Molybdenum in PDB 1xdq: Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase
Protein crystallography data
The structure of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, PDB code: 1xdq
was solved by
L.Loschi,
S.J.Brokx,
T.L.Hills,
G.Zhang,
M.G.Bertero,
A.L.Lovering,
J.H.Weiner,
N.C.Strynadka,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.75 /
2.55
|
Space group
|
I 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
110.345,
165.064,
181.447,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23 /
27.4
|
Molybdenum Binding Sites:
The binding sites of Molybdenum atom in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase
(pdb code 1xdq). This binding sites where shown within
5.0 Angstroms radius around Molybdenum atom.
In total 5 binding sites of Molybdenum where determined in the
Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase, PDB code: 1xdq:
Jump to Molybdenum binding site number:
1;
2;
3;
4;
5;
Molybdenum binding site 1 out
of 5 in 1xdq
Go back to
Molybdenum Binding Sites List in 1xdq
Molybdenum binding site 1 out
of 5 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase
Mono view
Stereo pair view
|
A full contact list of Molybdenum with other atoms in the Mo binding
site number 1 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mo501
b:40.7
occ:1.00
|
O
|
A:O601
|
1.7
|
35.3
|
1.0
|
O
|
A:HOH645
|
2.2
|
13.8
|
1.0
|
S2'
|
A:MTE301
|
2.4
|
44.4
|
1.0
|
S1'
|
A:MTE301
|
2.4
|
36.7
|
1.0
|
SG
|
A:CYS102
|
2.5
|
39.8
|
1.0
|
C1'
|
A:MTE301
|
3.2
|
41.8
|
1.0
|
C2'
|
A:MTE301
|
3.4
|
42.9
|
1.0
|
CB
|
A:CYS102
|
3.5
|
39.0
|
1.0
|
ND2
|
A:ASN45
|
3.6
|
46.6
|
1.0
|
N
|
A:VAL103
|
3.8
|
49.0
|
1.0
|
N
|
A:PHE203
|
3.9
|
41.1
|
1.0
|
CA
|
A:CYS102
|
3.9
|
41.7
|
1.0
|
CG1
|
A:VAL103
|
4.3
|
37.8
|
1.0
|
CA
|
A:GLY202
|
4.3
|
37.4
|
1.0
|
C
|
A:GLY202
|
4.3
|
40.5
|
1.0
|
C
|
A:CYS102
|
4.3
|
47.9
|
1.0
|
CA
|
A:PHE203
|
4.6
|
41.4
|
1.0
|
CB
|
A:PHE203
|
4.6
|
36.6
|
1.0
|
N
|
A:GLY202
|
4.7
|
40.2
|
1.0
|
C6
|
A:MTE301
|
4.7
|
41.0
|
1.0
|
CG
|
A:ASN45
|
4.7
|
46.2
|
1.0
|
N
|
A:GLU104
|
4.7
|
39.4
|
1.0
|
CA
|
A:VAL103
|
4.8
|
46.3
|
1.0
|
CD2
|
A:PHE203
|
4.8
|
40.8
|
1.0
|
CB
|
A:VAL103
|
4.9
|
45.9
|
1.0
|
|
Molybdenum binding site 2 out
of 5 in 1xdq
Go back to
Molybdenum Binding Sites List in 1xdq
Molybdenum binding site 2 out
of 5 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase
Mono view
Stereo pair view
|
A full contact list of Molybdenum with other atoms in the Mo binding
site number 2 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mo502
b:41.2
occ:1.00
|
O
|
B:O602
|
1.7
|
32.2
|
1.0
|
S1'
|
B:MTE302
|
2.3
|
40.1
|
1.0
|
S2'
|
B:MTE302
|
2.4
|
44.2
|
1.0
|
SG
|
B:CYS102
|
2.5
|
47.1
|
1.0
|
O
|
B:HOH628
|
2.5
|
17.1
|
1.0
|
C1'
|
B:MTE302
|
3.2
|
46.0
|
1.0
|
CB
|
B:CYS102
|
3.4
|
50.0
|
1.0
|
C2'
|
B:MTE302
|
3.4
|
42.6
|
1.0
|
ND2
|
B:ASN45
|
3.6
|
63.4
|
1.0
|
N
|
B:VAL103
|
3.8
|
46.1
|
1.0
|
CA
|
B:CYS102
|
3.9
|
45.9
|
1.0
|
N
|
B:PHE203
|
3.9
|
40.8
|
1.0
|
CG1
|
B:VAL103
|
4.2
|
34.3
|
1.0
|
C
|
B:CYS102
|
4.3
|
47.0
|
1.0
|
CA
|
B:GLY202
|
4.4
|
44.9
|
1.0
|
C
|
B:GLY202
|
4.4
|
42.1
|
1.0
|
C6
|
B:MTE302
|
4.6
|
33.6
|
1.0
|
CA
|
B:PHE203
|
4.6
|
42.5
|
1.0
|
CB
|
B:PHE203
|
4.7
|
41.7
|
1.0
|
N
|
B:GLY202
|
4.7
|
42.6
|
1.0
|
CG
|
B:ASN45
|
4.7
|
61.2
|
1.0
|
N
|
B:GLU104
|
4.8
|
44.7
|
1.0
|
CA
|
B:VAL103
|
4.8
|
46.7
|
1.0
|
CD2
|
B:PHE203
|
4.8
|
35.8
|
1.0
|
CB
|
B:VAL103
|
4.8
|
42.7
|
1.0
|
CG
|
B:GLU104
|
5.0
|
45.5
|
1.0
|
|
Molybdenum binding site 3 out
of 5 in 1xdq
Go back to
Molybdenum Binding Sites List in 1xdq
Molybdenum binding site 3 out
of 5 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase
Mono view
Stereo pair view
|
A full contact list of Molybdenum with other atoms in the Mo binding
site number 3 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mo503
b:41.4
occ:1.00
|
O
|
C:O603
|
1.7
|
42.6
|
1.0
|
O
|
C:HOH621
|
2.2
|
15.9
|
1.0
|
S2'
|
C:MTE303
|
2.3
|
45.3
|
1.0
|
S1'
|
C:MTE303
|
2.3
|
43.5
|
1.0
|
SG
|
C:CYS102
|
2.4
|
44.0
|
1.0
|
C1'
|
C:MTE303
|
3.2
|
49.8
|
1.0
|
CB
|
C:CYS102
|
3.4
|
43.3
|
1.0
|
C2'
|
C:MTE303
|
3.4
|
47.3
|
1.0
|
ND2
|
C:ASN45
|
3.8
|
51.4
|
1.0
|
N
|
C:VAL103
|
3.8
|
46.7
|
1.0
|
CA
|
C:CYS102
|
3.9
|
46.2
|
1.0
|
N
|
C:PHE203
|
3.9
|
46.2
|
1.0
|
CG1
|
C:VAL103
|
4.2
|
28.8
|
1.0
|
C
|
C:GLY202
|
4.3
|
44.8
|
1.0
|
C
|
C:CYS102
|
4.3
|
47.2
|
1.0
|
CA
|
C:GLY202
|
4.3
|
41.5
|
1.0
|
CB
|
C:PHE203
|
4.6
|
43.5
|
1.0
|
CA
|
C:PHE203
|
4.6
|
45.2
|
1.0
|
N
|
C:GLY202
|
4.6
|
44.8
|
1.0
|
C6
|
C:MTE303
|
4.6
|
45.2
|
1.0
|
CD2
|
C:PHE203
|
4.7
|
40.2
|
1.0
|
N
|
C:GLU104
|
4.8
|
47.4
|
1.0
|
CA
|
C:VAL103
|
4.8
|
42.0
|
1.0
|
CG
|
C:ASN45
|
4.8
|
46.0
|
1.0
|
CB
|
C:VAL103
|
4.9
|
43.7
|
1.0
|
|
Molybdenum binding site 4 out
of 5 in 1xdq
Go back to
Molybdenum Binding Sites List in 1xdq
Molybdenum binding site 4 out
of 5 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase
Mono view
Stereo pair view
|
A full contact list of Molybdenum with other atoms in the Mo binding
site number 4 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mo504
b:41.9
occ:1.00
|
O
|
D:O604
|
1.7
|
31.2
|
1.0
|
O
|
D:HOH629
|
2.3
|
19.8
|
1.0
|
S2'
|
D:MTE304
|
2.3
|
47.4
|
1.0
|
S1'
|
D:MTE304
|
2.4
|
46.9
|
1.0
|
SG
|
D:CYS102
|
2.4
|
45.0
|
1.0
|
C1'
|
D:MTE304
|
3.2
|
50.6
|
1.0
|
C2'
|
D:MTE304
|
3.4
|
50.4
|
1.0
|
CB
|
D:CYS102
|
3.5
|
44.4
|
1.0
|
ND2
|
D:ASN45
|
3.7
|
51.2
|
1.0
|
N
|
D:VAL103
|
3.7
|
43.2
|
1.0
|
N
|
D:PHE203
|
3.8
|
45.0
|
1.0
|
CA
|
D:CYS102
|
3.8
|
44.8
|
1.0
|
CA
|
D:GLY202
|
4.2
|
46.0
|
1.0
|
C
|
D:GLY202
|
4.3
|
46.9
|
1.0
|
C
|
D:CYS102
|
4.3
|
46.0
|
1.0
|
CG1
|
D:VAL103
|
4.3
|
44.6
|
1.0
|
N
|
D:GLY202
|
4.5
|
39.1
|
1.0
|
CA
|
D:PHE203
|
4.6
|
46.0
|
1.0
|
CB
|
D:PHE203
|
4.6
|
43.0
|
1.0
|
C6
|
D:MTE304
|
4.7
|
47.0
|
1.0
|
CA
|
D:VAL103
|
4.8
|
43.3
|
1.0
|
CB
|
D:VAL103
|
4.8
|
41.2
|
1.0
|
N
|
D:GLU104
|
4.8
|
42.3
|
1.0
|
CG
|
D:ASN45
|
4.8
|
56.9
|
1.0
|
CD2
|
D:PHE203
|
4.9
|
45.3
|
1.0
|
|
Molybdenum binding site 5 out
of 5 in 1xdq
Go back to
Molybdenum Binding Sites List in 1xdq
Molybdenum binding site 5 out
of 5 in the Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase
Mono view
Stereo pair view
|
A full contact list of Molybdenum with other atoms in the Mo binding
site number 5 of Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mo505
b:49.0
occ:1.00
|
O
|
E:O605
|
1.7
|
32.2
|
1.0
|
S2'
|
E:MTE305
|
2.3
|
49.2
|
1.0
|
S1'
|
E:MTE305
|
2.3
|
43.3
|
1.0
|
O
|
E:HOH630
|
2.4
|
29.2
|
1.0
|
SG
|
E:CYS102
|
2.5
|
53.4
|
1.0
|
C1'
|
E:MTE305
|
3.2
|
50.5
|
1.0
|
C2'
|
E:MTE305
|
3.4
|
49.3
|
1.0
|
CB
|
E:CYS102
|
3.5
|
51.2
|
1.0
|
ND2
|
E:ASN45
|
3.6
|
47.1
|
1.0
|
N
|
E:VAL103
|
3.8
|
52.4
|
1.0
|
CA
|
E:CYS102
|
3.9
|
53.8
|
1.0
|
N
|
E:PHE203
|
3.9
|
40.6
|
1.0
|
CA
|
E:GLY202
|
4.2
|
43.2
|
1.0
|
C
|
E:GLY202
|
4.3
|
45.8
|
1.0
|
CG1
|
E:VAL103
|
4.3
|
46.1
|
1.0
|
C
|
E:CYS102
|
4.3
|
55.9
|
1.0
|
N
|
E:GLY202
|
4.6
|
45.8
|
1.0
|
CA
|
E:PHE203
|
4.6
|
41.4
|
1.0
|
C6
|
E:MTE305
|
4.7
|
45.9
|
1.0
|
CB
|
E:PHE203
|
4.7
|
45.2
|
1.0
|
N
|
E:GLU104
|
4.7
|
47.8
|
1.0
|
CG
|
E:ASN45
|
4.7
|
52.7
|
1.0
|
CA
|
E:VAL103
|
4.8
|
46.7
|
1.0
|
CD2
|
E:PHE203
|
4.8
|
46.6
|
1.0
|
CB
|
E:VAL103
|
4.8
|
45.7
|
1.0
|
|
Reference:
L.Loschi,
S.J.Brokx,
T.L.Hills,
G.Zhang,
M.G.Bertero,
A.L.Lovering,
J.H.Weiner,
N.C.Strynadka.
Structural and Biochemical Identification of A Novel Bacterial Oxidoreductase. J.Biol.Chem. V. 279 50391 2004.
ISSN: ISSN 0021-9258
PubMed: 15355966
DOI: 10.1074/JBC.M408876200
Page generated: Sun Oct 6 15:33:30 2024
|