Molybdenum in PDB 5wa0: Crystal Structure of the Sulfite Dehydrogenase, Sort R78Q Mutant From Sinorhizobium Meliloti
Enzymatic activity of Crystal Structure of the Sulfite Dehydrogenase, Sort R78Q Mutant From Sinorhizobium Meliloti
All present enzymatic activity of Crystal Structure of the Sulfite Dehydrogenase, Sort R78Q Mutant From Sinorhizobium Meliloti:
1.8.3.1;
Protein crystallography data
The structure of Crystal Structure of the Sulfite Dehydrogenase, Sort R78Q Mutant From Sinorhizobium Meliloti, PDB code: 5wa0
was solved by
M.J.Maher,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.94 /
2.10
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
95.520,
91.780,
109.670,
90.00,
90.56,
90.00
|
R / Rfree (%)
|
21.7 /
27.1
|
Molybdenum Binding Sites:
The binding sites of Molybdenum atom in the Crystal Structure of the Sulfite Dehydrogenase, Sort R78Q Mutant From Sinorhizobium Meliloti
(pdb code 5wa0). This binding sites where shown within
5.0 Angstroms radius around Molybdenum atom.
In total 4 binding sites of Molybdenum where determined in the
Crystal Structure of the Sulfite Dehydrogenase, Sort R78Q Mutant From Sinorhizobium Meliloti, PDB code: 5wa0:
Jump to Molybdenum binding site number:
1;
2;
3;
4;
Molybdenum binding site 1 out
of 4 in 5wa0
Go back to
Molybdenum Binding Sites List in 5wa0
Molybdenum binding site 1 out
of 4 in the Crystal Structure of the Sulfite Dehydrogenase, Sort R78Q Mutant From Sinorhizobium Meliloti
Mono view
Stereo pair view
|
A full contact list of Molybdenum with other atoms in the Mo binding
site number 1 of Crystal Structure of the Sulfite Dehydrogenase, Sort R78Q Mutant From Sinorhizobium Meliloti within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mo401
b:17.9
occ:1.00
|
MOM1
|
A:MSS401
|
0.0
|
17.9
|
1.0
|
OM1
|
A:MSS401
|
1.9
|
17.0
|
1.0
|
S2'
|
A:MSS401
|
2.3
|
18.2
|
1.0
|
S1'
|
A:MSS401
|
2.3
|
17.2
|
1.0
|
O
|
A:HOH503
|
2.3
|
33.4
|
1.0
|
SG
|
A:CYS127
|
2.4
|
13.8
|
1.0
|
OE1
|
A:GLN78
|
2.8
|
18.5
|
0.5
|
C1'
|
A:MSS401
|
3.3
|
16.8
|
1.0
|
C2'
|
A:MSS401
|
3.3
|
16.9
|
1.0
|
CB
|
A:CYS127
|
3.6
|
13.3
|
1.0
|
CA
|
A:CYS127
|
3.7
|
13.0
|
1.0
|
N
|
A:SER128
|
3.8
|
13.0
|
1.0
|
OG
|
A:SER128
|
3.9
|
13.3
|
1.0
|
CD
|
A:GLN78
|
3.9
|
18.8
|
0.5
|
CG
|
A:GLN78
|
4.0
|
17.8
|
0.5
|
OH
|
A:TYR267
|
4.0
|
16.7
|
1.0
|
N
|
A:VAL242
|
4.0
|
12.3
|
1.0
|
CE1
|
A:TYR267
|
4.2
|
16.1
|
1.0
|
CB
|
A:VAL242
|
4.3
|
13.0
|
1.0
|
C
|
A:CYS127
|
4.3
|
13.0
|
1.0
|
CA
|
A:VAL242
|
4.4
|
12.7
|
1.0
|
CZ
|
A:TYR267
|
4.5
|
16.4
|
1.0
|
NE2
|
A:GLN78
|
4.6
|
19.3
|
0.5
|
C
|
A:GLY241
|
4.6
|
12.1
|
1.0
|
C6
|
A:MSS401
|
4.7
|
16.2
|
1.0
|
C3'
|
A:MSS401
|
4.7
|
16.6
|
1.0
|
CA
|
A:GLY241
|
4.8
|
11.9
|
1.0
|
CB
|
A:SER128
|
4.8
|
13.3
|
1.0
|
CB
|
A:GLN78
|
4.8
|
17.8
|
0.5
|
CA
|
A:SER128
|
4.9
|
13.2
|
1.0
|
N
|
A:GLY129
|
4.9
|
14.2
|
1.0
|
N
|
A:CYS127
|
4.9
|
12.8
|
1.0
|
O
|
A:HOH575
|
5.0
|
14.0
|
1.0
|
|
Molybdenum binding site 2 out
of 4 in 5wa0
Go back to
Molybdenum Binding Sites List in 5wa0
Molybdenum binding site 2 out
of 4 in the Crystal Structure of the Sulfite Dehydrogenase, Sort R78Q Mutant From Sinorhizobium Meliloti
Mono view
Stereo pair view
|
A full contact list of Molybdenum with other atoms in the Mo binding
site number 2 of Crystal Structure of the Sulfite Dehydrogenase, Sort R78Q Mutant From Sinorhizobium Meliloti within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mo401
b:18.8
occ:1.00
|
MOM1
|
B:MSS401
|
0.0
|
18.8
|
1.0
|
OM1
|
B:MSS401
|
1.9
|
16.7
|
1.0
|
S2'
|
B:MSS401
|
2.3
|
18.2
|
1.0
|
S1'
|
B:MSS401
|
2.3
|
18.9
|
1.0
|
O
|
B:HOH501
|
2.4
|
35.9
|
1.0
|
SG
|
B:CYS127
|
2.5
|
15.9
|
1.0
|
OE1
|
B:GLN78
|
2.8
|
21.0
|
0.5
|
NE2
|
B:GLN78
|
3.1
|
20.5
|
0.5
|
C2'
|
B:MSS401
|
3.3
|
18.4
|
1.0
|
C1'
|
B:MSS401
|
3.3
|
18.2
|
1.0
|
CD
|
B:GLN78
|
3.3
|
20.7
|
0.5
|
CB
|
B:CYS127
|
3.5
|
15.2
|
1.0
|
CA
|
B:CYS127
|
3.7
|
14.9
|
1.0
|
N
|
B:SER128
|
3.9
|
15.2
|
1.0
|
N
|
B:VAL242
|
3.9
|
14.8
|
1.0
|
O
|
B:HOH715
|
4.1
|
15.3
|
1.0
|
CG
|
B:GLN78
|
4.1
|
20.2
|
0.5
|
OG
|
B:SER128
|
4.2
|
15.9
|
1.0
|
OH
|
B:TYR267
|
4.3
|
17.1
|
1.0
|
CE1
|
B:TYR267
|
4.3
|
16.9
|
1.0
|
C
|
B:CYS127
|
4.3
|
15.1
|
1.0
|
CB
|
B:VAL242
|
4.3
|
15.4
|
1.0
|
CA
|
B:VAL242
|
4.4
|
15.2
|
1.0
|
C
|
B:GLY241
|
4.6
|
14.8
|
1.0
|
CZ
|
B:TYR267
|
4.7
|
17.1
|
1.0
|
CG
|
B:GLN78
|
4.7
|
21.0
|
0.5
|
C6
|
B:MSS401
|
4.7
|
17.9
|
1.0
|
CA
|
B:GLY241
|
4.7
|
14.7
|
1.0
|
C3'
|
B:MSS401
|
4.7
|
18.1
|
1.0
|
N
|
B:GLY129
|
4.8
|
16.4
|
1.0
|
CB
|
B:GLN78
|
4.9
|
20.1
|
0.5
|
O
|
B:HOH716
|
4.9
|
19.6
|
1.0
|
CA
|
B:SER128
|
5.0
|
15.6
|
1.0
|
N
|
B:CYS127
|
5.0
|
14.8
|
1.0
|
CB
|
B:SER128
|
5.0
|
15.7
|
1.0
|
|
Molybdenum binding site 3 out
of 4 in 5wa0
Go back to
Molybdenum Binding Sites List in 5wa0
Molybdenum binding site 3 out
of 4 in the Crystal Structure of the Sulfite Dehydrogenase, Sort R78Q Mutant From Sinorhizobium Meliloti
Mono view
Stereo pair view
|
A full contact list of Molybdenum with other atoms in the Mo binding
site number 3 of Crystal Structure of the Sulfite Dehydrogenase, Sort R78Q Mutant From Sinorhizobium Meliloti within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mo401
b:18.6
occ:1.00
|
MOM1
|
C:MSS401
|
0.0
|
18.6
|
1.0
|
OM1
|
C:MSS401
|
1.9
|
17.6
|
1.0
|
O
|
C:HOH510
|
2.2
|
20.7
|
1.0
|
S1'
|
C:MSS401
|
2.3
|
17.0
|
1.0
|
S2'
|
C:MSS401
|
2.3
|
16.4
|
1.0
|
SG
|
C:CYS127
|
2.4
|
15.1
|
1.0
|
OE1
|
C:GLN78
|
2.8
|
18.0
|
0.5
|
C1'
|
C:MSS401
|
3.3
|
16.6
|
1.0
|
C2'
|
C:MSS401
|
3.3
|
16.6
|
1.0
|
CB
|
C:CYS127
|
3.5
|
14.6
|
1.0
|
CA
|
C:CYS127
|
3.7
|
14.4
|
1.0
|
N
|
C:SER128
|
3.9
|
15.1
|
1.0
|
CG
|
C:GLN78
|
4.0
|
17.8
|
0.5
|
CD
|
C:GLN78
|
4.0
|
18.3
|
0.5
|
OG
|
C:SER128
|
4.0
|
16.0
|
1.0
|
OH
|
C:TYR267
|
4.1
|
16.6
|
1.0
|
N
|
C:VAL242
|
4.1
|
12.9
|
1.0
|
CE1
|
C:TYR267
|
4.3
|
16.4
|
1.0
|
C
|
C:CYS127
|
4.3
|
14.7
|
1.0
|
O
|
C:HOH672
|
4.4
|
21.2
|
1.0
|
CB
|
C:VAL242
|
4.5
|
13.4
|
1.0
|
CA
|
C:VAL242
|
4.5
|
13.0
|
1.0
|
C
|
C:GLY241
|
4.6
|
12.6
|
1.0
|
CA
|
C:GLY241
|
4.6
|
12.6
|
1.0
|
CZ
|
C:TYR267
|
4.6
|
16.6
|
1.0
|
NE2
|
C:GLN78
|
4.6
|
18.5
|
0.5
|
C6
|
C:MSS401
|
4.7
|
16.5
|
1.0
|
C3'
|
C:MSS401
|
4.7
|
16.1
|
1.0
|
CB
|
C:GLN78
|
4.8
|
17.7
|
0.5
|
N
|
C:GLY129
|
4.8
|
16.3
|
1.0
|
CB
|
C:SER128
|
4.9
|
15.7
|
1.0
|
CA
|
C:SER128
|
5.0
|
15.4
|
1.0
|
N
|
C:CYS127
|
5.0
|
14.1
|
1.0
|
O
|
C:HOH656
|
5.0
|
20.4
|
1.0
|
|
Molybdenum binding site 4 out
of 4 in 5wa0
Go back to
Molybdenum Binding Sites List in 5wa0
Molybdenum binding site 4 out
of 4 in the Crystal Structure of the Sulfite Dehydrogenase, Sort R78Q Mutant From Sinorhizobium Meliloti
Mono view
Stereo pair view
|
A full contact list of Molybdenum with other atoms in the Mo binding
site number 4 of Crystal Structure of the Sulfite Dehydrogenase, Sort R78Q Mutant From Sinorhizobium Meliloti within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mo401
b:17.9
occ:1.00
|
MOM1
|
D:MSS401
|
0.0
|
17.9
|
1.0
|
OM1
|
D:MSS401
|
1.9
|
16.0
|
1.0
|
S1'
|
D:MSS401
|
2.3
|
16.6
|
1.0
|
S2'
|
D:MSS401
|
2.3
|
15.7
|
1.0
|
SG
|
D:CYS127
|
2.4
|
13.3
|
1.0
|
O
|
D:HOH524
|
2.4
|
16.0
|
1.0
|
OE1
|
D:GLN78
|
2.8
|
18.6
|
0.5
|
C1'
|
D:MSS401
|
3.3
|
16.4
|
1.0
|
C2'
|
D:MSS401
|
3.3
|
16.4
|
1.0
|
CB
|
D:CYS127
|
3.4
|
13.0
|
1.0
|
CA
|
D:CYS127
|
3.7
|
12.7
|
1.0
|
N
|
D:SER128
|
3.8
|
13.2
|
1.0
|
CD
|
D:GLN78
|
4.0
|
18.8
|
0.5
|
N
|
D:VAL242
|
4.0
|
14.6
|
1.0
|
CG
|
D:GLN78
|
4.0
|
18.0
|
0.5
|
OG
|
D:SER128
|
4.0
|
13.9
|
1.0
|
OH
|
D:TYR267
|
4.2
|
17.1
|
1.0
|
O
|
D:HOH534
|
4.2
|
26.0
|
1.0
|
C
|
D:CYS127
|
4.2
|
12.9
|
1.0
|
CE1
|
D:TYR267
|
4.3
|
16.8
|
1.0
|
CB
|
D:VAL242
|
4.4
|
15.2
|
1.0
|
CA
|
D:VAL242
|
4.5
|
14.8
|
1.0
|
C
|
D:GLY241
|
4.6
|
14.3
|
1.0
|
CA
|
D:GLY241
|
4.6
|
14.3
|
1.0
|
CZ
|
D:TYR267
|
4.7
|
17.1
|
1.0
|
CB
|
D:GLN78
|
4.7
|
17.9
|
0.5
|
CG
|
D:GLN78
|
4.7
|
18.8
|
0.5
|
C6
|
D:MSS401
|
4.7
|
16.4
|
1.0
|
C3'
|
D:MSS401
|
4.8
|
16.4
|
1.0
|
O
|
D:HOH688
|
4.8
|
10.8
|
1.0
|
CB
|
D:GLN78
|
4.8
|
18.2
|
0.5
|
CA
|
D:SER128
|
4.9
|
13.7
|
1.0
|
CB
|
D:SER128
|
4.9
|
13.8
|
1.0
|
NE2
|
D:GLN78
|
4.9
|
19.2
|
0.5
|
N
|
D:CYS127
|
4.9
|
12.4
|
1.0
|
N
|
D:GLY129
|
5.0
|
14.5
|
1.0
|
|
Reference:
J.C.Hsiao,
A.P.Mcgrath,
L.Kielmann,
P.Kalimuthu,
F.Darain,
P.V.Bernhardt,
J.Harmer,
M.Lee,
K.Meyers,
M.J.Maher,
U.Kappler.
The Central Active Site Arginine in Sulfite Oxidizing Enzymes Alters Kinetic Properties By Controlling Electron Transfer and Redox Interactions. Biochim. Biophys. Acta V.1859 19 2017.
ISSN: ISSN 0006-3002
PubMed: 28986298
DOI: 10.1016/J.BBABIO.2017.10.001
Page generated: Sun Oct 6 16:28:38 2024
|