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Iodine in PDB 5g5h: Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant

Enzymatic activity of Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant

All present enzymatic activity of Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant:
1.17.1.4;

Protein crystallography data

The structure of Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant, PDB code: 5g5h 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) 48.27 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.839, 78.263, 151.732, 90.00, 99.93, 90.00
R / Rfree (%) 16.4 / 22

Other elements in 5g5h:

The structure of Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant also contains other interesting chemical elements:

Molybdenum (Mo) 1 atom
Iron (Fe) 8 atoms
Chlorine (Cl) 10 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant (pdb code 5g5h). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant, PDB code: 5g5h:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 5g5h

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Iodine binding site 1 out of 8 in the Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1228

b:25.0
occ:0.61
 O C:ACT1743 3.4 18.8 1.0
N C:ARG272 3.6 20.9 1.0
C A:CYS99 3.8 17.2 1.0
C C:ACT1743 3.8 18.6 1.0
O A:CYS99 3.8 17.4 1.0
CD A:LYS97 3.9 20.4 1.0
CG C:PRO192 4.0 17.5 1.0
CH3 C:ACT1743 4.0 22.8 1.0
CA C:PRO271 4.1 21.9 1.0
CG A:LYS97 4.1 19.5 1.0
CB A:ASP100 4.1 17.1 1.0
CA A:CYS99 4.1 16.7 1.0
CB C:ARG272 4.2 20.1 1.0
SD C:MET269 4.3 31.1 1.0
N A:ASP100 4.3 16.6 1.0
C C:PRO271 4.3 21.4 1.0
CA C:ARG272 4.4 20.4 1.0
N A:CYS99 4.4 17.3 1.0
O A:GLY98 4.4 20.2 1.0
O C:LEU270 4.5 21.9 1.0
C A:GLY98 4.6 17.9 1.0
CB C:PRO192 4.6 17.4 1.0
OXT C:ACT1743 4.6 16.1 1.0
OD2 A:ASP100 4.7 17.3 1.0
CG C:MET269 4.7 29.1 1.0
O A:LYS97 4.8 17.8 1.0
CA A:ASP100 4.9 16.9 1.0
CG A:ASP100 4.9 17.0 1.0
CB C:PRO271 4.9 22.7 1.0

Iodine binding site 2 out of 8 in 5g5h

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Iodine binding site 2 out of 8 in the Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1319

b:36.8
occ:0.72
 NE2 B:GLN249 3.5 38.2 1.0
NE B:ARG255 3.8 32.5 1.0
O B:HOH2137 3.9 37.3 1.0
CA B:GLY254 4.1 32.0 1.0
CG B:GLN249 4.1 38.0 1.0
CG B:ARG255 4.2 31.7 1.0
C B:GLY254 4.3 31.8 1.0
CD1 B:LEU222 4.3 33.0 1.0
CD B:GLN249 4.3 38.2 1.0
O B:ILE247 4.4 32.7 1.0
NH2 B:ARG255 4.4 34.5 1.0
N B:ARG255 4.4 31.4 1.0
CZ B:ARG255 4.5 33.2 1.0
CG2 B:ILE247 4.5 31.7 1.0
CD B:ARG255 4.5 31.7 1.0
CD2 B:LEU222 4.7 34.7 1.0
CB B:LEU222 4.7 33.4 1.0
O B:GLY254 4.8 31.9 1.0
CG B:LEU222 4.8 33.6 1.0
CB B:ARG255 4.9 31.6 1.0
N B:GLY254 4.9 33.4 1.0

Iodine binding site 3 out of 8 in 5g5h

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Iodine binding site 3 out of 8 in the Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1320

b:54.6
occ:0.70
 O B:HOH2066 3.4 18.1 1.0
O B:GLN147 3.6 29.4 1.0
OG1 B:THR160 3.7 26.0 1.0
CD2 B:HIS148 3.7 29.3 1.0
OG1 B:THR117 3.7 24.8 1.0
NE2 B:HIS148 3.8 28.7 1.0
CA B:CYS119 3.8 22.7 1.0
N B:CYS119 3.8 22.7 1.0
CG B:HIS148 3.9 29.2 1.0
N B:THR160 3.9 24.6 1.0
CE1 B:HIS148 4.0 29.2 1.0
ND1 B:HIS148 4.1 29.2 1.0
CB B:CYS119 4.1 23.6 1.0
CA B:HIS148 4.2 28.9 1.0
C B:GLN147 4.2 29.4 1.0
CA B:ALA159 4.4 22.8 1.0
C B:ARG118 4.5 22.6 1.0
N B:HIS148 4.5 30.1 1.0
CB B:THR160 4.6 26.0 1.0
CB B:HIS148 4.6 29.1 1.0
CG2 B:THR160 4.7 26.1 1.0
C B:ALA159 4.7 23.6 1.0
O B:THR160 4.8 25.7 1.0
CA B:THR160 4.8 25.3 1.0
CB B:ALA159 4.9 22.7 1.0
O B:ARG118 4.9 22.9 1.0
N B:ARG118 4.9 22.9 1.0
O B:HOH2053 4.9 22.5 1.0

Iodine binding site 4 out of 8 in 5g5h

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Iodine binding site 4 out of 8 in the Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1323

b:37.7
occ:0.72
 CE1 B:HIS263 3.9 27.6 1.0
CH2 B:TRP266 4.0 33.4 1.0
CZ3 B:TRP266 4.2 32.5 1.0
CA B:GLY152 4.2 27.2 1.0
CB B:PRO196 4.4 36.6 1.0
O B:HOH2114 4.4 27.5 1.0
NZ B:LYS264 4.5 27.9 1.0
CE B:LYS264 4.5 26.8 1.0
NE2 B:HIS263 4.5 27.4 1.0
O B:GLY152 4.6 27.3 1.0
C B:GLY152 4.9 26.9 1.0
ND1 B:HIS263 5.0 26.9 1.0

Iodine binding site 5 out of 8 in 5g5h

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Iodine binding site 5 out of 8 in the Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I1734

b:33.0
occ:0.48
 OE1 A:GLN103 2.1 25.4 1.0
CD A:GLN103 3.1 25.9 1.0
CB C:ASP655 3.4 30.3 1.0
NE2 A:GLN103 3.4 27.1 1.0
O C:HOH2379 3.5 7.5 1.0
CG C:ARG272 3.6 19.4 1.0
N C:MET656 3.8 30.9 1.0
OD2 C:ASP655 3.9 34.0 1.0
CG C:ASP655 3.9 32.4 1.0
CD2 A:HIS101 4.0 23.1 1.0
CB C:ARG272 4.0 20.1 1.0
CB A:CYS99 4.1 16.1 1.0
CB A:HIS101 4.1 20.2 1.0
O A:CYS99 4.2 17.4 1.0
CB C:MET656 4.2 32.7 1.0
CG A:HIS101 4.2 21.9 1.0
CG C:PRO273 4.3 20.9 1.0
CA C:ASP655 4.3 28.3 1.0
CD C:PRO273 4.4 19.8 1.0
CG A:GLN103 4.4 23.4 1.0
N C:PRO273 4.5 20.2 1.0
C C:ASP655 4.5 28.4 1.0
CA C:MET656 4.6 30.3 1.0
C C:ARG272 4.8 19.8 1.0
CB A:GLN103 4.8 21.4 1.0
OD1 C:ASP655 4.8 33.1 1.0
CA A:CYS99 4.9 16.7 1.0
C A:CYS99 4.9 17.2 1.0
CA C:PRO273 4.9 20.5 1.0
SG A:CYS99 5.0 15.2 1.0
CD C:ARG272 5.0 18.9 1.0

Iodine binding site 6 out of 8 in 5g5h

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Iodine binding site 6 out of 8 in the Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I1735

b:29.9
occ:0.69
 N C:ASN47 3.4 22.4 1.0
ND2 C:ASN47 3.6 24.0 0.5
CB C:ASN47 3.6 23.4 0.5
CG C:PRO265 3.8 21.4 1.0
CA C:ASN47 3.8 22.7 0.5
CD C:PRO265 3.9 21.6 1.0
CA C:ASN47 3.9 22.9 0.5
C C:ASN47 3.9 21.8 1.0
CB C:ASN47 3.9 24.0 0.5
CD C:PRO46 4.0 22.7 1.0
C C:ALA45 4.0 22.1 1.0
N C:PRO46 4.0 22.3 1.0
CA C:ALA45 4.0 23.0 1.0
CG C:ASN47 4.1 23.9 0.5
CB C:ALA45 4.2 22.9 1.0
N C:ALA48 4.2 20.4 1.0
O C:ASN47 4.3 21.4 1.0
C C:PRO46 4.5 22.7 1.0
O C:ALA45 4.6 21.4 1.0
CB C:PRO265 4.6 21.3 1.0
CG C:PRO46 4.8 23.3 1.0
CA C:PRO46 4.8 22.5 1.0
CA C:ALA48 4.9 20.0 1.0

Iodine binding site 7 out of 8 in 5g5h

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Iodine binding site 7 out of 8 in the Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I1736

b:37.4
occ:0.85
 NH1 C:ARG606 3.8 29.1 1.0
NZ C:LYS411 3.8 40.5 1.0
CD1 C:PHE412 4.1 27.2 1.0
O C:HOH2382 4.1 27.5 1.0
NZ C:LYS669 4.1 40.5 1.0
CD C:ARG606 4.1 30.3 1.0
CG C:GLU671 4.1 35.4 1.0
CB C:LEU608 4.2 21.4 1.0
CG C:ARG606 4.3 29.4 1.0
CD2 C:LEU608 4.4 21.7 1.0
CA C:PHE412 4.4 27.9 1.0
O C:LYS411 4.5 29.9 1.0
CE C:LYS669 4.5 38.6 1.0
CG C:LYS411 4.5 34.0 1.0
CB C:GLU671 4.5 30.5 1.0
CE1 C:PHE412 4.6 27.7 1.0
CG C:LEU608 4.7 21.7 1.0
CZ C:ARG606 4.8 30.3 1.0
CD1 C:LEU608 4.8 21.9 1.0
C C:LYS411 4.8 29.3 1.0
N C:PHE412 4.9 28.2 1.0
NE C:ARG606 4.9 31.1 1.0
CG C:PHE412 5.0 27.3 1.0

Iodine binding site 8 out of 8 in 5g5h

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Iodine binding site 8 out of 8 in the Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Escherichia Coli Periplasmic Aldehyde Oxidase R440H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I1737

b:35.6
occ:0.64
 O C:HOH2008 3.7 30.5 1.0
CB C:ALA7 3.8 28.9 1.0
CB C:PRO684 3.9 23.6 1.0
O C:HOH2340 3.9 30.1 1.0
ND2 C:ASN10 3.9 24.6 1.0
CA C:ALA7 3.9 28.9 1.0
CG C:PRO684 4.0 23.2 1.0
OH C:TYR520 4.1 22.6 1.0
CA C:PRO684 4.3 23.0 1.0
N C:GLY8 4.5 30.3 1.0
CE1 C:PHE3 4.5 24.9 1.0
CZ C:TYR520 4.7 22.1 1.0
CB C:ASN10 4.7 25.6 1.0
C C:ALA7 4.8 29.1 1.0
CD1 C:PHE3 4.8 25.6 1.0
CG C:ASN10 4.8 25.3 1.0
CE1 C:TYR520 4.8 22.0 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 Aug 11 20:59:18 2024

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