Iron in PDB 1n5x: Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound
Enzymatic activity of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound
All present enzymatic activity of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound:
1.1.1.204;
Protein crystallography data
The structure of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound, PDB code: 1n5x
was solved by
K.Okamoto,
B.T.Eger,
T.Nishino,
S.Kondo,
E.F.Pai,
T.Nishino,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.80
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
168.269,
124.659,
147.325,
90.00,
90.99,
90.00
|
R / Rfree (%)
|
24.4 /
27.5
|
Other elements in 1n5x:
The structure of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound
(pdb code 1n5x). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound, PDB code: 1n5x:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 1n5x
Go back to
Iron Binding Sites List in 1n5x
Iron binding site 1 out
of 8 in the Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe3001
b:6.3
occ:1.00
|
FE1
|
A:FES3001
|
0.0
|
6.3
|
1.0
|
S2
|
A:FES3001
|
2.2
|
6.3
|
1.0
|
S1
|
A:FES3001
|
2.2
|
6.3
|
1.0
|
SG
|
A:CYS150
|
2.4
|
20.9
|
1.0
|
SG
|
A:CYS113
|
2.4
|
20.9
|
1.0
|
FE2
|
A:FES3001
|
2.7
|
6.3
|
1.0
|
CB
|
A:CYS150
|
3.3
|
20.9
|
1.0
|
CB
|
A:CYS113
|
3.4
|
20.9
|
1.0
|
N
|
A:CYS113
|
3.7
|
20.9
|
1.0
|
N
|
A:GLY114
|
3.9
|
20.9
|
1.0
|
CA
|
A:CYS113
|
4.0
|
20.9
|
1.0
|
N
|
A:CYS150
|
4.0
|
20.9
|
1.0
|
C
|
A:CYS113
|
4.3
|
20.9
|
1.0
|
CA
|
A:CYS150
|
4.3
|
20.9
|
1.0
|
N
|
A:PHE115
|
4.4
|
20.9
|
1.0
|
SG
|
A:CYS148
|
4.5
|
20.9
|
1.0
|
N
|
A:ARG149
|
4.7
|
20.9
|
1.0
|
SG
|
A:CYS116
|
4.7
|
20.9
|
1.0
|
CA
|
A:GLY114
|
4.8
|
20.9
|
1.0
|
C
|
A:GLN112
|
4.9
|
20.9
|
1.0
|
N
|
A:CYS116
|
4.9
|
20.9
|
1.0
|
C
|
A:ARG149
|
4.9
|
20.9
|
1.0
|
CB
|
A:GLN112
|
4.9
|
20.9
|
1.0
|
|
Iron binding site 2 out
of 8 in 1n5x
Go back to
Iron Binding Sites List in 1n5x
Iron binding site 2 out
of 8 in the Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe3001
b:6.3
occ:1.00
|
FE2
|
A:FES3001
|
0.0
|
6.3
|
1.0
|
S2
|
A:FES3001
|
2.1
|
6.3
|
1.0
|
S1
|
A:FES3001
|
2.2
|
6.3
|
1.0
|
SG
|
A:CYS116
|
2.3
|
20.9
|
1.0
|
SG
|
A:CYS148
|
2.4
|
20.9
|
1.0
|
FE1
|
A:FES3001
|
2.7
|
6.3
|
1.0
|
CB
|
A:CYS116
|
3.3
|
20.9
|
1.0
|
CB
|
A:CYS148
|
3.4
|
20.9
|
1.0
|
CA
|
A:CYS148
|
3.8
|
20.9
|
1.0
|
N
|
A:ARG149
|
4.1
|
20.9
|
1.0
|
N
|
A:CYS116
|
4.2
|
20.9
|
1.0
|
N
|
A:CYS150
|
4.3
|
20.9
|
1.0
|
CB
|
A:CYS150
|
4.3
|
20.9
|
1.0
|
CA
|
A:CYS116
|
4.3
|
20.9
|
1.0
|
C
|
A:CYS148
|
4.4
|
20.9
|
1.0
|
SG
|
A:CYS150
|
4.4
|
20.9
|
1.0
|
SG
|
A:CYS113
|
4.7
|
20.9
|
1.0
|
CG2
|
A:THR151
|
4.9
|
20.9
|
1.0
|
CA
|
A:CYS150
|
4.9
|
20.9
|
1.0
|
N
|
A:THR117
|
4.9
|
20.9
|
1.0
|
C
|
A:CYS116
|
4.9
|
20.9
|
1.0
|
N
|
A:THR151
|
4.9
|
20.9
|
1.0
|
N
|
A:GLY114
|
4.9
|
20.9
|
1.0
|
|
Iron binding site 3 out
of 8 in 1n5x
Go back to
Iron Binding Sites List in 1n5x
Iron binding site 3 out
of 8 in the Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe3002
b:8.9
occ:1.00
|
FE1
|
A:FES3002
|
0.0
|
8.9
|
1.0
|
S1
|
A:FES3002
|
2.2
|
8.9
|
1.0
|
S2
|
A:FES3002
|
2.2
|
8.9
|
1.0
|
SG
|
A:CYS73
|
2.4
|
20.9
|
1.0
|
SG
|
A:CYS51
|
2.4
|
20.9
|
1.0
|
FE2
|
A:FES3002
|
2.7
|
8.9
|
1.0
|
CB
|
A:CYS73
|
3.3
|
20.9
|
1.0
|
CB
|
A:CYS51
|
3.5
|
20.9
|
1.0
|
N
|
A:GLY46
|
4.2
|
20.9
|
1.0
|
CB
|
A:ASN71
|
4.2
|
20.9
|
1.0
|
SG
|
A:CYS43
|
4.3
|
20.9
|
1.0
|
CA
|
A:GLY46
|
4.3
|
20.9
|
1.0
|
N
|
A:GLY44
|
4.3
|
20.9
|
1.0
|
N
|
A:CYS73
|
4.3
|
20.9
|
1.0
|
N
|
A:CYS51
|
4.3
|
20.9
|
1.0
|
CA
|
A:CYS73
|
4.4
|
20.9
|
1.0
|
CA
|
A:CYS51
|
4.5
|
20.9
|
1.0
|
CA
|
A:GLY44
|
4.5
|
20.9
|
1.0
|
OD1
|
A:ASN71
|
4.5
|
20.9
|
1.0
|
SG
|
A:CYS48
|
4.8
|
20.9
|
1.0
|
N
|
A:GLY49
|
4.8
|
20.9
|
1.0
|
CG
|
A:ASN71
|
4.8
|
20.9
|
1.0
|
N
|
A:ALA50
|
4.9
|
20.9
|
1.0
|
C
|
A:GLY44
|
4.9
|
20.9
|
1.0
|
N
|
A:GLU45
|
4.9
|
20.9
|
1.0
|
CA
|
A:ASN71
|
5.0
|
20.9
|
1.0
|
C
|
A:GLY46
|
5.0
|
20.9
|
1.0
|
|
Iron binding site 4 out
of 8 in 1n5x
Go back to
Iron Binding Sites List in 1n5x
Iron binding site 4 out
of 8 in the Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe3002
b:8.9
occ:1.00
|
FE2
|
A:FES3002
|
0.0
|
8.9
|
1.0
|
S2
|
A:FES3002
|
2.2
|
8.9
|
1.0
|
S1
|
A:FES3002
|
2.2
|
8.9
|
1.0
|
SG
|
A:CYS48
|
2.3
|
20.9
|
1.0
|
SG
|
A:CYS43
|
2.4
|
20.9
|
1.0
|
FE1
|
A:FES3002
|
2.7
|
8.9
|
1.0
|
CB
|
A:CYS48
|
3.5
|
20.9
|
1.0
|
N
|
A:CYS48
|
3.5
|
20.9
|
1.0
|
N
|
A:CYS43
|
3.6
|
20.9
|
1.0
|
CB
|
A:CYS43
|
3.6
|
20.9
|
1.0
|
N
|
A:GLY49
|
3.6
|
20.9
|
1.0
|
CA
|
A:CYS48
|
3.8
|
20.9
|
1.0
|
N
|
A:GLY44
|
3.9
|
20.9
|
1.0
|
CA
|
A:CYS43
|
4.0
|
20.9
|
1.0
|
C
|
A:GLY42
|
4.1
|
20.9
|
1.0
|
C
|
A:CYS48
|
4.1
|
20.9
|
1.0
|
N
|
A:ALA50
|
4.2
|
20.9
|
1.0
|
N
|
A:GLY42
|
4.3
|
20.9
|
1.0
|
N
|
A:GLY47
|
4.3
|
20.9
|
1.0
|
CA
|
A:GLY42
|
4.4
|
20.9
|
1.0
|
N
|
A:GLY46
|
4.4
|
20.9
|
1.0
|
C
|
A:CYS43
|
4.4
|
20.9
|
1.0
|
CA
|
A:GLY49
|
4.6
|
20.9
|
1.0
|
C
|
A:GLY47
|
4.6
|
20.9
|
1.0
|
SG
|
A:CYS73
|
4.7
|
20.9
|
1.0
|
SG
|
A:CYS51
|
4.7
|
20.9
|
1.0
|
CA
|
A:GLY46
|
4.7
|
20.9
|
1.0
|
C
|
A:GLY46
|
4.7
|
20.9
|
1.0
|
N
|
A:GLU45
|
4.8
|
20.9
|
1.0
|
CB
|
A:ALA50
|
4.8
|
20.9
|
1.0
|
CA
|
A:GLY44
|
4.8
|
20.9
|
1.0
|
C
|
A:GLY49
|
4.9
|
20.9
|
1.0
|
O
|
A:GLY42
|
5.0
|
20.9
|
1.0
|
N
|
A:CYS51
|
5.0
|
20.9
|
1.0
|
|
Iron binding site 5 out
of 8 in 1n5x
Go back to
Iron Binding Sites List in 1n5x
Iron binding site 5 out
of 8 in the Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe4001
b:6.3
occ:1.00
|
FE1
|
B:FES4001
|
0.0
|
6.3
|
1.0
|
S2
|
B:FES4001
|
2.2
|
6.3
|
1.0
|
S1
|
B:FES4001
|
2.2
|
6.3
|
1.0
|
SG
|
B:CYS150
|
2.4
|
20.9
|
1.0
|
SG
|
B:CYS113
|
2.4
|
20.9
|
1.0
|
FE2
|
B:FES4001
|
2.7
|
6.3
|
1.0
|
CB
|
B:CYS150
|
3.3
|
20.9
|
1.0
|
CB
|
B:CYS113
|
3.4
|
20.9
|
1.0
|
N
|
B:CYS113
|
3.7
|
20.9
|
1.0
|
N
|
B:GLY114
|
3.9
|
20.9
|
1.0
|
CA
|
B:CYS113
|
4.0
|
20.9
|
1.0
|
N
|
B:CYS150
|
4.0
|
20.9
|
1.0
|
C
|
B:CYS113
|
4.3
|
20.9
|
1.0
|
CA
|
B:CYS150
|
4.3
|
20.9
|
1.0
|
N
|
B:PHE115
|
4.4
|
20.9
|
1.0
|
SG
|
B:CYS148
|
4.5
|
20.9
|
1.0
|
N
|
B:ARG149
|
4.7
|
20.9
|
1.0
|
SG
|
B:CYS116
|
4.7
|
20.9
|
1.0
|
CA
|
B:GLY114
|
4.8
|
20.9
|
1.0
|
C
|
B:GLN112
|
4.9
|
20.9
|
1.0
|
N
|
B:CYS116
|
4.9
|
20.9
|
1.0
|
C
|
B:ARG149
|
4.9
|
20.9
|
1.0
|
CB
|
B:GLN112
|
4.9
|
20.9
|
1.0
|
|
Iron binding site 6 out
of 8 in 1n5x
Go back to
Iron Binding Sites List in 1n5x
Iron binding site 6 out
of 8 in the Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe4001
b:6.3
occ:1.00
|
FE2
|
B:FES4001
|
0.0
|
6.3
|
1.0
|
S2
|
B:FES4001
|
2.1
|
6.3
|
1.0
|
S1
|
B:FES4001
|
2.2
|
6.3
|
1.0
|
SG
|
B:CYS116
|
2.3
|
20.9
|
1.0
|
SG
|
B:CYS148
|
2.4
|
20.9
|
1.0
|
FE1
|
B:FES4001
|
2.7
|
6.3
|
1.0
|
CB
|
B:CYS116
|
3.3
|
20.9
|
1.0
|
CB
|
B:CYS148
|
3.4
|
20.9
|
1.0
|
CA
|
B:CYS148
|
3.8
|
20.9
|
1.0
|
N
|
B:ARG149
|
4.1
|
20.9
|
1.0
|
N
|
B:CYS116
|
4.2
|
20.9
|
1.0
|
N
|
B:CYS150
|
4.3
|
20.9
|
1.0
|
CB
|
B:CYS150
|
4.3
|
20.9
|
1.0
|
CA
|
B:CYS116
|
4.3
|
20.9
|
1.0
|
C
|
B:CYS148
|
4.4
|
20.9
|
1.0
|
SG
|
B:CYS150
|
4.4
|
20.9
|
1.0
|
SG
|
B:CYS113
|
4.7
|
20.9
|
1.0
|
CG2
|
B:THR151
|
4.9
|
20.9
|
1.0
|
CA
|
B:CYS150
|
4.9
|
20.9
|
1.0
|
N
|
B:THR117
|
4.9
|
20.9
|
1.0
|
C
|
B:CYS116
|
4.9
|
20.9
|
1.0
|
N
|
B:THR151
|
4.9
|
20.9
|
1.0
|
N
|
B:GLY114
|
4.9
|
20.9
|
1.0
|
O
|
B:LEU147
|
5.0
|
20.9
|
1.0
|
|
Iron binding site 7 out
of 8 in 1n5x
Go back to
Iron Binding Sites List in 1n5x
Iron binding site 7 out
of 8 in the Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe4002
b:8.9
occ:1.00
|
FE1
|
B:FES4002
|
0.0
|
8.9
|
1.0
|
S1
|
B:FES4002
|
2.2
|
8.9
|
1.0
|
S2
|
B:FES4002
|
2.2
|
8.9
|
1.0
|
SG
|
B:CYS73
|
2.4
|
20.9
|
1.0
|
SG
|
B:CYS51
|
2.4
|
20.9
|
1.0
|
FE2
|
B:FES4002
|
2.7
|
8.9
|
1.0
|
CB
|
B:CYS73
|
3.3
|
20.9
|
1.0
|
CB
|
B:CYS51
|
3.5
|
20.9
|
1.0
|
N
|
B:GLY46
|
4.2
|
20.9
|
1.0
|
CB
|
B:ASN71
|
4.2
|
20.9
|
1.0
|
SG
|
B:CYS43
|
4.3
|
20.9
|
1.0
|
CA
|
B:GLY46
|
4.3
|
20.9
|
1.0
|
N
|
B:GLY44
|
4.3
|
20.9
|
1.0
|
N
|
B:CYS73
|
4.3
|
20.9
|
1.0
|
N
|
B:CYS51
|
4.3
|
20.9
|
1.0
|
CA
|
B:CYS73
|
4.4
|
20.9
|
1.0
|
CA
|
B:CYS51
|
4.5
|
20.9
|
1.0
|
CA
|
B:GLY44
|
4.5
|
20.9
|
1.0
|
OD1
|
B:ASN71
|
4.5
|
20.9
|
1.0
|
SG
|
B:CYS48
|
4.8
|
20.9
|
1.0
|
N
|
B:GLY49
|
4.8
|
20.9
|
1.0
|
CG
|
B:ASN71
|
4.8
|
20.9
|
1.0
|
N
|
B:ALA50
|
4.9
|
20.9
|
1.0
|
C
|
B:GLY44
|
4.9
|
20.9
|
1.0
|
N
|
B:GLU45
|
4.9
|
20.9
|
1.0
|
CA
|
B:ASN71
|
5.0
|
20.9
|
1.0
|
C
|
B:GLY46
|
5.0
|
20.9
|
1.0
|
|
Iron binding site 8 out
of 8 in 1n5x
Go back to
Iron Binding Sites List in 1n5x
Iron binding site 8 out
of 8 in the Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe4002
b:8.9
occ:1.00
|
FE2
|
B:FES4002
|
0.0
|
8.9
|
1.0
|
S2
|
B:FES4002
|
2.2
|
8.9
|
1.0
|
S1
|
B:FES4002
|
2.2
|
8.9
|
1.0
|
SG
|
B:CYS48
|
2.3
|
20.9
|
1.0
|
SG
|
B:CYS43
|
2.4
|
20.9
|
1.0
|
FE1
|
B:FES4002
|
2.7
|
8.9
|
1.0
|
CB
|
B:CYS48
|
3.5
|
20.9
|
1.0
|
N
|
B:CYS48
|
3.5
|
20.9
|
1.0
|
N
|
B:CYS43
|
3.6
|
20.9
|
1.0
|
CB
|
B:CYS43
|
3.6
|
20.9
|
1.0
|
N
|
B:GLY49
|
3.6
|
20.9
|
1.0
|
CA
|
B:CYS48
|
3.8
|
20.9
|
1.0
|
N
|
B:GLY44
|
3.9
|
20.9
|
1.0
|
CA
|
B:CYS43
|
4.0
|
20.9
|
1.0
|
C
|
B:GLY42
|
4.1
|
20.9
|
1.0
|
C
|
B:CYS48
|
4.1
|
20.9
|
1.0
|
N
|
B:ALA50
|
4.2
|
20.9
|
1.0
|
N
|
B:GLY42
|
4.3
|
20.9
|
1.0
|
N
|
B:GLY47
|
4.3
|
20.9
|
1.0
|
CA
|
B:GLY42
|
4.4
|
20.9
|
1.0
|
N
|
B:GLY46
|
4.4
|
20.9
|
1.0
|
C
|
B:CYS43
|
4.4
|
20.9
|
1.0
|
CA
|
B:GLY49
|
4.6
|
20.9
|
1.0
|
C
|
B:GLY47
|
4.6
|
20.9
|
1.0
|
SG
|
B:CYS73
|
4.7
|
20.9
|
1.0
|
SG
|
B:CYS51
|
4.7
|
20.9
|
1.0
|
CA
|
B:GLY46
|
4.7
|
20.9
|
1.0
|
C
|
B:GLY46
|
4.7
|
20.9
|
1.0
|
N
|
B:GLU45
|
4.8
|
20.9
|
1.0
|
CB
|
B:ALA50
|
4.8
|
20.9
|
1.0
|
CA
|
B:GLY44
|
4.8
|
20.9
|
1.0
|
C
|
B:GLY49
|
4.9
|
20.9
|
1.0
|
O
|
B:GLY42
|
5.0
|
20.9
|
1.0
|
N
|
B:CYS51
|
5.0
|
20.9
|
1.0
|
|
Reference:
K.Okamoto,
B.T.Eger,
T.Nishino,
S.Kondo,
E.F.Pai,
T.Nishino.
An Extremely Potent Inhibitor of Xanthine Oxidoreductase: Crystal Structure of the Enzyme-Inhibitor Complex and Mechanism of Inhibition J.Biol.Chem. V. 278 1848 2003.
ISSN: ISSN 0021-9258
PubMed: 12421831
DOI: 10.1074/JBC.M208307200
Page generated: Sat Aug 3 11:25:13 2024
|