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:
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
Go back to
Iron Binding Sites List in 5g5g
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
Go back to
Iron Binding Sites List in 5g5g
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
Go back to
Iron Binding Sites List in 5g5g
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
Go back to
Iron Binding Sites List in 5g5g
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
Go back to
Iron Binding Sites List in 5g5g
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
Go back to
Iron Binding Sites List in 5g5g
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
Go back to
Iron Binding Sites List in 5g5g
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
Go back to
Iron Binding Sites List in 5g5g
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: Tue Aug 6 01:25:13 2024
|