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Iron in PDB 5hr7: X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna

Enzymatic activity of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna

All present enzymatic activity of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna:
2.1.1.192;

Protein crystallography data

The structure of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna, PDB code: 5hr7 was solved by E.L.Schwalm, T.L.Grove, S.J.Booker, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.717, 70.383, 151.810, 90.00, 90.11, 90.00
R / Rfree (%) 21.6 / 24.8

Other elements in 5hr7:

The structure of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms
Arsenic (As) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna (pdb code 5hr7). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna, PDB code: 5hr7:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5hr7

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Iron binding site 1 out of 8 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:47.1
occ:1.00
 FE1 B:SF4501 0.0 47.1 1.0
S2 B:SF4501 2.1 44.8 1.0
S3 B:SF4501 2.1 45.4 1.0
S4 B:SF4501 2.1 45.1 1.0
SG B:CYS132 2.2 43.3 1.0
CB B:CYS132 3.0 42.8 1.0
FE4 B:SF4501 3.0 47.5 1.0
FE2 B:SF4501 3.1 47.4 1.0
FE3 B:SF4501 3.1 49.5 1.0
S1 B:SF4501 3.7 48.7 1.0
SD B:MET503 4.1 59.0 1.0
CE B:MET503 4.1 60.2 1.0
CB B:THR134 4.2 42.1 1.0
N B:ALA135 4.3 46.1 1.0
CB B:CYS129 4.5 49.0 1.0
CA B:CYS132 4.5 42.1 1.0
CB B:ALA135 4.7 44.5 1.0
OG1 B:THR134 4.7 40.9 1.0
C8 B:5AD502 4.8 47.9 1.0
SG B:CYS129 4.9 49.7 1.0
CG2 B:THR134 4.9 42.5 1.0
CB B:CYS125 5.0 46.0 1.0
CA B:THR134 5.0 43.0 1.0
SG B:CYS125 5.0 45.1 1.0

Iron binding site 2 out of 8 in 5hr7

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Iron binding site 2 out of 8 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:47.4
occ:1.00
 FE2 B:SF4501 0.0 47.4 1.0
S4 B:SF4501 2.1 45.1 1.0
S1 B:SF4501 2.1 48.7 1.0
S3 B:SF4501 2.1 45.4 1.0
SG B:CYS129 2.2 49.7 1.0
CB B:CYS129 3.0 49.0 1.0
FE3 B:SF4501 3.0 49.5 1.0
FE1 B:SF4501 3.1 47.1 1.0
FE4 B:SF4501 3.1 47.5 1.0
O B:HOH602 3.4 53.6 1.0
S2 B:SF4501 3.7 44.8 1.0
OG B:SER213 3.8 57.7 1.0
OXT B:MET503 4.0 60.2 1.0
N B:CYS129 4.1 50.8 1.0
CA B:CYS129 4.1 49.6 1.0
CB B:LEU127 4.4 53.9 1.0
CB B:CYS132 4.8 42.8 1.0
CB B:SER213 4.8 52.6 1.0
SG B:CYS132 4.9 43.3 1.0
SG B:CYS125 4.9 45.1 1.0

Iron binding site 3 out of 8 in 5hr7

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Iron binding site 3 out of 8 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:49.5
occ:1.00
 FE3 B:SF4501 0.0 49.5 1.0
S1 B:SF4501 2.1 48.7 1.0
S4 B:SF4501 2.1 45.1 1.0
S2 B:SF4501 2.2 44.8 1.0
SD B:MET503 2.3 59.0 1.0
OXT B:MET503 2.4 60.2 1.0
N B:MET503 2.4 57.1 1.0
C B:MET503 3.0 58.2 1.0
FE2 B:SF4501 3.0 47.4 1.0
FE1 B:SF4501 3.1 47.1 1.0
FE4 B:SF4501 3.1 47.5 1.0
CA B:MET503 3.1 57.9 1.0
CG B:MET503 3.5 59.6 1.0
CE B:MET503 3.7 60.2 1.0
S3 B:SF4501 3.7 45.4 1.0
CB B:MET503 3.8 57.1 1.0
O B:MET503 4.1 59.3 1.0
O B:HOH602 4.3 53.6 1.0
OG B:SER213 4.3 57.7 1.0
O2' B:5AD502 4.6 52.3 1.0
C2' B:5AD502 4.6 52.0 1.0
O B:GLY179 4.7 40.6 1.0
SG B:CYS132 5.0 43.3 1.0
OE2 B:GLU180 5.0 41.8 1.0

Iron binding site 4 out of 8 in 5hr7

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Iron binding site 4 out of 8 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:47.5
occ:1.00
 FE4 B:SF4501 0.0 47.5 1.0
S2 B:SF4501 2.1 44.8 1.0
S3 B:SF4501 2.1 45.4 1.0
SG B:CYS125 2.1 45.1 1.0
S1 B:SF4501 2.2 48.7 1.0
CB B:CYS125 3.0 46.0 1.0
FE1 B:SF4501 3.0 47.1 1.0
FE2 B:SF4501 3.1 47.4 1.0
FE3 B:SF4501 3.1 49.5 1.0
S4 B:SF4501 3.7 45.1 1.0
CB B:LEU127 4.1 53.9 1.0
N B:MET503 4.2 57.1 1.0
N B:GLU180 4.4 42.8 1.0
CA B:CYS125 4.4 48.5 1.0
C B:GLY179 4.5 41.1 1.0
CA B:GLY179 4.6 42.5 1.0
N B:LEU127 4.6 56.4 1.0
CG B:LEU127 4.7 55.7 1.0
CB B:GLU180 4.8 43.2 1.0
N B:GLY179 4.8 41.3 1.0
CA B:LEU127 4.9 56.1 1.0
C B:CYS125 4.9 50.4 1.0
CA B:GLU180 5.0 43.6 1.0
CD1 B:LEU127 5.0 55.0 1.0
O B:GLY179 5.0 40.6 1.0

Iron binding site 5 out of 8 in 5hr7

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Iron binding site 5 out of 8 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:52.2
occ:1.00
 FE1 A:SF4501 0.0 52.2 1.0
S2 A:SF4501 2.1 51.9 1.0
S4 A:SF4501 2.1 49.5 1.0
S3 A:SF4501 2.2 47.1 1.0
SD A:MET503 2.3 62.2 1.0
O A:MET503 2.4 61.5 1.0
N A:MET503 2.4 58.0 1.0
C A:MET503 3.1 59.0 1.0
FE2 A:SF4501 3.1 51.1 1.0
FE3 A:SF4501 3.1 51.7 1.0
FE4 A:SF4501 3.1 51.3 1.0
CA A:MET503 3.2 58.8 1.0
CE A:MET503 3.5 62.3 1.0
CG A:MET503 3.5 60.7 1.0
S1 A:SF4501 3.7 48.7 1.0
CB A:MET503 3.9 58.3 1.0
OXT A:MET503 4.2 60.3 1.0
O2' A:5AD502 4.3 56.5 1.0
OG A:SER213 4.4 62.5 1.0
O A:HOH604 4.5 54.5 1.0
O A:GLY179 4.7 42.8 1.0
C2' A:5AD502 4.8 54.5 1.0
SG A:CYS132 4.9 46.3 1.0
C A:GLY179 5.0 43.8 1.0

Iron binding site 6 out of 8 in 5hr7

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Iron binding site 6 out of 8 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:51.1
occ:1.00
 FE2 A:SF4501 0.0 51.1 1.0
S3 A:SF4501 2.1 47.1 1.0
S1 A:SF4501 2.1 48.7 1.0
S4 A:SF4501 2.1 49.5 1.0
SG A:CYS132 2.2 46.3 1.0
CB A:CYS132 3.1 46.5 1.0
FE4 A:SF4501 3.1 51.3 1.0
FE1 A:SF4501 3.1 52.2 1.0
FE3 A:SF4501 3.1 51.7 1.0
S2 A:SF4501 3.7 51.9 1.0
CE A:MET503 3.9 62.3 1.0
CB A:THR134 4.1 45.8 1.0
SD A:MET503 4.1 62.2 1.0
N A:ALA135 4.3 48.6 1.0
CB A:CYS129 4.5 50.8 1.0
CA A:CYS132 4.5 45.5 1.0
OG1 A:THR134 4.7 43.4 1.0
CB A:ALA135 4.7 46.4 1.0
C8 A:5AD502 4.9 51.2 1.0
SG A:CYS129 4.9 50.7 1.0
CG2 A:THR134 4.9 46.2 1.0
SG A:CYS125 4.9 46.1 1.0
CB A:CYS125 4.9 47.8 1.0
CA A:THR134 4.9 46.1 1.0
C A:THR134 5.0 48.4 1.0
CA A:ALA135 5.0 46.7 1.0

Iron binding site 7 out of 8 in 5hr7

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Iron binding site 7 out of 8 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:51.7
occ:1.00
 FE3 A:SF4501 0.0 51.7 1.0
S2 A:SF4501 2.1 51.9 1.0
S4 A:SF4501 2.1 49.5 1.0
S1 A:SF4501 2.2 48.7 1.0
SG A:CYS129 2.2 50.7 1.0
CB A:CYS129 3.0 50.8 1.0
FE1 A:SF4501 3.1 52.2 1.0
FE4 A:SF4501 3.1 51.3 1.0
FE2 A:SF4501 3.1 51.1 1.0
O A:HOH604 3.6 54.5 1.0
S3 A:SF4501 3.7 47.1 1.0
OG A:SER213 3.9 62.5 1.0
N A:CYS129 4.1 52.5 1.0
O A:MET503 4.1 61.5 1.0
CA A:CYS129 4.1 52.0 1.0
CB A:LEU127 4.3 55.3 1.0
CB A:CYS132 4.9 46.5 1.0
CB A:SER213 4.9 56.2 1.0
SG A:CYS125 4.9 46.1 1.0
O2' A:5AD502 5.0 56.5 1.0
SG A:CYS132 5.0 46.3 1.0

Iron binding site 8 out of 8 in 5hr7

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Iron binding site 8 out of 8 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with Cross-Linked in Vitro Transcribed Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:51.3
occ:1.00
 FE4 A:SF4501 0.0 51.3 1.0
SG A:CYS125 2.1 46.1 1.0
S3 A:SF4501 2.1 47.1 1.0
S1 A:SF4501 2.1 48.7 1.0
S2 A:SF4501 2.2 51.9 1.0
CB A:CYS125 3.0 47.8 1.0
FE2 A:SF4501 3.1 51.1 1.0
FE3 A:SF4501 3.1 51.7 1.0
FE1 A:SF4501 3.1 52.2 1.0
S4 A:SF4501 3.7 49.5 1.0
CB A:LEU127 4.1 55.3 1.0
N A:MET503 4.2 58.0 1.0
N A:GLU180 4.4 45.8 1.0
CA A:CYS125 4.4 49.2 1.0
C A:GLY179 4.5 43.8 1.0
CA A:GLY179 4.6 46.1 1.0
N A:LEU127 4.6 58.0 1.0
CG A:LEU127 4.7 57.3 1.0
CB A:GLU180 4.8 45.7 1.0
N A:GLY179 4.8 45.2 1.0
CA A:LEU127 4.8 57.8 1.0
C A:CYS125 4.9 51.2 1.0
O A:GLY179 5.0 42.8 1.0
CA A:GLU180 5.0 46.1 1.0

Reference:

E.L.Schwalm, T.L.Grove, S.J.Booker, A.K.Boal. Crystallographic Capture of A Radical S-Adenosylmethionine Enzyme in the Act of Modifying Trna. Science V. 352 309 2016.
ISSN: ESSN 1095-9203
PubMed: 27081063
DOI: 10.1126/SCIENCE.AAD5367
Page generated: Tue Aug 5 21:56:22 2025

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