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Iron in PDB 4pl1: X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with S- Adenosylmethionine

Enzymatic activity of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with S- Adenosylmethionine

All present enzymatic activity of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with S- Adenosylmethionine:
2.1.1.192;

Protein crystallography data

The structure of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with S- Adenosylmethionine, PDB code: 4pl1 was solved by A.K.Boal, A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.85 / 2.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.627, 55.729, 254.032, 90.00, 90.00, 90.00
R / Rfree (%) 26.3 / 30

Iron Binding Sites:

The binding sites of Iron atom in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with S- Adenosylmethionine (pdb code 4pl1). 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 S- Adenosylmethionine, PDB code: 4pl1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4pl1

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Iron binding site 1 out of 8 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with S- Adenosylmethionine


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 S- Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:56.1
occ:1.00
 FE1 B:SF4402 0.0 56.1 1.0
S2 B:SF4402 2.2 54.5 1.0
S4 B:SF4402 2.2 54.3 1.0
S3 B:SF4402 2.2 54.2 1.0
SG B:CYS129 2.2 53.5 1.0
FE3 B:SF4402 2.8 53.7 1.0
FE4 B:SF4402 2.8 53.5 1.0
FE2 B:SF4402 2.9 55.6 1.0
CB B:CYS129 3.1 55.2 1.0
S1 B:SF4402 3.8 54.6 1.0
N B:CYS129 4.2 57.1 1.0
CA B:CYS129 4.2 56.0 1.0
OXT B:SAM401 4.4 54.4 1.0
CB B:LEU127 4.4 55.8 1.0
CB B:CYS132 4.7 52.2 1.0
SG B:CYS125 4.7 46.2 1.0
N B:SAM401 4.8 55.3 1.0
SG B:CYS132 4.9 50.2 1.0
CB B:SER213 5.0 45.0 1.0

Iron binding site 2 out of 8 in 4pl1

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Iron binding site 2 out of 8 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with S- Adenosylmethionine


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 S- Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:55.6
occ:1.00
 FE2 B:SF4402 0.0 55.6 1.0
S1 B:SF4402 2.2 54.6 1.0
S3 B:SF4402 2.2 54.2 1.0
S4 B:SF4402 2.2 54.3 1.0
SG B:CYS132 2.3 50.2 1.0
FE4 B:SF4402 2.8 53.5 1.0
FE1 B:SF4402 2.9 56.1 1.0
FE3 B:SF4402 2.9 53.7 1.0
CB B:CYS132 3.0 52.2 1.0
S2 B:SF4402 3.8 54.5 1.0
CE B:SAM401 4.2 56.4 1.0
SD B:SAM401 4.5 56.3 1.0
CA B:CYS132 4.5 53.1 1.0
CB B:CYS129 4.5 55.2 1.0
SG B:CYS129 4.7 53.5 1.0
SG B:CYS125 4.8 46.2 1.0
CB B:THR134 4.8 59.4 1.0
C8 B:SAM401 4.9 59.9 1.0
CB B:CYS125 4.9 48.2 1.0

Iron binding site 3 out of 8 in 4pl1

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Iron binding site 3 out of 8 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with S- Adenosylmethionine


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 S- Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:53.7
occ:1.00
 FE3 B:SF4402 0.0 53.7 1.0
SG B:CYS125 2.1 46.2 1.0
S4 B:SF4402 2.2 54.3 1.0
S2 B:SF4402 2.2 54.5 1.0
S1 B:SF4402 2.2 54.6 1.0
FE1 B:SF4402 2.8 56.1 1.0
FE2 B:SF4402 2.9 55.6 1.0
FE4 B:SF4402 2.9 53.5 1.0
CB B:CYS125 3.1 48.2 1.0
S3 B:SF4402 3.8 54.2 1.0
N B:SAM401 4.1 55.3 1.0
CB B:LEU127 4.2 55.8 1.0
CA B:CYS125 4.5 49.1 1.0
C B:GLY179 4.6 43.1 1.0
O B:GLY179 4.6 44.0 1.0
N B:GLU180 4.7 42.8 1.0
CD2 B:LEU127 4.8 54.9 1.0
N B:LEU127 4.8 54.7 1.0
CB B:GLU180 4.9 42.2 1.0
SG B:CYS129 4.9 53.5 1.0
CA B:LEU127 5.0 56.0 1.0
CA B:GLY179 5.0 43.1 1.0
C B:CYS125 5.0 49.5 1.0

Iron binding site 4 out of 8 in 4pl1

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Iron binding site 4 out of 8 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with S- Adenosylmethionine


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 S- Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:53.5
occ:1.00
 FE4 B:SF4402 0.0 53.5 1.0
S3 B:SF4402 2.2 54.2 1.0
S1 B:SF4402 2.2 54.6 1.0
S2 B:SF4402 2.2 54.5 1.0
N B:SAM401 2.5 55.3 1.0
OXT B:SAM401 2.6 54.4 1.0
FE2 B:SF4402 2.8 55.6 1.0
FE1 B:SF4402 2.8 56.1 1.0
FE3 B:SF4402 2.9 53.7 1.0
SD B:SAM401 3.1 56.3 1.0
C B:SAM401 3.2 55.2 1.0
CA B:SAM401 3.3 55.6 1.0
CG B:SAM401 3.4 55.6 1.0
S4 B:SF4402 3.8 54.3 1.0
CB B:SAM401 3.8 55.4 1.0
CE B:SAM401 3.9 56.4 1.0
O B:GLY179 4.3 44.0 1.0
O B:SAM401 4.4 55.8 1.0
C5' B:SAM401 4.7 57.7 1.0
SG B:CYS125 4.8 46.2 1.0
SG B:CYS132 4.9 50.2 1.0
SG B:CYS129 4.9 53.5 1.0
OE1 B:GLU180 4.9 42.2 1.0

Iron binding site 5 out of 8 in 4pl1

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Iron binding site 5 out of 8 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with S- Adenosylmethionine


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 S- Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:59.5
occ:1.00
 FE1 A:SF4402 0.0 59.5 1.0
S4 A:SF4402 2.2 56.1 1.0
S2 A:SF4402 2.2 58.0 1.0
S3 A:SF4402 2.2 59.7 1.0
SG A:CYS125 2.3 59.5 1.0
FE2 A:SF4402 2.8 59.0 1.0
FE3 A:SF4402 2.8 58.5 1.0
FE4 A:SF4402 2.9 58.0 1.0
CB A:CYS125 3.0 59.0 1.0
S1 A:SF4402 3.8 57.6 1.0
N A:SAM401 4.1 58.1 1.0
CB A:LEU127 4.2 66.5 1.0
O A:GLY179 4.4 58.2 1.0
C A:GLY179 4.4 59.0 1.0
CA A:CYS125 4.5 59.1 1.0
CD2 A:LEU127 4.6 66.9 1.0
CA A:GLY179 4.8 58.9 1.0
N A:GLU180 4.8 58.8 1.0
CG A:LEU127 4.9 66.6 1.0
SG A:CYS132 4.9 64.4 1.0
N A:GLY179 4.9 60.0 1.0
N A:LEU127 5.0 64.7 1.0
SG A:CYS129 5.0 64.0 1.0

Iron binding site 6 out of 8 in 4pl1

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Iron binding site 6 out of 8 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with S- Adenosylmethionine


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 S- Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:59.0
occ:1.00
 FE2 A:SF4402 0.0 59.0 1.0
S3 A:SF4402 2.2 59.7 1.0
S1 A:SF4402 2.2 57.6 1.0
S4 A:SF4402 2.2 56.1 1.0
SG A:CYS129 2.4 64.0 1.0
FE4 A:SF4402 2.8 58.0 1.0
FE1 A:SF4402 2.8 59.5 1.0
FE3 A:SF4402 2.8 58.5 1.0
CB A:CYS129 3.1 65.2 1.0
S2 A:SF4402 3.8 58.0 1.0
CB A:LEU127 4.2 66.5 1.0
CA A:CYS129 4.3 66.6 1.0
N A:CYS129 4.3 67.1 1.0
OXT A:SAM401 4.4 58.8 1.0
CB A:CYS132 4.7 66.4 1.0
CD2 A:LEU127 4.7 66.9 1.0
SG A:CYS125 4.8 59.5 1.0
OG A:SER213 4.8 55.4 1.0
SG A:CYS132 4.9 64.4 1.0
N A:SAM401 4.9 58.1 1.0
CB A:SER213 5.0 54.3 1.0

Iron binding site 7 out of 8 in 4pl1

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Iron binding site 7 out of 8 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with S- Adenosylmethionine


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 S- Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:58.5
occ:1.00
 FE3 A:SF4402 0.0 58.5 1.0
S2 A:SF4402 2.2 58.0 1.0
S1 A:SF4402 2.2 57.6 1.0
S4 A:SF4402 2.2 56.1 1.0
SG A:CYS132 2.4 64.4 1.0
FE1 A:SF4402 2.8 59.5 1.0
FE2 A:SF4402 2.8 59.0 1.0
FE4 A:SF4402 2.9 58.0 1.0
CB A:CYS132 3.1 66.4 1.0
S3 A:SF4402 3.8 59.7 1.0
CE A:SAM401 4.0 56.8 1.0
CB A:CYS129 4.5 65.2 1.0
SD A:SAM401 4.5 56.2 1.0
CA A:CYS132 4.6 67.3 1.0
CB A:THR134 4.7 75.4 1.0
C8 A:SAM401 4.7 59.6 1.0
SG A:CYS129 4.8 64.0 1.0
CB A:CYS125 4.9 59.0 1.0
SG A:CYS125 5.0 59.5 1.0

Iron binding site 8 out of 8 in 4pl1

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Iron binding site 8 out of 8 in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli with S- Adenosylmethionine


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 S- Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:58.0
occ:1.00
 FE4 A:SF4402 0.0 58.0 1.0
S3 A:SF4402 2.2 59.7 1.0
S1 A:SF4402 2.2 57.6 1.0
S2 A:SF4402 2.3 58.0 1.0
OXT A:SAM401 2.4 58.8 1.0
N A:SAM401 2.6 58.1 1.0
FE2 A:SF4402 2.8 59.0 1.0
FE1 A:SF4402 2.9 59.5 1.0
FE3 A:SF4402 2.9 58.5 1.0
SD A:SAM401 3.1 56.2 1.0
C A:SAM401 3.2 58.3 1.0
CA A:SAM401 3.3 58.2 1.0
CG A:SAM401 3.6 56.5 1.0
S4 A:SF4402 3.8 56.1 1.0
CE A:SAM401 3.9 56.8 1.0
CB A:SAM401 4.0 57.1 1.0
O A:SAM401 4.3 57.8 1.0
O A:GLY179 4.4 58.2 1.0
OE1 A:GLU180 4.6 55.4 1.0
C5' A:SAM401 4.8 58.0 1.0
C3' A:SAM401 4.9 58.9 1.0
C2' A:SAM401 4.9 59.3 1.0
OG A:SER213 5.0 55.4 1.0
SG A:CYS129 5.0 64.0 1.0
SG A:CYS125 5.0 59.5 1.0

Reference:

A.Silakov, T.L.Grove, M.I.Radle, M.R.Bauerle, M.T.Green, A.C.Rosenzweig, A.K.Boal, S.J.Booker. Characterization of A Cross-Linked Protein-Nucleic Acid Substrate Radical in the Reaction Catalyzed By Rlmn. J.Am.Chem.Soc. V. 136 8221 2014.
ISSN: ESSN 1520-5126
PubMed: 24806349
DOI: 10.1021/JA410560P
Page generated: Mon Aug 5 08:28:35 2024

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