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Iron in PDB 5c4i: Structure of An Oxalate Oxidoreductase

Enzymatic activity of Structure of An Oxalate Oxidoreductase

All present enzymatic activity of Structure of An Oxalate Oxidoreductase:
1.2.7.10;

Protein crystallography data

The structure of Structure of An Oxalate Oxidoreductase, PDB code: 5c4i was solved by M.I.Gibson, E.J.Brignole, E.Pierce, M.Can, S.W.Ragsdale, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.66 / 2.27
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.351, 152.203, 171.824, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 21.6

Other elements in 5c4i:

The structure of Structure of An Oxalate Oxidoreductase also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Sodium (Na) 2 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Structure of An Oxalate Oxidoreductase (pdb code 5c4i). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Structure of An Oxalate Oxidoreductase, PDB code: 5c4i:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in 5c4i

Go back to Iron Binding Sites List in 5c4i
Iron binding site 1 out of 24 in the Structure of An Oxalate Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of An Oxalate Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:10.4
occ:1.00
 FE1 B:SF4401 0.0 10.4 1.0
SG B:CYS290 2.3 12.6 1.0
S2 B:SF4401 2.3 12.1 1.0
S4 B:SF4401 2.3 7.6 1.0
S3 B:SF4401 2.3 11.1 1.0
FE3 B:SF4401 2.7 9.1 1.0
FE2 B:SF4401 2.7 8.7 1.0
FE4 B:SF4401 2.7 9.9 1.0
CB B:CYS290 3.4 11.1 1.0
CA B:CYS290 3.8 11.4 1.0
S1 B:SF4401 3.9 10.3 1.0
N B:GLY292 3.9 9.9 1.0
N B:LYS291 4.0 10.7 1.0
C B:CYS290 4.2 12.0 1.0
CG B:PRO254 4.3 6.8 1.0
CA B:GLY292 4.4 12.1 1.0
CD B:PRO254 4.5 9.0 1.0
N B:CYS293 4.7 9.6 1.0
SG B:CYS296 4.8 10.0 1.0
CB B:CYS275 4.8 10.7 1.0
SG B:CYS271 4.8 11.0 1.0
C B:LYS291 4.9 11.5 1.0
SG B:CYS293 4.9 11.1 1.0

Iron binding site 2 out of 24 in 5c4i

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Iron binding site 2 out of 24 in the Structure of An Oxalate Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of An Oxalate Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:8.7
occ:1.00
 FE2 B:SF4401 0.0 8.7 1.0
S1 B:SF4401 2.3 10.3 1.0
S4 B:SF4401 2.3 7.6 1.0
S3 B:SF4401 2.3 11.1 1.0
SG B:CYS296 2.3 10.0 1.0
FE1 B:SF4401 2.7 10.4 1.0
FE3 B:SF4401 2.7 9.1 1.0
FE4 B:SF4401 2.7 9.9 1.0
CB B:CYS296 3.2 6.4 1.0
S2 B:SF4401 3.9 12.1 1.0
N B:CYS296 3.9 7.6 1.0
CA B:CYS296 4.2 10.7 1.0
CG B:PRO254 4.2 6.8 1.0
SG B:CYS290 4.6 12.6 1.0
SG B:CYS293 4.6 11.1 1.0
CB B:PRO254 4.6 9.3 1.0
N B:LEU295 4.7 10.2 1.0
CE1 B:PHE285 4.8 7.5 1.0
N B:GLY294 4.8 11.4 1.0
SG B:CYS271 4.8 11.0 1.0
CD1 B:ILE276 4.9 8.4 1.0
CD1 B:PHE285 5.0 8.3 1.0
CD B:PRO254 5.0 9.0 1.0

Iron binding site 3 out of 24 in 5c4i

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Iron binding site 3 out of 24 in the Structure of An Oxalate Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of An Oxalate Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:9.1
occ:1.00
 FE3 B:SF4401 0.0 9.1 1.0
SG B:CYS293 2.3 11.1 1.0
S2 B:SF4401 2.3 12.1 1.0
S4 B:SF4401 2.3 7.6 1.0
S1 B:SF4401 2.3 10.3 1.0
FE1 B:SF4401 2.7 10.4 1.0
FE4 B:SF4401 2.7 9.9 1.0
FE2 B:SF4401 2.7 8.7 1.0
N B:CYS293 3.5 9.6 1.0
CB B:CYS293 3.5 11.3 1.0
O B:HOH542 3.7 7.4 1.0
N B:GLY294 3.7 11.4 1.0
S3 B:SF4401 3.9 11.1 1.0
CA B:CYS293 3.9 13.0 1.0
N B:LEU295 4.2 10.2 1.0
C B:CYS293 4.3 15.4 1.0
C B:GLY292 4.4 8.1 1.0
N B:GLY292 4.5 9.9 1.0
SG B:CYS296 4.6 10.0 1.0
CA B:GLY292 4.7 12.1 1.0
CA B:GLY294 4.7 13.1 1.0
SG B:CYS271 4.7 11.0 1.0
SG B:CYS290 4.7 12.6 1.0
CB B:LEU295 4.8 8.8 1.0
CD B:PRO272 4.8 8.1 1.0
N B:CYS296 4.9 7.6 1.0
C B:GLY294 5.0 11.6 1.0

Iron binding site 4 out of 24 in 5c4i

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Iron binding site 4 out of 24 in the Structure of An Oxalate Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of An Oxalate Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:9.9
occ:1.00
 FE4 B:SF4401 0.0 9.9 1.0
S2 B:SF4401 2.3 12.1 1.0
S3 B:SF4401 2.3 11.1 1.0
S1 B:SF4401 2.3 10.3 1.0
SG B:CYS271 2.3 11.0 1.0
FE3 B:SF4401 2.7 9.1 1.0
FE1 B:SF4401 2.7 10.4 1.0
FE2 B:SF4401 2.7 8.7 1.0
CB B:CYS271 3.3 7.1 1.0
S4 B:SF4401 3.9 7.6 1.0
CA B:CYS271 4.1 9.8 1.0
CB B:CYS275 4.3 10.7 1.0
CD B:PRO272 4.5 8.1 1.0
SG B:CYS293 4.6 11.1 1.0
O B:HOH542 4.7 7.4 1.0
C B:CYS271 4.8 9.6 1.0
N B:PRO272 4.9 9.8 1.0
SG B:CYS290 4.9 12.6 1.0
SG B:CYS296 4.9 10.0 1.0
CG1 B:ILE276 4.9 11.2 1.0
SG B:CYS275 5.0 15.4 1.0
N B:CYS275 5.0 14.1 1.0

Iron binding site 5 out of 24 in 5c4i

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Iron binding site 5 out of 24 in the Structure of An Oxalate Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of An Oxalate Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:14.4
occ:1.00
 FE1 B:SF4402 0.0 14.4 1.0
S2 B:SF4402 2.3 10.9 1.0
S4 B:SF4402 2.3 12.6 1.0
S3 B:SF4402 2.3 8.2 1.0
SG B:CYS261 2.3 14.9 1.0
FE2 B:SF4402 2.7 9.3 1.0
FE3 B:SF4402 2.7 10.3 1.0
FE4 B:SF4402 2.7 8.8 1.0
CB B:CYS261 3.5 11.3 1.0
CA B:CYS261 3.8 20.5 1.0
N B:GLU263 3.9 18.3 1.0
N B:THR262 3.9 15.2 1.0
S1 B:SF4402 3.9 9.3 1.0
C B:CYS261 4.3 19.8 1.0
CA B:GLU263 4.3 16.3 1.0
CD1 B:ILE256 4.3 10.2 1.0
CG B:PRO283 4.4 15.4 1.0
N B:CYS264 4.6 15.6 1.0
CB B:ALA304 4.7 13.8 1.0
C B:THR262 4.8 18.9 1.0
CD B:PRO283 4.8 12.9 1.0
SG B:CYS300 4.8 13.2 1.0
OG1 B:THR262 4.9 13.9 1.0
SG B:CYS264 4.9 13.6 1.0
CA B:THR262 4.9 22.1 1.0
SG B:CYS267 4.9 12.2 1.0

Iron binding site 6 out of 24 in 5c4i

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Iron binding site 6 out of 24 in the Structure of An Oxalate Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of An Oxalate Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:9.3
occ:1.00
 FE2 B:SF4402 0.0 9.3 1.0
SG B:CYS264 2.3 13.6 1.0
S3 B:SF4402 2.3 8.2 1.0
S1 B:SF4402 2.3 9.3 1.0
S4 B:SF4402 2.3 12.6 1.0
FE3 B:SF4402 2.7 10.3 1.0
FE4 B:SF4402 2.7 8.8 1.0
FE1 B:SF4402 2.7 14.4 1.0
N B:CYS264 3.5 15.6 1.0
N B:TYR265 3.6 14.2 1.0
CB B:CYS264 3.6 14.9 1.0
S2 B:SF4402 3.9 10.9 1.0
CA B:CYS264 3.9 15.8 1.0
N B:THR266 4.1 11.8 1.0
C B:CYS264 4.1 13.2 1.0
OG1 B:THR262 4.2 13.9 1.0
CD B:PRO301 4.2 11.3 1.0
CA B:TYR265 4.5 9.8 1.0
N B:GLU263 4.5 18.3 1.0
C B:GLU263 4.6 13.0 1.0
SG B:CYS300 4.6 13.2 1.0
SG B:CYS267 4.7 12.2 1.0
CA B:GLU263 4.7 16.3 1.0
CB B:THR266 4.7 9.8 1.0
OG1 B:THR266 4.8 14.6 1.0
SG B:CYS261 4.8 14.9 1.0
C B:TYR265 4.8 14.2 1.0
N B:THR262 4.9 15.2 1.0
N B:CYS267 4.9 10.9 1.0
CG B:PRO301 5.0 19.1 1.0
CA B:THR266 5.0 9.0 1.0

Iron binding site 7 out of 24 in 5c4i

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Iron binding site 7 out of 24 in the Structure of An Oxalate Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of An Oxalate Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:10.3
occ:1.00
 FE3 B:SF4402 0.0 10.3 1.0
S2 B:SF4402 2.3 10.9 1.0
S1 B:SF4402 2.3 9.3 1.0
S4 B:SF4402 2.3 12.6 1.0
SG B:CYS300 2.3 13.2 1.0
FE2 B:SF4402 2.7 9.3 1.0
FE4 B:SF4402 2.7 8.8 1.0
FE1 B:SF4402 2.7 14.4 1.0
CB B:CYS300 3.3 14.3 1.0
S3 B:SF4402 3.9 8.2 1.0
CA B:CYS300 4.0 9.0 1.0
CB B:ALA304 4.2 13.8 1.0
CD B:PRO301 4.2 11.3 1.0
C B:CYS300 4.7 13.1 1.0
SG B:CYS264 4.7 13.6 1.0
N B:PRO301 4.7 15.8 1.0
CG B:LEU305 4.7 10.5 1.0
CD1 B:LEU305 4.8 9.6 1.0
SG B:CYS267 4.8 12.2 1.0
CB B:SER302 4.8 17.6 1.0
N B:SER302 4.8 15.2 1.0
N B:ALA304 4.8 11.7 1.0
SG B:CYS261 4.9 14.9 1.0

Iron binding site 8 out of 24 in 5c4i

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Iron binding site 8 out of 24 in the Structure of An Oxalate Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of An Oxalate Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:8.8
occ:1.00
 FE4 B:SF4402 0.0 8.8 1.0
S3 B:SF4402 2.3 8.2 1.0
S1 B:SF4402 2.3 9.3 1.0
S2 B:SF4402 2.3 10.9 1.0
SG B:CYS267 2.3 12.2 1.0
FE3 B:SF4402 2.7 10.3 1.0
FE2 B:SF4402 2.7 9.3 1.0
FE1 B:SF4402 2.7 14.4 1.0
CB B:CYS267 3.4 11.1 1.0
S4 B:SF4402 3.9 12.6 1.0
N B:CYS267 4.1 10.9 1.0
CA B:CYS267 4.4 8.1 1.0
CG B:PRO283 4.5 15.4 1.0
N B:TYR265 4.5 14.2 1.0
CA B:TYR265 4.6 9.8 1.0
N B:THR266 4.6 11.8 1.0
SG B:CYS264 4.7 13.6 1.0
SG B:CYS261 4.7 14.9 1.0
CD1 B:LEU305 4.8 9.6 1.0
SG B:CYS300 4.8 13.2 1.0

Iron binding site 9 out of 24 in 5c4i

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Iron binding site 9 out of 24 in the Structure of An Oxalate Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of An Oxalate Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:10.0
occ:1.00
 FE1 C:SF4401 0.0 10.0 1.0
SG C:CYS225 2.3 15.2 1.0
S3 C:SF4401 2.3 12.0 1.0
S4 C:SF4401 2.3 7.1 1.0
S2 C:SF4401 2.3 9.6 1.0
FE4 C:SF4401 2.7 9.5 1.0
FE3 C:SF4401 2.7 7.4 1.0
FE2 C:SF4401 2.7 6.6 1.0
CB C:CYS225 3.4 10.6 1.0
S1 C:SF4401 3.9 7.9 1.0
CA C:CYS225 4.0 9.7 1.0
CB C:ALA142 4.4 16.1 1.0
ND2 C:ASN138 4.5 13.2 1.0
CB C:LYS227 4.5 8.2 1.0
C C:CYS225 4.6 12.2 1.0
SG C:CYS52 4.7 14.0 1.0
SG C:CYS27 4.8 7.1 1.0
CD C:PRO226 4.8 9.7 1.0
SG C:CYS24 4.8 13.9 1.0
N C:LYS227 4.9 9.3 1.0
CD C:PRO29 4.9 7.3 1.0
N C:PRO226 4.9 10.2 1.0

Iron binding site 10 out of 24 in 5c4i

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Iron binding site 10 out of 24 in the Structure of An Oxalate Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of An Oxalate Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:6.6
occ:1.00
 FE2 C:SF4401 0.0 6.6 1.0
SG C:CYS27 2.3 7.1 1.0
S4 C:SF4401 2.3 7.1 1.0
S3 C:SF4401 2.3 12.0 1.0
S1 C:SF4401 2.3 7.9 1.0
FE4 C:SF4401 2.7 9.5 1.0
FE3 C:SF4401 2.7 7.4 1.0
FE1 C:SF4401 2.7 10.0 1.0
CB C:CYS27 3.3 9.4 1.0
S2 C:SF4401 3.9 9.6 1.0
CA C:CYS27 4.1 7.8 1.0
CD C:PRO29 4.1 7.3 1.0
CE C:MET53 4.3 6.7 1.0
CB C:CYS24 4.3 9.1 1.0
CG C:PRO29 4.4 8.6 1.0
N C:CYS24 4.5 9.0 1.0
SG C:CYS24 4.5 13.9 1.0
C C:CYS27 4.7 9.5 1.0
CB C:PRO29 4.8 6.5 1.0
SG C:CYS52 4.8 14.0 1.0
N C:GLY28 4.8 7.0 1.0
SG C:CYS225 4.9 15.2 1.0
CB C:CYS52 4.9 13.3 1.0

Reference:

M.I.Gibson, E.J.Brignole, E.Pierce, M.Can, S.W.Ragsdale, C.L.Drennan. The Structure of An Oxalate Oxidoreductase Provides Insight Into Microbial 2-Oxoacid Metabolism. Biochemistry V. 54 4112 2015.
ISSN: ISSN 0006-2960
PubMed: 26061898
DOI: 10.1021/ACS.BIOCHEM.5B00521
Page generated: Mon Aug 5 20:48:05 2024

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