Iron in PDB 7dqx: Crystal Structure of Xanthine Dehydrogenase Family Protein
Enzymatic activity of Crystal Structure of Xanthine Dehydrogenase Family Protein
All present enzymatic activity of Crystal Structure of Xanthine Dehydrogenase Family Protein:
1.5.99.14;
Protein crystallography data
The structure of Crystal Structure of Xanthine Dehydrogenase Family Protein, PDB code: 7dqx
was solved by
W.Lei,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
147.24 /
3.44
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
112.86,
126.792,
294.49,
90,
90,
90
|
R / Rfree (%)
|
28.8 /
32.6
|
Other elements in 7dqx:
The structure of Crystal Structure of Xanthine Dehydrogenase Family Protein also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Xanthine Dehydrogenase Family Protein
(pdb code 7dqx). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Crystal Structure of Xanthine Dehydrogenase Family Protein, PDB code: 7dqx:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 7dqx
Go back to
Iron Binding Sites List in 7dqx
Iron binding site 1 out
of 8 in the Crystal Structure of Xanthine Dehydrogenase Family Protein
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Xanthine Dehydrogenase Family Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:66.4
occ:1.00
|
FE1
|
C:FES201
|
0.0
|
66.4
|
1.0
|
CB
|
C:CYS62
|
2.0
|
65.3
|
1.0
|
S1
|
C:FES201
|
2.2
|
64.0
|
1.0
|
S2
|
C:FES201
|
2.2
|
65.4
|
1.0
|
SG
|
C:CYS50
|
2.3
|
61.9
|
1.0
|
SG
|
C:CYS62
|
2.3
|
65.3
|
1.0
|
FE2
|
C:FES201
|
3.2
|
64.8
|
1.0
|
CB
|
C:CYS50
|
3.2
|
58.5
|
1.0
|
CA
|
C:CYS62
|
3.4
|
63.9
|
1.0
|
N
|
C:CYS62
|
4.0
|
60.8
|
1.0
|
C
|
C:CYS62
|
4.1
|
63.9
|
1.0
|
N
|
C:GLY45
|
4.1
|
56.0
|
1.0
|
SG
|
C:CYS42
|
4.3
|
64.0
|
1.0
|
O
|
C:CYS62
|
4.4
|
64.1
|
1.0
|
CA
|
C:CYS50
|
4.5
|
56.2
|
1.0
|
CA
|
C:GLY45
|
4.6
|
56.3
|
1.0
|
N
|
C:HIS44
|
4.6
|
60.9
|
1.0
|
SG
|
C:CYS47
|
4.6
|
62.7
|
1.0
|
CB
|
C:ARG60
|
4.7
|
54.2
|
1.0
|
C
|
C:GLU43
|
4.7
|
64.8
|
1.0
|
CG1
|
C:VAL40
|
4.7
|
61.4
|
1.0
|
N
|
C:THR63
|
4.8
|
63.0
|
1.0
|
CA
|
C:GLU43
|
4.8
|
70.8
|
1.0
|
OE1
|
C:GLU43
|
4.8
|
82.1
|
1.0
|
O
|
C:CYS42
|
5.0
|
70.9
|
1.0
|
C
|
C:SER61
|
5.0
|
59.4
|
1.0
|
|
Iron binding site 2 out
of 8 in 7dqx
Go back to
Iron Binding Sites List in 7dqx
Iron binding site 2 out
of 8 in the Crystal Structure of Xanthine Dehydrogenase Family Protein
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Xanthine Dehydrogenase Family Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:64.8
occ:1.00
|
FE2
|
C:FES201
|
0.0
|
64.8
|
1.0
|
S1
|
C:FES201
|
2.2
|
64.0
|
1.0
|
S2
|
C:FES201
|
2.2
|
65.4
|
1.0
|
SG
|
C:CYS47
|
2.3
|
62.7
|
1.0
|
SG
|
C:CYS42
|
2.3
|
64.0
|
1.0
|
SG
|
C:CYS50
|
2.8
|
61.9
|
1.0
|
FE1
|
C:FES201
|
3.2
|
66.4
|
1.0
|
N
|
C:CYS47
|
3.2
|
58.1
|
1.0
|
CB
|
C:CYS50
|
3.3
|
58.5
|
1.0
|
N
|
C:GLY48
|
3.4
|
56.0
|
1.0
|
N
|
C:VAL46
|
3.4
|
55.7
|
1.0
|
CB
|
C:CYS47
|
3.6
|
60.2
|
1.0
|
CA
|
C:CYS47
|
3.8
|
58.4
|
1.0
|
C
|
C:VAL46
|
3.9
|
56.6
|
1.0
|
CA
|
C:GLY45
|
4.0
|
56.3
|
1.0
|
C
|
C:GLY45
|
4.0
|
56.0
|
1.0
|
N
|
C:GLY45
|
4.1
|
56.0
|
1.0
|
CB
|
C:CYS42
|
4.1
|
64.8
|
1.0
|
C
|
C:CYS47
|
4.1
|
58.5
|
1.0
|
CA
|
C:VAL46
|
4.2
|
55.4
|
1.0
|
CA
|
C:GLY48
|
4.4
|
54.5
|
1.0
|
NH1
|
C:ARG60
|
4.5
|
51.6
|
1.0
|
CA
|
C:CYS50
|
4.5
|
56.2
|
1.0
|
N
|
C:CYS50
|
4.6
|
54.4
|
1.0
|
N
|
C:CYS42
|
4.6
|
64.2
|
1.0
|
O
|
C:VAL46
|
4.7
|
56.7
|
1.0
|
C
|
C:GLY48
|
4.7
|
52.5
|
1.0
|
CD
|
C:ARG60
|
4.8
|
55.6
|
1.0
|
CA
|
C:CYS42
|
4.8
|
65.9
|
1.0
|
SG
|
C:CYS62
|
4.9
|
65.3
|
1.0
|
C
|
C:CYS42
|
4.9
|
68.0
|
1.0
|
O
|
C:GLY45
|
4.9
|
56.7
|
1.0
|
|
Iron binding site 3 out
of 8 in 7dqx
Go back to
Iron Binding Sites List in 7dqx
Iron binding site 3 out
of 8 in the Crystal Structure of Xanthine Dehydrogenase Family Protein
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Xanthine Dehydrogenase Family Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe202
b:43.3
occ:1.00
|
FE1
|
C:FES202
|
0.0
|
43.3
|
1.0
|
S2
|
C:FES202
|
2.2
|
49.4
|
1.0
|
S1
|
C:FES202
|
2.2
|
47.7
|
1.0
|
SG
|
C:CYS104
|
2.3
|
45.2
|
1.0
|
SG
|
C:CYS137
|
2.3
|
45.8
|
1.0
|
FE2
|
C:FES202
|
3.2
|
47.2
|
1.0
|
CB
|
C:CYS139
|
3.6
|
45.3
|
1.0
|
SG
|
C:CYS101
|
3.7
|
49.1
|
1.0
|
CB
|
C:CYS137
|
3.8
|
46.7
|
1.0
|
SG
|
C:CYS139
|
3.9
|
48.1
|
1.0
|
CB
|
C:CYS104
|
4.1
|
43.6
|
1.0
|
N
|
C:CYS139
|
4.2
|
44.5
|
1.0
|
N
|
C:ARG138
|
4.3
|
45.4
|
1.0
|
OG1
|
C:THR140
|
4.3
|
41.9
|
1.0
|
N
|
C:GLN100
|
4.4
|
45.5
|
1.0
|
CA
|
C:CYS139
|
4.4
|
44.2
|
1.0
|
CA
|
C:CYS137
|
4.5
|
45.4
|
1.0
|
N
|
C:CYS101
|
4.5
|
48.2
|
1.0
|
N
|
C:CYS104
|
4.7
|
41.9
|
1.0
|
N
|
C:THR140
|
4.7
|
42.7
|
1.0
|
C
|
C:CYS137
|
4.8
|
47.6
|
1.0
|
CB
|
C:CYS101
|
4.9
|
50.0
|
1.0
|
CA
|
C:CYS104
|
4.9
|
43.2
|
1.0
|
C
|
C:ARG138
|
5.0
|
45.7
|
1.0
|
|
Iron binding site 4 out
of 8 in 7dqx
Go back to
Iron Binding Sites List in 7dqx
Iron binding site 4 out
of 8 in the Crystal Structure of Xanthine Dehydrogenase Family Protein
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Xanthine Dehydrogenase Family Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe202
b:47.2
occ:1.00
|
FE2
|
C:FES202
|
0.0
|
47.2
|
1.0
|
S2
|
C:FES202
|
2.2
|
49.4
|
1.0
|
S1
|
C:FES202
|
2.2
|
47.7
|
1.0
|
SG
|
C:CYS139
|
2.3
|
48.1
|
1.0
|
SG
|
C:CYS101
|
2.3
|
49.1
|
1.0
|
CB
|
C:CYS101
|
2.9
|
50.0
|
1.0
|
FE1
|
C:FES202
|
3.2
|
43.3
|
1.0
|
CB
|
C:CYS139
|
3.5
|
45.3
|
1.0
|
N
|
C:CYS101
|
4.0
|
48.2
|
1.0
|
CA
|
C:CYS101
|
4.0
|
48.1
|
1.0
|
N2'
|
A:MCN801
|
4.4
|
66.7
|
1.0
|
O
|
A:GLY266
|
4.4
|
57.6
|
1.0
|
N
|
C:CYS139
|
4.5
|
44.5
|
1.0
|
C
|
C:ARG138
|
4.5
|
45.7
|
1.0
|
N
|
C:ARG138
|
4.6
|
45.4
|
1.0
|
CA
|
C:CYS139
|
4.6
|
44.2
|
1.0
|
SG
|
C:CYS104
|
4.6
|
45.2
|
1.0
|
C
|
A:GLY266
|
4.7
|
57.4
|
1.0
|
CG
|
A:MET216
|
4.8
|
54.6
|
1.0
|
N3'
|
A:MCN801
|
4.8
|
71.1
|
1.0
|
SG
|
C:CYS137
|
4.8
|
45.8
|
1.0
|
CZ
|
A:PHE269
|
4.8
|
47.2
|
1.0
|
O
|
C:ARG138
|
4.8
|
46.0
|
1.0
|
N
|
A:GLY267
|
4.9
|
57.0
|
1.0
|
CA
|
C:ARG138
|
4.9
|
45.8
|
1.0
|
N
|
C:GLY102
|
4.9
|
44.4
|
1.0
|
CA
|
A:GLY267
|
4.9
|
57.0
|
1.0
|
CB
|
C:ARG138
|
4.9
|
46.7
|
1.0
|
|
Iron binding site 5 out
of 8 in 7dqx
Go back to
Iron Binding Sites List in 7dqx
Iron binding site 5 out
of 8 in the Crystal Structure of Xanthine Dehydrogenase Family Protein
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of Xanthine Dehydrogenase Family Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe201
b:58.4
occ:1.00
|
FE1
|
F:FES201
|
0.0
|
58.4
|
1.0
|
CB
|
F:CYS62
|
2.0
|
56.9
|
1.0
|
S1
|
F:FES201
|
2.2
|
55.8
|
1.0
|
S2
|
F:FES201
|
2.2
|
57.6
|
1.0
|
SG
|
F:CYS50
|
2.3
|
55.7
|
1.0
|
SG
|
F:CYS62
|
2.3
|
57.5
|
1.0
|
CB
|
F:CYS50
|
3.1
|
54.3
|
1.0
|
FE2
|
F:FES201
|
3.2
|
54.5
|
1.0
|
CA
|
F:CYS62
|
3.5
|
54.6
|
1.0
|
N
|
F:CYS62
|
4.0
|
53.2
|
1.0
|
C
|
F:CYS62
|
4.1
|
52.9
|
1.0
|
N
|
F:GLY45
|
4.1
|
51.2
|
1.0
|
CB
|
F:ARG60
|
4.4
|
50.2
|
1.0
|
O
|
F:CYS62
|
4.4
|
54.1
|
1.0
|
SG
|
F:CYS42
|
4.5
|
54.1
|
1.0
|
CA
|
F:GLY45
|
4.5
|
51.4
|
1.0
|
CA
|
F:CYS50
|
4.5
|
53.3
|
1.0
|
N
|
F:HIS44
|
4.6
|
53.2
|
1.0
|
N
|
F:THR63
|
4.7
|
53.4
|
1.0
|
SG
|
F:CYS47
|
4.8
|
53.2
|
1.0
|
C
|
F:GLU43
|
4.8
|
54.4
|
1.0
|
CA
|
F:GLU43
|
4.9
|
56.9
|
1.0
|
O
|
F:CYS42
|
5.0
|
58.0
|
1.0
|
CG1
|
F:VAL40
|
5.0
|
56.0
|
1.0
|
|
Iron binding site 6 out
of 8 in 7dqx
Go back to
Iron Binding Sites List in 7dqx
Iron binding site 6 out
of 8 in the Crystal Structure of Xanthine Dehydrogenase Family Protein
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of Xanthine Dehydrogenase Family Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe201
b:54.5
occ:1.00
|
FE2
|
F:FES201
|
0.0
|
54.5
|
1.0
|
S1
|
F:FES201
|
2.2
|
55.8
|
1.0
|
S2
|
F:FES201
|
2.2
|
57.6
|
1.0
|
SG
|
F:CYS47
|
2.3
|
53.2
|
1.0
|
SG
|
F:CYS42
|
2.3
|
54.1
|
1.0
|
SG
|
F:CYS50
|
2.9
|
55.7
|
1.0
|
N
|
F:CYS47
|
3.0
|
51.8
|
1.0
|
FE1
|
F:FES201
|
3.2
|
58.4
|
1.0
|
N
|
F:VAL46
|
3.3
|
50.6
|
1.0
|
CB
|
F:CYS47
|
3.5
|
53.1
|
1.0
|
N
|
F:GLY48
|
3.6
|
53.1
|
1.0
|
CB
|
F:CYS50
|
3.6
|
54.3
|
1.0
|
CA
|
F:CYS47
|
3.6
|
52.6
|
1.0
|
CB
|
F:CYS42
|
3.7
|
55.0
|
1.0
|
C
|
F:VAL46
|
3.8
|
50.7
|
1.0
|
N
|
F:GLY45
|
4.0
|
51.2
|
1.0
|
C
|
F:GLY45
|
4.1
|
51.0
|
1.0
|
CA
|
F:VAL46
|
4.1
|
50.1
|
1.0
|
CA
|
F:GLY45
|
4.1
|
51.4
|
1.0
|
C
|
F:CYS47
|
4.2
|
53.7
|
1.0
|
N
|
F:CYS42
|
4.2
|
55.6
|
1.0
|
C
|
F:CYS42
|
4.3
|
56.4
|
1.0
|
CA
|
F:CYS42
|
4.3
|
55.5
|
1.0
|
O
|
F:CYS42
|
4.5
|
58.0
|
1.0
|
N
|
F:GLU43
|
4.7
|
55.9
|
1.0
|
O
|
F:VAL46
|
4.7
|
50.7
|
1.0
|
CA
|
F:GLY48
|
4.7
|
52.7
|
1.0
|
N
|
F:HIS44
|
4.7
|
53.2
|
1.0
|
NH1
|
F:ARG60
|
4.8
|
52.7
|
1.0
|
N
|
F:CYS50
|
4.9
|
52.7
|
1.0
|
CA
|
F:CYS50
|
4.9
|
53.3
|
1.0
|
SG
|
F:CYS62
|
5.0
|
57.5
|
1.0
|
|
Iron binding site 7 out
of 8 in 7dqx
Go back to
Iron Binding Sites List in 7dqx
Iron binding site 7 out
of 8 in the Crystal Structure of Xanthine Dehydrogenase Family Protein
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Crystal Structure of Xanthine Dehydrogenase Family Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe202
b:48.6
occ:1.00
|
FE1
|
F:FES202
|
0.0
|
48.6
|
1.0
|
S2
|
F:FES202
|
2.2
|
51.5
|
1.0
|
S1
|
F:FES202
|
2.2
|
46.6
|
1.0
|
SG
|
F:CYS104
|
2.3
|
50.2
|
1.0
|
SG
|
F:CYS137
|
2.3
|
53.9
|
1.0
|
FE2
|
F:FES202
|
3.1
|
50.3
|
1.0
|
CB
|
F:CYS139
|
3.5
|
56.3
|
1.0
|
SG
|
F:CYS101
|
3.7
|
51.0
|
1.0
|
CB
|
F:CYS137
|
3.9
|
54.7
|
1.0
|
SG
|
F:CYS139
|
3.9
|
56.4
|
1.0
|
CB
|
F:CYS104
|
4.0
|
48.9
|
1.0
|
N
|
F:CYS139
|
4.3
|
55.8
|
1.0
|
N
|
F:ARG138
|
4.4
|
55.6
|
1.0
|
CA
|
F:CYS139
|
4.4
|
56.0
|
1.0
|
CA
|
F:CYS137
|
4.5
|
55.8
|
1.0
|
OG1
|
F:THR140
|
4.5
|
56.7
|
1.0
|
N
|
F:CYS101
|
4.5
|
51.5
|
1.0
|
N
|
F:GLN100
|
4.6
|
51.9
|
1.0
|
N
|
F:CYS104
|
4.7
|
49.6
|
1.0
|
CB
|
F:CYS101
|
4.8
|
50.9
|
1.0
|
C
|
F:CYS137
|
4.8
|
56.4
|
1.0
|
N
|
F:THR140
|
4.9
|
55.5
|
1.0
|
CA
|
F:CYS104
|
4.9
|
50.6
|
1.0
|
CG
|
F:GLN100
|
5.0
|
54.9
|
1.0
|
C
|
F:ARG138
|
5.0
|
55.6
|
1.0
|
|
Iron binding site 8 out
of 8 in 7dqx
Go back to
Iron Binding Sites List in 7dqx
Iron binding site 8 out
of 8 in the Crystal Structure of Xanthine Dehydrogenase Family Protein
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Crystal Structure of Xanthine Dehydrogenase Family Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe202
b:50.3
occ:1.00
|
FE2
|
F:FES202
|
0.0
|
50.3
|
1.0
|
S2
|
F:FES202
|
2.2
|
51.5
|
1.0
|
S1
|
F:FES202
|
2.2
|
46.6
|
1.0
|
SG
|
F:CYS139
|
2.3
|
56.4
|
1.0
|
SG
|
F:CYS101
|
2.3
|
51.0
|
1.0
|
CB
|
F:CYS101
|
2.8
|
50.9
|
1.0
|
FE1
|
F:FES202
|
3.1
|
48.6
|
1.0
|
CB
|
F:CYS139
|
3.5
|
56.3
|
1.0
|
CA
|
F:CYS101
|
4.0
|
50.9
|
1.0
|
N
|
F:CYS101
|
4.0
|
51.5
|
1.0
|
N2'
|
D:MCN801
|
4.1
|
68.8
|
1.0
|
N3'
|
D:MCN801
|
4.6
|
74.0
|
1.0
|
N
|
F:CYS139
|
4.6
|
55.8
|
1.0
|
C
|
F:ARG138
|
4.6
|
55.6
|
1.0
|
CA
|
F:CYS139
|
4.6
|
56.0
|
1.0
|
CA
|
D:GLY267
|
4.6
|
55.5
|
1.0
|
O
|
D:GLY266
|
4.6
|
55.3
|
1.0
|
SG
|
F:CYS104
|
4.7
|
50.2
|
1.0
|
N
|
F:ARG138
|
4.8
|
55.6
|
1.0
|
C2'
|
D:MCN801
|
4.8
|
74.5
|
1.0
|
N
|
D:GLY267
|
4.8
|
54.7
|
1.0
|
C
|
D:GLY266
|
4.8
|
55.7
|
1.0
|
SG
|
F:CYS137
|
4.8
|
53.9
|
1.0
|
O
|
F:ARG138
|
4.8
|
55.5
|
1.0
|
N
|
F:GLY102
|
4.9
|
51.0
|
1.0
|
C
|
F:CYS101
|
4.9
|
51.7
|
1.0
|
CZ
|
D:PHE269
|
4.9
|
49.5
|
1.0
|
CG
|
D:MET216
|
5.0
|
56.7
|
1.0
|
|
Reference:
W.Lei,
W.Lei.
N/A N/A.
Page generated: Thu Aug 8 04:04:42 2024
|