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Iron in PDB 3rfa: X-Ray Structure of Rlmn From Escherichia Coli in Complex with S- Adenosylmethionine

Enzymatic activity of X-Ray Structure of Rlmn From Escherichia Coli in Complex with S- Adenosylmethionine

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

Protein crystallography data

The structure of X-Ray Structure of Rlmn From Escherichia Coli in Complex with S- Adenosylmethionine, PDB code: 3rfa was solved by A.K.Boal, T.L.Grove, M.I.Mclaughlin, N.Yennawar, S.J.Booker, A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.180, 55.621, 252.179, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 24.1

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 3rfa

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Iron binding site 1 out of 8 in the X-Ray Structure of Rlmn From Escherichia Coli in Complex 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 Structure of Rlmn From Escherichia Coli in Complex with S- Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe405

b:27.2
occ:1.00
 FE1 A:SF4405 0.0 27.2 1.0
S3 A:SF4405 2.2 27.7 1.0
S2 A:SF4405 2.3 27.0 1.0
SG A:CYS125 2.3 26.4 1.0
S4 A:SF4405 2.4 26.6 1.0
FE4 A:SF4405 2.7 29.0 1.0
FE2 A:SF4405 2.7 27.3 1.0
FE3 A:SF4405 2.8 26.7 1.0
CB A:CYS125 3.2 27.8 1.0
S1 A:SF4405 3.9 27.5 1.0
N A:SAM406 4.0 26.9 1.0
CB A:LEU127 4.0 30.7 1.0
C A:GLY179 4.6 25.7 1.0
N A:GLU180 4.6 25.6 1.0
CA A:CYS125 4.6 28.7 1.0
N A:LEU127 4.7 31.0 1.0
SG A:CYS132 4.7 33.8 1.0
SG A:CYS129 4.8 29.7 1.0
CB A:GLU180 4.8 25.7 1.0
CA A:LEU127 4.8 31.5 1.0
CA A:GLY179 4.8 26.3 1.0
O A:GLY179 4.8 25.3 1.0
CD2 A:LEU127 4.9 31.6 1.0

Iron binding site 2 out of 8 in 3rfa

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Iron binding site 2 out of 8 in the X-Ray Structure of Rlmn From Escherichia Coli in Complex 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 Structure of Rlmn From Escherichia Coli in Complex with S- Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe405

b:27.3
occ:1.00
 FE2 A:SF4405 0.0 27.3 1.0
SG A:CYS129 2.2 29.7 1.0
S3 A:SF4405 2.3 27.7 1.0
S4 A:SF4405 2.3 26.6 1.0
S1 A:SF4405 2.4 27.5 1.0
FE4 A:SF4405 2.7 29.0 1.0
FE1 A:SF4405 2.7 27.2 1.0
FE3 A:SF4405 2.8 26.7 1.0
CB A:CYS129 3.1 30.5 1.0
S2 A:SF4405 3.9 27.0 1.0
N A:CYS129 4.1 31.7 1.0
CA A:CYS129 4.2 31.5 1.0
CB A:LEU127 4.4 30.7 1.0
O A:SAM406 4.4 27.1 1.0
SG A:CYS132 4.5 33.8 1.0
CB A:CYS132 4.5 35.2 1.0
O A:HOH432 4.7 20.4 1.0
OG A:SER213 4.8 28.3 1.0
CB A:SER213 4.8 25.8 1.0
N A:SAM406 4.8 26.9 1.0
SG A:CYS125 4.8 26.4 1.0

Iron binding site 3 out of 8 in 3rfa

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Iron binding site 3 out of 8 in the X-Ray Structure of Rlmn From Escherichia Coli in Complex 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 Structure of Rlmn From Escherichia Coli in Complex with S- Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe405

b:26.7
occ:1.00
 FE3 A:SF4405 0.0 26.7 1.0
N A:SAM406 2.3 26.9 1.0
S1 A:SF4405 2.3 27.5 1.0
S4 A:SF4405 2.3 26.6 1.0
S2 A:SF4405 2.3 27.0 1.0
O A:SAM406 2.6 27.1 1.0
FE1 A:SF4405 2.8 27.2 1.0
FE2 A:SF4405 2.8 27.3 1.0
FE4 A:SF4405 2.8 29.0 1.0
CA A:SAM406 3.2 27.2 1.0
C A:SAM406 3.2 27.2 1.0
SD A:SAM406 3.3 28.5 1.0
CG A:SAM406 3.7 27.4 1.0
S3 A:SF4405 3.9 27.7 1.0
CB A:SAM406 4.0 27.1 1.0
CE A:SAM406 4.3 27.8 1.0
OXT A:SAM406 4.4 27.1 1.0
O A:GLY179 4.5 25.3 1.0
OE1 A:GLU180 4.7 23.0 1.0
SG A:CYS129 4.8 29.7 1.0
CB A:SER213 4.8 25.8 1.0
C3' A:SAM406 4.8 29.7 1.0
SG A:CYS125 4.8 26.4 1.0
OG A:SER213 4.8 28.3 1.0
SG A:CYS132 4.9 33.8 1.0
C5' A:SAM406 4.9 28.4 1.0
C2' A:SAM406 4.9 30.0 1.0
C A:GLY179 4.9 25.7 1.0

Iron binding site 4 out of 8 in 3rfa

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Iron binding site 4 out of 8 in the X-Ray Structure of Rlmn From Escherichia Coli in Complex 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 Structure of Rlmn From Escherichia Coli in Complex with S- Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe405

b:29.0
occ:1.00
 FE4 A:SF4405 0.0 29.0 1.0
SG A:CYS132 2.2 33.8 1.0
S3 A:SF4405 2.3 27.7 1.0
S1 A:SF4405 2.3 27.5 1.0
S2 A:SF4405 2.3 27.0 1.0
FE1 A:SF4405 2.7 27.2 1.0
FE2 A:SF4405 2.7 27.3 1.0
FE3 A:SF4405 2.8 26.7 1.0
CB A:CYS132 3.2 35.2 1.0
S4 A:SF4405 3.9 26.6 1.0
CE A:SAM406 4.3 27.8 1.0
SD A:SAM406 4.4 28.5 1.0
CB A:CYS129 4.6 30.5 1.0
CB A:THR134 4.6 41.2 1.0
SG A:CYS129 4.6 29.7 1.0
CA A:CYS132 4.7 35.7 1.0
SG A:CYS125 4.8 26.4 1.0
CB A:CYS125 4.8 27.8 1.0
N A:SAM406 4.8 26.9 1.0
C8 A:SAM406 4.8 30.1 1.0

Iron binding site 5 out of 8 in 3rfa

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Iron binding site 5 out of 8 in the X-Ray Structure of Rlmn From Escherichia Coli in Complex 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 Structure of Rlmn From Escherichia Coli in Complex with S- Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe405

b:22.5
occ:1.00
 FE1 B:SF4405 0.0 22.5 1.0
S4 B:SF4405 2.2 22.3 1.0
S3 B:SF4405 2.3 21.7 1.0
SG B:CYS129 2.3 26.1 1.0
S2 B:SF4405 2.4 22.0 1.0
FE2 B:SF4405 2.7 21.3 1.0
FE3 B:SF4405 2.7 21.9 1.0
FE4 B:SF4405 2.7 23.0 1.0
CB B:CYS129 3.1 26.4 1.0
O B:HOH489 3.6 23.5 1.0
S1 B:SF4405 3.9 21.6 1.0
N B:CYS129 4.1 27.6 1.0
CA B:CYS129 4.2 27.4 1.0
OXT B:SAM406 4.3 23.4 1.0
CB B:LEU127 4.4 26.4 1.0
CB B:CYS132 4.4 28.5 1.0
SG B:CYS132 4.5 26.6 1.0
N B:SAM406 4.7 23.1 1.0
SG B:CYS125 4.8 24.3 1.0
CB B:SER213 4.8 22.7 1.0
OG B:SER213 4.9 25.1 1.0
O B:HOH497 4.9 17.1 1.0

Iron binding site 6 out of 8 in 3rfa

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Iron binding site 6 out of 8 in the X-Ray Structure of Rlmn From Escherichia Coli in Complex 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 Structure of Rlmn From Escherichia Coli in Complex with S- Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe405

b:21.3
occ:1.00
 FE2 B:SF4405 0.0 21.3 1.0
S3 B:SF4405 2.2 21.7 1.0
S4 B:SF4405 2.3 22.3 1.0
N B:SAM406 2.3 23.1 1.0
S1 B:SF4405 2.4 21.6 1.0
OXT B:SAM406 2.5 23.4 1.0
FE1 B:SF4405 2.7 22.5 1.0
FE3 B:SF4405 2.8 21.9 1.0
FE4 B:SF4405 2.8 23.0 1.0
SD B:SAM406 3.2 22.7 1.0
CA B:SAM406 3.2 23.0 1.0
C B:SAM406 3.2 23.1 1.0
CG B:SAM406 3.6 22.9 1.0
S2 B:SF4405 4.0 22.0 1.0
CB B:SAM406 4.0 22.6 1.0
O B:HOH489 4.1 23.5 1.0
CE B:SAM406 4.1 22.8 1.0
O B:SAM406 4.4 23.1 1.0
O B:GLY179 4.5 19.1 1.0
OE1 B:GLU180 4.6 21.2 1.0
SG B:CYS125 4.8 24.3 1.0
SG B:CYS129 4.8 26.1 1.0
SG B:CYS132 4.8 26.6 1.0
C3' B:SAM406 4.8 25.3 1.0
CB B:SER213 4.8 22.7 1.0
C5' B:SAM406 4.9 23.5 1.0
OG B:SER213 4.9 25.1 1.0
C2' B:SAM406 5.0 26.0 1.0
C B:GLY179 5.0 19.6 1.0

Iron binding site 7 out of 8 in 3rfa

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Iron binding site 7 out of 8 in the X-Ray Structure of Rlmn From Escherichia Coli in Complex 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 Structure of Rlmn From Escherichia Coli in Complex with S- Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe405

b:21.9
occ:1.00
 FE3 B:SF4405 0.0 21.9 1.0
S2 B:SF4405 2.2 22.0 1.0
SG B:CYS125 2.3 24.3 1.0
S1 B:SF4405 2.3 21.6 1.0
S4 B:SF4405 2.4 22.3 1.0
FE4 B:SF4405 2.7 23.0 1.0
FE1 B:SF4405 2.7 22.5 1.0
FE2 B:SF4405 2.8 21.3 1.0
CB B:CYS125 3.2 24.4 1.0
S3 B:SF4405 3.9 21.7 1.0
N B:SAM406 4.0 23.1 1.0
CB B:LEU127 4.0 26.4 1.0
CA B:CYS125 4.6 24.8 1.0
C B:GLY179 4.7 19.6 1.0
N B:LEU127 4.7 26.6 1.0
N B:GLU180 4.7 19.5 1.0
SG B:CYS132 4.7 26.6 1.0
CD1 B:LEU127 4.7 29.1 1.0
CA B:LEU127 4.8 27.2 1.0
SG B:CYS129 4.8 26.1 1.0
CG B:LEU127 4.9 27.8 1.0
CB B:GLU180 4.9 20.1 1.0
O B:GLY179 4.9 19.1 1.0
CA B:GLY179 4.9 19.9 1.0

Iron binding site 8 out of 8 in 3rfa

Go back to Iron Binding Sites List in 3rfa
Iron binding site 8 out of 8 in the X-Ray Structure of Rlmn From Escherichia Coli in Complex 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 Structure of Rlmn From Escherichia Coli in Complex with S- Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe405

b:23.0
occ:1.00
 FE4 B:SF4405 0.0 23.0 1.0
SG B:CYS132 2.2 26.6 1.0
S1 B:SF4405 2.2 21.6 1.0
S2 B:SF4405 2.3 22.0 1.0
S3 B:SF4405 2.3 21.7 1.0
FE3 B:SF4405 2.7 21.9 1.0
FE1 B:SF4405 2.7 22.5 1.0
FE2 B:SF4405 2.8 21.3 1.0
CB B:CYS132 3.1 28.5 1.0
S4 B:SF4405 3.9 22.3 1.0
CE B:SAM406 4.1 22.8 1.0
SD B:SAM406 4.5 22.7 1.0
CB B:CYS129 4.5 26.4 1.0
CA B:CYS132 4.6 29.1 1.0
CB B:THR134 4.6 34.4 1.0
SG B:CYS129 4.7 26.1 1.0
SG B:CYS125 4.7 24.3 1.0
N B:ALA135 4.8 36.3 1.0
CB B:CYS125 4.8 24.4 1.0
C8 B:SAM406 4.8 26.0 1.0
N B:SAM406 4.9 23.1 1.0

Reference:

A.K.Boal, T.L.Grove, M.I.Mclaughlin, N.H.Yennawar, S.J.Booker, A.C.Rosenzweig. Structural Basis For Methyl Transfer By A Radical Sam Enzyme. Science V. 332 1089 2011.
ISSN: ISSN 0036-8075
PubMed: 21527678
DOI: 10.1126/SCIENCE.1205358
Page generated: Sun Aug 4 19:13:37 2024

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