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Iron in PDB 5g5g: Escherichia Coli Periplasmic Aldehyde Oxidase

Protein crystallography data

The structure of Escherichia Coli Periplasmic Aldehyde Oxidase, PDB code: 5g5g was solved by M.A.S.Correia, A.R.Otrelo-Cardoso, M.J.Romao, T.Santos-Silva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.32 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.681, 78.342, 151.909, 90.00, 99.69, 90.00
R / Rfree (%) 13.8 / 16.7

Other elements in 5g5g:

The structure of Escherichia Coli Periplasmic Aldehyde Oxidase also contains other interesting chemical elements:

Molybdenum (Mo) 1 atom
Iodine (I) 7 atoms
Chlorine (Cl) 12 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Escherichia Coli Periplasmic Aldehyde Oxidase (pdb code 5g5g). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Escherichia Coli Periplasmic Aldehyde Oxidase, PDB code: 5g5g:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5g5g

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Iron binding site 1 out of 8 in the Escherichia Coli Periplasmic Aldehyde Oxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Escherichia Coli Periplasmic Aldehyde Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe230

b:10.6
occ:1.00
FE1 A:FES230 0.0 10.6 1.0
SG A:CYS161 2.2 11.2 1.0
SG A:CYS208 2.2 10.1 1.0
S2 A:FES230 2.2 11.1 1.0
S1 A:FES230 2.2 11.6 1.0
CB A:CYS208 3.1 10.2 1.0
FE2 A:FES230 3.1 10.3 1.0
CB A:CYS161 3.3 10.3 1.0
CA A:CYS208 3.4 10.0 1.0
O A:HOH2122 4.1 11.3 1.0
C A:CYS208 4.2 10.3 1.0
N A:CYS161 4.2 10.0 1.0
N A:ARG209 4.3 9.9 1.0
CA A:CYS161 4.3 10.6 1.0
CB A:CYS210 4.4 10.0 1.0
N A:CYS210 4.5 9.4 1.0
SG A:CYS210 4.5 10.0 1.0
O A:ILE207 4.6 10.9 1.0
N A:CYS208 4.6 10.6 1.0
C A:CYS161 4.9 10.0 1.0
SG A:CYS158 4.9 9.8 1.0
O A:CYS208 5.0 9.7 1.0
CA A:CYS210 5.0 9.6 1.0
NE2 A:GLN165 5.0 11.1 1.0

Iron binding site 2 out of 8 in 5g5g

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Iron binding site 2 out of 8 in the Escherichia Coli Periplasmic Aldehyde Oxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Escherichia Coli Periplasmic Aldehyde Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe230

b:10.3
occ:1.00
FE2 A:FES230 0.0 10.3 1.0
SG A:CYS158 2.2 9.8 1.0
SG A:CYS210 2.2 10.0 1.0
S1 A:FES230 2.2 11.6 1.0
S2 A:FES230 2.2 11.1 1.0
FE1 A:FES230 3.1 10.6 1.0
CB A:CYS158 3.1 10.1 1.0
CB A:CYS210 3.4 10.0 1.0
N A:CYS158 3.4 9.9 1.0
O A:HOH2126 3.6 10.2 1.0
CA A:CYS158 3.7 9.9 1.0
N A:GLY159 3.9 9.5 1.0
N A:CYS210 4.1 9.4 1.0
C A:CYS158 4.2 9.8 1.0
CA A:CYS210 4.3 9.6 1.0
N A:TYR160 4.3 9.5 1.0
SG A:CYS208 4.5 10.1 1.0
C A:GLN157 4.6 10.3 1.0
N A:GLN157 4.8 10.1 1.0
CB A:GLN157 4.8 10.9 1.0
N A:CYS161 4.8 10.0 1.0
SG A:CYS161 4.9 11.2 1.0
CA A:GLN157 5.0 10.5 1.0
CA A:GLY159 5.0 9.9 1.0

Iron binding site 3 out of 8 in 5g5g

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Iron binding site 3 out of 8 in the Escherichia Coli Periplasmic Aldehyde Oxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Escherichia Coli Periplasmic Aldehyde Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe231

b:10.6
occ:1.00
FE1 A:FES231 0.0 10.6 1.0
S2 A:FES231 2.2 9.8 1.0
S1 A:FES231 2.2 9.7 1.0
SG A:CYS107 2.3 12.3 1.0
SG A:CYS119 2.3 11.4 1.0
FE2 A:FES231 2.7 10.2 1.0
CB A:CYS119 3.3 11.5 1.0
CB A:CYS107 3.3 10.8 1.0
N A:CYS119 4.2 11.1 1.0
N A:GLY102 4.3 10.6 1.0
N A:CYS107 4.3 11.0 1.0
CA A:CYS119 4.3 11.7 1.0
SG A:CYS99 4.3 11.2 1.0
CB A:ASN117 4.3 12.5 1.0
CA A:CYS107 4.5 10.8 1.0
N A:ASP100 4.5 11.2 1.0
CA A:GLY102 4.5 10.4 1.0
SG A:CYS104 4.6 10.2 1.0
CG A:ASN117 4.6 13.0 1.0
CA A:ASP100 4.7 11.4 1.0
N A:GLY105 4.8 10.9 1.0
N A:HIS101 4.8 10.9 1.0
CD2 A:LEU83 4.8 11.0 1.0
N A:ALA106 4.9 10.5 1.0
C A:ASP100 5.0 11.1 1.0

Iron binding site 4 out of 8 in 5g5g

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Iron binding site 4 out of 8 in the Escherichia Coli Periplasmic Aldehyde Oxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Escherichia Coli Periplasmic Aldehyde Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe231

b:10.2
occ:1.00
FE2 A:FES231 0.0 10.2 1.0
S1 A:FES231 2.2 9.7 1.0
S2 A:FES231 2.3 9.8 1.0
SG A:CYS104 2.3 10.2 1.0
SG A:CYS99 2.4 11.2 1.0
FE1 A:FES231 2.7 10.6 1.0
CB A:CYS104 3.5 10.2 1.0
CB A:CYS99 3.5 11.2 1.0
N A:CYS99 3.5 11.1 1.0
N A:CYS104 3.6 11.3 1.0
N A:ASP100 3.9 11.2 1.0
CA A:CYS99 3.9 11.3 1.0
CA A:CYS104 3.9 10.6 1.0
N A:GLY105 3.9 10.9 1.0
N A:GLN103 4.1 10.7 1.0
C A:GLY98 4.2 11.2 1.0
N A:GLY98 4.3 10.7 1.0
C A:CYS104 4.3 10.5 1.0
C A:CYS99 4.3 11.8 1.0
N A:ALA106 4.3 10.5 1.0
CA A:GLY98 4.4 10.7 1.0
N A:GLY102 4.4 10.6 1.0
SG A:CYS119 4.4 11.4 1.0
SG A:CYS107 4.6 12.3 1.0
C A:GLN103 4.6 11.5 1.0
N A:HIS101 4.7 10.9 1.0
C A:GLY102 4.7 11.1 1.0
CA A:GLY102 4.8 10.4 1.0
CA A:GLN103 4.8 11.4 1.0
CA A:ASP100 4.9 11.4 1.0
CA A:GLY105 4.9 10.5 1.0

Iron binding site 5 out of 8 in 5g5g

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Iron binding site 5 out of 8 in the Escherichia Coli Periplasmic Aldehyde Oxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Escherichia Coli Periplasmic Aldehyde Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe320

b:16.9
occ:1.00
FE1 B:SF4320 0.0 16.9 1.0
SG B:CYS138 2.1 19.8 1.0
S4 B:SF4320 2.3 20.5 1.0
S2 B:SF4320 2.4 18.9 1.0
S3 B:SF4320 2.4 19.6 1.0
CB B:CYS138 3.0 21.5 1.0
FE4 B:SF4320 3.1 16.9 1.0
FE2 B:SF4320 3.2 17.9 1.0
CA B:CYS138 3.3 21.6 1.0
FE3 B:SF4320 3.3 16.0 1.0
C B:CYS138 3.9 21.6 1.0
S1 B:SF4320 4.0 17.6 1.0
N B:ALA139 4.0 21.1 1.0
N B:ALA140 4.2 20.0 1.0
O B:ALA156 4.3 22.3 1.0
CB B:ALA140 4.3 18.8 1.0
CA B:CYS157 4.3 20.3 1.0
N B:ILE158 4.6 18.5 1.0
SG B:CYS157 4.6 18.5 1.0
N B:CYS138 4.7 23.4 1.0
O B:CYS138 4.7 21.9 1.0
CB B:CYS157 4.8 20.0 1.0
CA B:ALA140 4.8 19.6 1.0
O B:GLY137 4.9 22.8 1.0
SG B:CYS129 4.9 18.8 1.0
CA B:CYS129 5.0 19.3 1.0
N B:ASN130 5.0 20.6 1.0

Iron binding site 6 out of 8 in 5g5g

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Iron binding site 6 out of 8 in the Escherichia Coli Periplasmic Aldehyde Oxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Escherichia Coli Periplasmic Aldehyde Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe320

b:17.9
occ:1.00
FE2 B:SF4320 0.0 17.9 1.0
SG B:CYS129 1.8 18.8 1.0
S4 B:SF4320 2.2 20.5 1.0
S3 B:SF4320 2.3 19.6 1.0
S1 B:SF4320 2.5 17.6 1.0
CB B:CYS129 2.9 18.7 1.0
FE1 B:SF4320 3.2 16.9 1.0
FE3 B:SF4320 3.2 16.0 1.0
CA B:CYS129 3.3 19.3 1.0
FE4 B:SF4320 3.4 16.9 1.0
C B:CYS129 3.7 20.3 1.0
N B:ASN130 3.8 20.6 1.0
N B:LYS131 3.9 21.2 1.0
CB B:LYS131 3.9 20.6 1.0
S2 B:SF4320 4.1 18.9 1.0
CB B:PHE122 4.4 16.6 1.0
CA B:PHE122 4.4 16.9 1.0
N B:PHE122 4.5 16.4 1.0
O B:CYS129 4.5 20.0 1.0
CA B:LYS131 4.6 21.8 1.0
N B:CYS129 4.6 20.3 1.0
SG B:CYS119 4.6 15.6 1.0
O B:PRO128 4.7 22.2 1.0
CA B:ASN130 4.9 21.6 1.0
C B:ASN130 4.9 21.9 1.0
N B:ARG132 4.9 24.3 1.0

Iron binding site 7 out of 8 in 5g5g

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Iron binding site 7 out of 8 in the Escherichia Coli Periplasmic Aldehyde Oxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Escherichia Coli Periplasmic Aldehyde Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe320

b:16.0
occ:1.00
FE3 B:SF4320 0.0 16.0 1.0
SG B:CYS119 2.0 15.6 1.0
S1 B:SF4320 2.2 17.6 1.0
S4 B:SF4320 2.3 20.5 1.0
S2 B:SF4320 2.4 18.9 1.0
CB B:CYS119 2.9 15.5 1.0
FE2 B:SF4320 3.2 17.9 1.0
FE4 B:SF4320 3.3 16.9 1.0
FE1 B:SF4320 3.3 16.9 1.0
NE2 B:HIS148 3.8 18.7 1.0
S3 B:SF4320 4.1 19.6 1.0
CD2 B:HIS148 4.2 18.8 1.0
CA B:CYS119 4.3 14.9 1.0
CB B:ALA140 4.3 18.8 1.0
N B:PHE122 4.4 16.4 1.0
CB B:PHE122 4.4 16.6 1.0
CB B:ALA159 4.5 16.4 1.0
SG B:CYS129 4.7 18.8 1.0
CB B:TYR121 4.8 17.3 1.0
C B:CYS119 4.9 15.0 1.0
CE1 B:HIS148 4.9 19.3 1.0
CA B:PHE122 4.9 16.9 1.0

Iron binding site 8 out of 8 in 5g5g

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Iron binding site 8 out of 8 in the Escherichia Coli Periplasmic Aldehyde Oxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Escherichia Coli Periplasmic Aldehyde Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe320

b:16.9
occ:1.00
FE4 B:SF4320 0.0 16.9 1.0
SG B:CYS157 1.9 18.5 1.0
S2 B:SF4320 2.2 18.9 1.0
S3 B:SF4320 2.3 19.6 1.0
S1 B:SF4320 2.4 17.6 1.0
CB B:CYS157 3.0 20.0 1.0
FE1 B:SF4320 3.1 16.9 1.0
FE3 B:SF4320 3.3 16.0 1.0
FE2 B:SF4320 3.4 17.9 1.0
CB B:ALA159 3.6 16.4 1.0
CA B:CYS157 3.6 20.3 1.0
N B:ALA159 3.9 17.1 1.0
N B:ILE158 4.0 18.5 1.0
S4 B:SF4320 4.0 20.5 1.0
C B:CYS157 4.1 19.7 1.0
CE B:LYS131 4.2 19.7 1.0
CA B:ALA159 4.3 16.6 1.0
CB B:LYS131 4.4 20.6 1.0
SG B:CYS138 4.7 19.8 1.0
O B:ALA156 4.7 22.3 1.0
C B:ILE158 4.8 17.7 1.0
CD B:LYS131 4.9 19.6 1.0
N B:CYS157 4.9 21.9 1.0
SG B:CYS129 4.9 18.8 1.0
CA B:ILE158 5.0 18.4 1.0
O B:HOH2141 5.0 38.6 1.0

Reference:

M.A.Correia, A.R.Otrelo-Cardoso, V.Schwuchow, K.G.Sigfridsson Clauss, M.Haumann, M.J.Romao, S.Leimkuhler, T.Santos-Silva. The Escherichia Coli Periplasmic Aldehyde Oxidoreductase Is An Exceptional Member of the Xanthine Oxidase Family of Molybdoenzymes. Acs Chem.Biol. V. 11 2923 2016.
ISSN: ISSN 1554-8929
PubMed: 27622978
DOI: 10.1021/ACSCHEMBIO.6B00572
Page generated: Sun Dec 13 16:01:59 2020

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