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Iron in PDB 3rf9: X-Ray Structure of Rlmn From Escherichia Coli

Enzymatic activity of X-Ray Structure of Rlmn From Escherichia Coli

All present enzymatic activity of X-Ray Structure of Rlmn From Escherichia Coli:
2.1.1.192;

Protein crystallography data

The structure of X-Ray Structure of Rlmn From Escherichia Coli, PDB code: 3rf9 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 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 72.152, 80.406, 312.242, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 26.7

Iron Binding Sites:

The binding sites of Iron atom in the X-Ray Structure of Rlmn From Escherichia Coli (pdb code 3rf9). 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, PDB code: 3rf9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3rf9

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Iron binding site 1 out of 8 in the X-Ray Structure of Rlmn From Escherichia Coli


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe405

b:36.3
occ:1.00
 FE1 A:SF4405 0.0 36.3 1.0
S2 A:SF4405 2.2 34.2 1.0
S4 A:SF4405 2.3 34.2 1.0
S3 A:SF4405 2.4 34.5 1.0
FE3 A:SF4405 2.6 34.3 1.0
FE4 A:SF4405 2.8 33.6 1.0
FE2 A:SF4405 2.8 36.0 1.0
O A:HOH412 3.6 32.8 1.0
S1 A:SF4405 3.9 34.3 1.0
O A:GLY177 4.5 40.7 1.0
O A:GLY179 4.5 36.3 1.0
SG A:CYS132 4.6 39.5 1.0
OG A:SER213 4.7 28.4 1.0
O A:HOH606 4.7 19.2 1.0
SG A:CYS125 4.8 34.1 1.0
C A:GLY179 4.8 36.2 1.0
SG A:CYS129 4.9 36.4 1.0

Iron binding site 2 out of 8 in 3rf9

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Iron binding site 2 out of 8 in the X-Ray Structure of Rlmn From Escherichia Coli


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe405

b:36.0
occ:1.00
 FE2 A:SF4405 0.0 36.0 1.0
S1 A:SF4405 2.2 34.3 1.0
SG A:CYS132 2.2 39.5 1.0
S3 A:SF4405 2.3 34.5 1.0
S4 A:SF4405 2.4 34.2 1.0
FE4 A:SF4405 2.5 33.6 1.0
FE3 A:SF4405 2.7 34.3 1.0
FE1 A:SF4405 2.8 36.3 1.0
CB A:CYS132 3.0 40.4 1.0
S2 A:SF4405 3.9 34.2 1.0
CB A:CYS129 4.2 36.5 1.0
CA A:CYS132 4.5 41.1 1.0
N A:ALA135 4.5 46.0 1.0
SG A:CYS129 4.5 36.4 1.0
CB A:THR134 4.6 44.2 1.0
CB A:ALA135 4.7 46.6 1.0
CB A:CYS125 4.8 34.6 1.0
SG A:CYS125 4.9 34.1 1.0
CA A:ALA135 5.0 46.7 1.0

Iron binding site 3 out of 8 in 3rf9

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Iron binding site 3 out of 8 in the X-Ray Structure of Rlmn From Escherichia Coli


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe405

b:34.3
occ:1.00
 FE3 A:SF4405 0.0 34.3 1.0
S4 A:SF4405 2.2 34.2 1.0
S2 A:SF4405 2.3 34.2 1.0
SG A:CYS125 2.3 34.1 1.0
S1 A:SF4405 2.4 34.3 1.0
FE1 A:SF4405 2.6 36.3 1.0
FE2 A:SF4405 2.7 36.0 1.0
FE4 A:SF4405 2.8 33.6 1.0
CB A:CYS125 3.0 34.6 1.0
S3 A:SF4405 3.9 34.5 1.0
CB A:LEU127 4.0 35.8 1.0
C A:GLY179 4.4 36.2 1.0
N A:GLU180 4.5 35.3 1.0
CA A:GLY179 4.5 37.5 1.0
CA A:CYS125 4.5 35.1 1.0
N A:GLY179 4.7 38.8 1.0
N A:LEU127 4.7 36.9 1.0
SG A:CYS132 4.7 39.5 1.0
CD2 A:LEU127 4.8 35.5 1.0
O A:GLY179 4.8 36.3 1.0
SG A:CYS129 4.9 36.4 1.0
CA A:LEU127 4.9 36.9 1.0
CB A:GLU180 4.9 34.2 1.0
CG A:LEU127 4.9 36.0 1.0
O A:HOH412 5.0 32.8 1.0

Iron binding site 4 out of 8 in 3rf9

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Iron binding site 4 out of 8 in the X-Ray Structure of Rlmn From Escherichia Coli


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe405

b:33.6
occ:1.00
 FE4 A:SF4405 0.0 33.6 1.0
S3 A:SF4405 2.2 34.5 1.0
S1 A:SF4405 2.3 34.3 1.0
SG A:CYS129 2.3 36.4 1.0
S2 A:SF4405 2.4 34.2 1.0
FE2 A:SF4405 2.5 36.0 1.0
FE1 A:SF4405 2.8 36.3 1.0
FE3 A:SF4405 2.8 34.3 1.0
CB A:CYS129 3.0 36.5 1.0
O A:HOH606 3.6 19.2 1.0
S4 A:SF4405 3.9 34.2 1.0
CB A:LEU127 4.2 35.8 1.0
N A:CYS129 4.2 37.8 1.0
CA A:CYS129 4.2 37.6 1.0
OG A:SER213 4.4 28.4 1.0
CB A:CYS132 4.5 40.4 1.0
SG A:CYS132 4.5 39.5 1.0
CD2 A:LEU127 4.7 35.5 1.0
O A:HOH447 4.8 18.0 1.0
SG A:CYS125 4.9 34.1 1.0

Iron binding site 5 out of 8 in 3rf9

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Iron binding site 5 out of 8 in the X-Ray Structure of Rlmn From Escherichia Coli


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe405

b:29.1
occ:1.00
 FE1 B:SF4405 0.0 29.1 1.0
S2 B:SF4405 2.2 29.2 1.0
SG B:CYS125 2.3 27.5 1.0
S4 B:SF4405 2.3 28.5 1.0
S3 B:SF4405 2.4 29.6 1.0
FE3 B:SF4405 2.7 30.7 1.0
FE4 B:SF4405 2.7 30.8 1.0
FE2 B:SF4405 2.8 28.2 1.0
CB B:CYS125 3.1 28.3 1.0
S1 B:SF4405 3.8 29.3 1.0
CB B:LEU127 4.0 29.2 1.0
C B:GLY179 4.3 28.8 1.0
CA B:GLY179 4.4 30.2 1.0
N B:GLU180 4.5 27.9 1.0
CA B:CYS125 4.5 29.0 1.0
N B:GLY179 4.6 31.6 1.0
O B:GLY179 4.6 28.6 1.0
N B:LEU127 4.7 30.0 1.0
SG B:CYS132 4.8 32.8 1.0
CD2 B:LEU127 4.8 29.9 1.0
CA B:LEU127 4.9 30.1 1.0
CG B:LEU127 4.9 29.4 1.0
CB B:GLU180 5.0 26.7 1.0

Iron binding site 6 out of 8 in 3rf9

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Iron binding site 6 out of 8 in the X-Ray Structure of Rlmn From Escherichia Coli


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe405

b:28.2
occ:1.00
 FE2 B:SF4405 0.0 28.2 1.0
S1 B:SF4405 2.2 29.3 1.0
S3 B:SF4405 2.3 29.6 1.0
S4 B:SF4405 2.4 28.5 1.0
SG B:CYS129 2.4 29.4 1.0
FE4 B:SF4405 2.6 30.8 1.0
FE1 B:SF4405 2.8 29.1 1.0
FE3 B:SF4405 2.8 30.7 1.0
CB B:CYS129 3.1 29.2 1.0
O B:HOH415 3.8 18.7 1.0
S2 B:SF4405 3.9 29.2 1.0
CB B:LEU127 4.1 29.2 1.0
N B:CYS129 4.1 30.5 1.0
CA B:CYS129 4.2 30.2 1.0
OG B:SER213 4.4 24.4 1.0
CB B:CYS132 4.5 32.7 1.0
SG B:CYS132 4.6 32.8 1.0
CD2 B:LEU127 4.7 29.9 1.0
SG B:CYS125 4.8 27.5 1.0

Iron binding site 7 out of 8 in 3rf9

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Iron binding site 7 out of 8 in the X-Ray Structure of Rlmn From Escherichia Coli


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe405

b:30.7
occ:1.00
 FE3 B:SF4405 0.0 30.7 1.0
S4 B:SF4405 2.3 28.5 1.0
S2 B:SF4405 2.3 29.2 1.0
S1 B:SF4405 2.3 29.3 1.0
FE1 B:SF4405 2.7 29.1 1.0
FE4 B:SF4405 2.7 30.8 1.0
FE2 B:SF4405 2.8 28.2 1.0
O B:HOH501 3.7 17.4 1.0
S3 B:SF4405 4.0 29.6 1.0
O B:GLY177 4.3 34.4 1.0
O B:GLY179 4.4 28.6 1.0
SG B:CYS132 4.6 32.8 1.0
OG B:SER213 4.7 24.4 1.0
SG B:CYS125 4.7 27.5 1.0
O B:HOH415 4.8 18.7 1.0
C B:GLY179 4.8 28.8 1.0

Iron binding site 8 out of 8 in 3rf9

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Iron binding site 8 out of 8 in the X-Ray Structure of Rlmn From Escherichia Coli


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe405

b:30.8
occ:1.00
 FE4 B:SF4405 0.0 30.8 1.0
S3 B:SF4405 2.2 29.6 1.0
SG B:CYS132 2.2 32.8 1.0
S1 B:SF4405 2.3 29.3 1.0
S2 B:SF4405 2.4 29.2 1.0
FE2 B:SF4405 2.6 28.2 1.0
FE1 B:SF4405 2.7 29.1 1.0
FE3 B:SF4405 2.7 30.7 1.0
CB B:CYS132 3.1 32.7 1.0
S4 B:SF4405 3.8 28.5 1.0
CB B:CYS129 4.4 29.2 1.0
CB B:THR134 4.4 37.8 1.0
N B:ALA135 4.4 39.9 1.0
CA B:CYS132 4.5 33.5 1.0
CB B:ALA135 4.6 40.5 1.0
SG B:CYS129 4.7 29.4 1.0
SG B:CYS125 4.7 27.5 1.0
CB B:CYS125 4.7 28.3 1.0
CA B:ALA135 4.9 40.8 1.0
CG2 B:THR134 5.0 37.9 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 Dec 13 15:20:01 2020

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