
SG B:CYS55 4.5 47.1 1.0
C B:TYR76 4.5 43.7 1.0
NE1 B:TRP79 4.6 40.5 1.0
CA B:HIS57 4.7 48.2 1.0
SG B:CYS74 4.7 40.5 1.0
CD1 B:TRP79 4.7 50.4 1.0
CE2 B:TRP79 4.8 35.9 1.0
C B:HIS57 4.8 48.4 1.0
CA B:TYR76 4.8 46.0 1.0
CA B:ARG58 5.0 44.1 1.0

Iron binding site 6 out of 9 in 7szg

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Iron binding site 6 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe505

b:51.6
occ:1.00
 NE2 B:HIS169 1.9 43.3 1.0
O B:HOH621 2.0 45.7 1.0
NE2 B:HIS164 2.1 38.4 1.0
O B:HOH637 2.2 39.9 1.0
OD1 B:ASP280 2.2 45.0 1.0
OD2 B:ASP280 2.5 43.6 1.0
CG B:ASP280 2.7 39.3 1.0
CD2 B:HIS169 2.8 48.8 1.0
CE1 B:HIS169 3.0 43.7 1.0
CE1 B:HIS164 3.0 39.4 1.0
CD2 B:HIS164 3.2 37.1 1.0
O B:HOH634 3.8 50.0 1.0
CG B:HIS169 4.0 48.5 1.0
ND1 B:HIS169 4.0 46.6 1.0
ND2 B:ASN158 4.1 40.4 1.0
CB B:ASP280 4.2 34.8 1.0
OD1 B:ASN158 4.2 44.9 1.0
ND1 B:HIS164 4.2 45.4 1.0
CG1 B:VAL276 4.3 49.7 1.0
CG B:HIS164 4.3 45.0 1.0
CD1 B:ILE168 4.4 39.9 1.0
O B:ASN158 4.5 42.4 1.0
CG B:ASN158 4.5 40.9 1.0
CE1 B:PHE165 4.6 54.5 1.0
CD1 B:PHE165 4.7 54.1 1.0
O B:HOH606 4.8 64.0 1.0
CG1 B:ILE168 4.9 43.5 1.0
CA B:ASP280 5.0 35.1 1.0
O B:VAL276 5.0 41.2 1.0

Iron binding site 7 out of 9 in 7szg

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Iron binding site 7 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:34.4
occ:1.00
 FE1 C:FES501 0.0 34.4 1.0
S2 C:FES501 2.1 35.6 1.0
S1 C:FES501 2.2 27.3 1.0
SG C:CYS74 2.4 37.0 1.0
SG C:CYS55 2.6 35.2 1.0
FE2 C:FES501 2.8 37.5 1.0
CB C:CYS74 3.1 26.0 1.0
CB C:CYS55 3.3 27.5 1.0
CB C:HIS57 4.2 31.6 1.0
CB C:TYR76 4.5 34.2 1.0
ND1 C:HIS57 4.5 33.2 1.0
CA C:CYS74 4.5 35.0 1.0
N C:HIS77 4.6 34.0 1.0
CA C:CYS55 4.7 35.3 1.0
CG C:HIS57 4.8 29.8 1.0
CB C:VAL60 4.9 40.1 1.0
N C:ARG58 4.9 36.0 1.0
N C:TYR76 4.9 32.4 1.0
CB C:TRP79 4.9 33.7 1.0
CG C:TRP79 4.9 42.8 1.0
C C:CYS74 5.0 32.0 1.0

Iron binding site 8 out of 9 in 7szg

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Iron binding site 8 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:37.5
occ:1.00
 FE2 C:FES501 0.0 37.5 1.0
ND1 C:HIS57 2.1 33.2 1.0
S2 C:FES501 2.2 35.6 1.0
S1 C:FES501 2.2 27.3 1.0
ND1 C:HIS77 2.6 31.3 1.0
FE1 C:FES501 2.8 34.4 1.0
CE1 C:HIS57 3.1 34.5 1.0
CG C:HIS57 3.1 29.8 1.0
CG C:HIS77 3.3 42.6 1.0
CB C:HIS77 3.4 35.4 1.0
CB C:HIS57 3.4 31.6 1.0
CE1 C:HIS77 3.6 31.3 1.0
N C:HIS77 3.8 34.0 1.0
CB C:TYR76 3.9 34.2 1.0
CA C:HIS77 4.2 38.6 1.0
NE2 C:HIS57 4.2 34.3 1.0
CD2 C:HIS57 4.3 34.1 1.0
CD2 C:TYR76 4.3 38.7 1.0
N C:ARG58 4.3 36.0 1.0
CG C:TYR76 4.5 37.7 1.0
CD2 C:HIS77 4.5 46.6 1.0
CB C:ARG58 4.5 29.6 1.0
CG C:ARG58 4.5 29.9 1.0
C C:TYR76 4.5 30.7 1.0
NE1 C:TRP79 4.6 32.3 1.0
NE2 C:HIS77 4.6 37.7 1.0
CA C:HIS57 4.7 37.0 1.0
CD1 C:TRP79 4.7 38.7 1.0
SG C:CYS74 4.7 37.0 1.0
CE2 C:TRP79 4.7 34.5 1.0
SG C:CYS55 4.8 35.2 1.0
CA C:TYR76 4.8 35.3 1.0
C C:HIS57 4.8 37.8 1.0
CG C:TRP79 5.0 42.8 1.0
CD2 C:TRP79 5.0 46.4 1.0

Iron binding site 9 out of 9 in 7szg

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Iron binding site 9 out of 9 in the Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of the Rieske Non-Heme Iron Oxygenase Gxta Pressurized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe504

b:49.3
occ:1.00
 OD2 C:ASP280 2.1 43.1 1.0
NE2 C:HIS169 2.1 50.0 1.0
NE2 C:HIS164 2.2 43.5 1.0
O C:HOH660 2.2 47.1 1.0
OD1 C:ASP280 2.3 40.9 1.0
CG C:ASP280 2.5 44.0 1.0
O C:HOH610 2.5 43.0 1.0
CE1 C:HIS164 3.0 47.0 1.0
CD2 C:HIS169 3.1 47.7 1.0
CE1 C:HIS169 3.1 43.8 1.0
CD2 C:HIS164 3.2 41.8 1.0
CB C:ASP280 4.0 36.6 1.0
OD1 C:ASN158 4.0 45.2 1.0
ND2 C:ASN158 4.0 34.8 1.0
ND1 C:HIS169 4.2 47.0 1.0
ND1 C:HIS164 4.2 43.3 1.0
CG C:HIS169 4.2 45.1 1.0
CG C:HIS164 4.3 44.3 1.0
O C:HOH621 4.4 49.1 1.0
CG C:ASN158 4.4 38.7 1.0
CG1 C:VAL276 4.5 42.1 1.0
CD1 C:ILE168 4.5 46.4 1.0
CE1 C:PHE165 4.5 54.2 1.0
O C:HOH619 4.5 66.2 1.0
O C:ASN158 4.7 33.2 1.0
CD1 C:PHE165 4.8 49.8 1.0
O C:HOH602 4.8 53.5 1.0
CA C:ASP280 4.9 39.2 1.0
CG1 C:ILE168 5.0 47.2 1.0
O C:VAL276 5.0 43.3 1.0

Reference:

J.Liu, J.Tian, C.Perry, A.L.Lukowski, T.I.Doukov, A.R.H.Narayan, J.Bridwell-Rabb. Design Principles For Site-Selective Hydroxylation By A Rieske Oxygenase. Nat Commun V. 13 255 2022.
ISSN: ESSN 2041-1723
PubMed: 35017498
DOI: 10.1038/S41467-021-27822-3
Page generated: Fri Aug 9 00:58:29 2024

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