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Iron in PDB 4pl2: X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli

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

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

Protein crystallography data

The structure of X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli, PDB code: 4pl2 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) 39.21 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.438, 55.384, 262.377, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 24.4

Iron Binding Sites:

The binding sites of Iron atom in the X-Ray Crystal Structure of C118A Rlmn From Escherichia Coli (pdb code 4pl2). 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, PDB code: 4pl2:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4pl2

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Iron binding site 1 out of 8 in the X-Ray Crystal Structure of C118A 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 Crystal Structure of C118A Rlmn From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:32.3
occ:1.00
 FE1 B:SF4401 0.0 32.3 1.0
SG B:CYS129 2.3 35.4 1.0
S4 B:SF4401 2.3 34.5 1.0
S3 B:SF4401 2.3 34.7 1.0
S2 B:SF4401 2.3 32.2 1.0
FE2 B:SF4401 2.7 35.1 1.0
FE3 B:SF4401 2.7 32.9 1.0
FE4 B:SF4401 2.8 35.2 1.0
CB B:CYS129 3.0 35.2 1.0
O B:HOH614 3.6 41.6 1.0
S1 B:SF4401 3.9 34.3 1.0
OG B:SER213 4.0 30.8 1.0
N B:CYS129 4.1 36.0 1.0
CB B:LEU127 4.2 38.2 1.0
CA B:CYS129 4.2 35.5 1.0
SG B:CYS132 4.5 38.9 1.0
CB B:CYS132 4.6 38.9 1.0
CD2 B:LEU127 4.8 38.8 1.0
SG B:CYS125 4.8 31.8 1.0
CB B:SER213 5.0 30.8 1.0

Iron binding site 2 out of 8 in 4pl2

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Iron binding site 2 out of 8 in the X-Ray Crystal Structure of C118A 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 Crystal Structure of C118A Rlmn From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:35.1
occ:1.00
 FE2 B:SF4401 0.0 35.1 1.0
SG B:CYS132 2.1 38.9 1.0
S1 B:SF4401 2.3 34.3 1.0
S3 B:SF4401 2.3 34.7 1.0
S4 B:SF4401 2.4 34.5 1.0
FE1 B:SF4401 2.7 32.3 1.0
FE4 B:SF4401 2.7 35.2 1.0
FE3 B:SF4401 2.7 32.9 1.0
CB B:CYS132 3.0 38.9 1.0
S2 B:SF4401 3.9 32.2 1.0
CB B:CYS129 4.4 35.2 1.0
CA B:GLY177 4.4 36.9 1.0
CB B:THR134 4.5 47.4 1.0
CA B:CYS132 4.5 38.6 1.0
N B:ALA135 4.6 49.2 1.0
SG B:CYS129 4.6 35.4 1.0
C B:GLY177 4.6 36.5 1.0
CB B:ALA135 4.6 50.4 1.0
O B:GLY177 4.7 38.1 1.0
SG B:CYS125 4.8 31.8 1.0
CB B:CYS125 4.8 32.7 1.0

Iron binding site 3 out of 8 in 4pl2

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Iron binding site 3 out of 8 in the X-Ray Crystal Structure of C118A 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 Crystal Structure of C118A Rlmn From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:32.9
occ:1.00
 FE3 B:SF4401 0.0 32.9 1.0
S4 B:SF4401 2.2 34.5 1.0
S1 B:SF4401 2.3 34.3 1.0
SG B:CYS125 2.3 31.8 1.0
S2 B:SF4401 2.3 32.2 1.0
FE1 B:SF4401 2.7 32.3 1.0
FE2 B:SF4401 2.7 35.1 1.0
FE4 B:SF4401 2.7 35.2 1.0
CB B:CYS125 3.2 32.7 1.0
S3 B:SF4401 3.9 34.7 1.0
CB B:LEU127 4.0 38.2 1.0
N B:GLU180 4.3 28.6 1.0
C B:GLY179 4.6 30.1 1.0
CA B:GLY179 4.6 30.5 1.0
CA B:CYS125 4.7 33.5 1.0
N B:LEU127 4.7 37.6 1.0
SG B:CYS132 4.7 38.9 1.0
N B:GLY179 4.7 30.8 1.0
CD2 B:LEU127 4.7 38.8 1.0
SG B:CYS129 4.8 35.4 1.0
CB B:GLU180 4.8 27.5 1.0
CA B:LEU127 4.8 37.7 1.0
CA B:GLU180 4.9 28.0 1.0
CG B:LEU127 4.9 38.5 1.0

Iron binding site 4 out of 8 in 4pl2

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Iron binding site 4 out of 8 in the X-Ray Crystal Structure of C118A 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 Crystal Structure of C118A Rlmn From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:35.2
occ:1.00
 FE4 B:SF4401 0.0 35.2 1.0
S1 B:SF4401 2.3 34.3 1.0
S3 B:SF4401 2.3 34.7 1.0
S2 B:SF4401 2.3 32.2 1.0
FE2 B:SF4401 2.7 35.1 1.0
FE3 B:SF4401 2.7 32.9 1.0
FE1 B:SF4401 2.8 32.3 1.0
CA B:GLY177 3.7 36.9 1.0
S4 B:SF4401 3.9 34.5 1.0
N B:GLY177 4.0 37.4 1.0
OG B:SER213 4.2 30.8 1.0
C B:GLY177 4.4 36.5 1.0
O B:HOH614 4.4 41.6 1.0
SG B:CYS132 4.6 38.9 1.0
N B:MET178 4.7 35.5 1.0
SG B:CYS129 4.8 35.4 1.0
SG B:CYS125 4.8 31.8 1.0
C B:GLY179 4.9 30.1 1.0
O B:GLY179 4.9 31.6 1.0
N B:GLY179 4.9 30.8 1.0

Iron binding site 5 out of 8 in 4pl2

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Iron binding site 5 out of 8 in the X-Ray Crystal Structure of C118A 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 Crystal Structure of C118A Rlmn From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:32.3
occ:1.00
 FE1 A:SF4401 0.0 32.3 1.0
S3 A:SF4401 2.2 34.9 1.0
S4 A:SF4401 2.3 34.1 1.0
S2 A:SF4401 2.4 32.1 1.0
SG A:CYS125 2.4 31.8 1.0
FE4 A:SF4401 2.7 32.6 1.0
FE2 A:SF4401 2.7 34.9 1.0
FE3 A:SF4401 2.7 35.3 1.0
CB A:CYS125 3.2 32.9 1.0
S1 A:SF4401 3.9 35.0 1.0
CB A:LEU127 4.1 38.1 1.0
N A:GLU180 4.2 29.4 1.0
SG A:CYS132 4.6 36.4 1.0
C A:GLY179 4.6 30.8 1.0
CA A:GLY179 4.6 31.4 1.0
N A:GLY179 4.6 31.5 1.0
CA A:CYS125 4.7 33.6 1.0
N A:LEU127 4.7 38.3 1.0
CD2 A:LEU127 4.7 38.9 1.0
SG A:CYS129 4.7 33.1 1.0
CB A:GLU180 4.7 28.0 1.0
CA A:GLU180 4.8 28.1 1.0
CG A:LEU127 4.9 38.5 1.0
CA A:LEU127 4.9 38.0 1.0

Iron binding site 6 out of 8 in 4pl2

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Iron binding site 6 out of 8 in the X-Ray Crystal Structure of C118A 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 Crystal Structure of C118A Rlmn From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:34.9
occ:1.00
 FE2 A:SF4401 0.0 34.9 1.0
SG A:CYS132 2.1 36.4 1.0
S1 A:SF4401 2.3 35.0 1.0
S4 A:SF4401 2.3 34.1 1.0
S3 A:SF4401 2.3 34.9 1.0
FE4 A:SF4401 2.7 32.6 1.0
FE1 A:SF4401 2.7 32.3 1.0
FE3 A:SF4401 2.7 35.3 1.0
CB A:CYS132 3.0 37.7 1.0
S2 A:SF4401 3.9 32.1 1.0
CB A:CYS129 4.4 34.6 1.0
CA A:GLY177 4.4 34.9 1.0
CB A:THR134 4.5 46.5 1.0
CA A:CYS132 4.5 37.9 1.0
SG A:CYS129 4.5 33.1 1.0
O A:GLY177 4.6 35.6 1.0
C A:GLY177 4.6 34.8 1.0
CB A:ALA135 4.7 49.7 1.0
N A:ALA135 4.7 49.0 1.0
SG A:CYS125 4.8 31.8 1.0
CB A:CYS125 4.9 32.9 1.0
OG1 A:THR134 4.9 45.2 1.0

Iron binding site 7 out of 8 in 4pl2

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Iron binding site 7 out of 8 in the X-Ray Crystal Structure of C118A 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 Crystal Structure of C118A Rlmn From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:35.3
occ:1.00
 FE3 A:SF4401 0.0 35.3 1.0
S2 A:SF4401 2.3 32.1 1.0
S4 A:SF4401 2.3 34.1 1.0
S1 A:SF4401 2.3 35.0 1.0
FE4 A:SF4401 2.7 32.6 1.0
FE2 A:SF4401 2.7 34.9 1.0
FE1 A:SF4401 2.7 32.3 1.0
CA A:GLY177 3.7 34.9 1.0
S3 A:SF4401 3.9 34.9 1.0
N A:GLY177 4.1 34.7 1.0
C A:GLY177 4.4 34.8 1.0
O A:HOH568 4.5 34.4 1.0
SG A:CYS132 4.6 36.4 1.0
N A:MET178 4.7 35.3 1.0
SG A:CYS129 4.8 33.1 1.0
SG A:CYS125 4.9 31.8 1.0
N A:GLU180 4.9 29.4 1.0
N A:GLY179 4.9 31.5 1.0
C A:GLY179 4.9 30.8 1.0

Iron binding site 8 out of 8 in 4pl2

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Iron binding site 8 out of 8 in the X-Ray Crystal Structure of C118A 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 Crystal Structure of C118A Rlmn From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:32.6
occ:1.00
 FE4 A:SF4401 0.0 32.6 1.0
SG A:CYS129 2.2 33.1 1.0
S3 A:SF4401 2.3 34.9 1.0
S2 A:SF4401 2.3 32.1 1.0
S1 A:SF4401 2.3 35.0 1.0
FE2 A:SF4401 2.7 34.9 1.0
FE1 A:SF4401 2.7 32.3 1.0
FE3 A:SF4401 2.7 35.3 1.0
CB A:CYS129 3.1 34.6 1.0
O A:HOH568 3.7 34.4 1.0
S4 A:SF4401 3.9 34.1 1.0
N A:CYS129 4.1 35.8 1.0
CA A:CYS129 4.2 35.1 1.0
CB A:LEU127 4.2 38.1 1.0
SG A:CYS132 4.5 36.4 1.0
CB A:CYS132 4.5 37.7 1.0
CD2 A:LEU127 4.8 38.9 1.0
SG A:CYS125 4.9 31.8 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 08:28:37 2024

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