Magnesium in PDB 6rj4: Molybdenum Storage Protein - P6422, Adp
Protein crystallography data
The structure of Molybdenum Storage Protein - P6422, Adp, PDB code: 6rj4
was solved by
U.Ermler,
S.Bruenle,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.17 /
1.90
|
Space group
|
P 64 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
188.680,
188.680,
188.630,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
17.2 /
20
|
Other elements in 6rj4:
The structure of Molybdenum Storage Protein - P6422, Adp also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Molybdenum Storage Protein - P6422, Adp
(pdb code 6rj4). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Molybdenum Storage Protein - P6422, Adp, PDB code: 6rj4:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6rj4
Go back to
Magnesium Binding Sites List in 6rj4
Magnesium binding site 1 out
of 4 in the Molybdenum Storage Protein - P6422, Adp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Molybdenum Storage Protein - P6422, Adp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg302
b:27.2
occ:1.00
|
O1B
|
A:ATP301
|
2.0
|
28.6
|
1.0
|
O
|
A:PRO227
|
2.0
|
34.6
|
1.0
|
OE2
|
A:GLU190
|
2.0
|
41.3
|
1.0
|
O
|
A:HOH419
|
2.1
|
27.6
|
1.0
|
O2A
|
A:ATP301
|
2.1
|
27.5
|
1.0
|
O
|
A:HOH404
|
2.2
|
24.9
|
1.0
|
CD
|
A:GLU190
|
3.0
|
37.6
|
1.0
|
C
|
A:PRO227
|
3.2
|
32.3
|
1.0
|
PB
|
A:ATP301
|
3.3
|
32.1
|
1.0
|
OE1
|
A:GLU190
|
3.3
|
37.7
|
1.0
|
PA
|
A:ATP301
|
3.3
|
33.2
|
1.0
|
O3A
|
A:ATP301
|
3.7
|
38.0
|
1.0
|
O
|
B:HOH416
|
3.9
|
30.8
|
1.0
|
OD2
|
A:ASP171
|
3.9
|
32.1
|
1.0
|
NZ
|
A:LYS45
|
4.0
|
35.5
|
1.0
|
O
|
A:HOH457
|
4.0
|
30.9
|
1.0
|
CA
|
A:PRO227
|
4.1
|
32.3
|
1.0
|
O3G
|
A:ATP301
|
4.1
|
28.4
|
1.0
|
OD1
|
A:ASP171
|
4.2
|
30.4
|
1.0
|
N
|
A:VAL228
|
4.2
|
32.7
|
1.0
|
C5'
|
A:ATP301
|
4.3
|
35.2
|
1.0
|
O
|
A:HOH458
|
4.3
|
31.2
|
1.0
|
O5'
|
A:ATP301
|
4.3
|
39.6
|
1.0
|
O2B
|
A:ATP301
|
4.4
|
32.5
|
1.0
|
CG
|
A:GLU190
|
4.4
|
31.5
|
1.0
|
CB
|
A:PRO227
|
4.4
|
33.0
|
1.0
|
CA
|
A:VAL228
|
4.4
|
28.1
|
1.0
|
O3B
|
A:ATP301
|
4.4
|
29.1
|
1.0
|
O1A
|
A:ATP301
|
4.4
|
42.4
|
1.0
|
CG
|
A:ASP171
|
4.5
|
31.7
|
1.0
|
PG
|
A:ATP301
|
4.8
|
28.2
|
1.0
|
CG1
|
A:VAL228
|
4.9
|
26.4
|
1.0
|
O
|
A:HOH415
|
5.0
|
25.4
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6rj4
Go back to
Magnesium Binding Sites List in 6rj4
Magnesium binding site 2 out
of 4 in the Molybdenum Storage Protein - P6422, Adp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Molybdenum Storage Protein - P6422, Adp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg302
b:40.9
occ:1.00
|
O3B
|
D:ADP301
|
1.9
|
33.4
|
0.7
|
O1A
|
D:ADP301
|
2.0
|
38.7
|
0.7
|
O
|
D:HOH433
|
2.2
|
40.5
|
1.0
|
O
|
D:HOH442
|
2.2
|
35.6
|
1.0
|
O
|
D:HOH526
|
2.3
|
44.7
|
1.0
|
O
|
D:HOH408
|
2.4
|
35.8
|
1.0
|
PA
|
D:ADP301
|
3.1
|
37.7
|
0.7
|
PB
|
D:ADP301
|
3.1
|
26.4
|
0.7
|
O3A
|
D:ADP301
|
3.1
|
37.1
|
0.7
|
O2
|
D:PO4303
|
3.7
|
27.0
|
1.0
|
O
|
D:HOH420
|
3.9
|
39.5
|
1.0
|
O5'
|
D:ADP301
|
3.9
|
38.1
|
0.7
|
O2B
|
D:ADP301
|
4.0
|
30.7
|
0.7
|
NZ
|
D:LYS42
|
4.1
|
25.2
|
1.0
|
O1B
|
D:ADP301
|
4.1
|
36.5
|
0.7
|
OD2
|
D:ASP170
|
4.3
|
27.4
|
1.0
|
O2A
|
D:ADP301
|
4.4
|
39.9
|
0.7
|
OD1
|
D:ASP170
|
4.5
|
27.5
|
1.0
|
O3
|
D:PO4303
|
4.6
|
33.5
|
1.0
|
NZ
|
D:LYS189
|
4.7
|
45.6
|
1.0
|
OE1
|
D:GLU227
|
4.7
|
31.1
|
1.0
|
CG
|
D:ASP170
|
4.7
|
28.9
|
1.0
|
P
|
D:PO4303
|
4.8
|
31.2
|
1.0
|
CE
|
D:LYS189
|
4.8
|
49.9
|
1.0
|
O
|
D:HOH514
|
4.9
|
49.5
|
1.0
|
OE1
|
D:GLN46
|
4.9
|
51.7
|
0.5
|
|
Magnesium binding site 3 out
of 4 in 6rj4
Go back to
Magnesium Binding Sites List in 6rj4
Magnesium binding site 3 out
of 4 in the Molybdenum Storage Protein - P6422, Adp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Molybdenum Storage Protein - P6422, Adp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg302
b:26.1
occ:1.00
|
O1B
|
C:ATP301
|
2.0
|
23.3
|
1.0
|
O
|
C:HOH406
|
2.0
|
26.4
|
1.0
|
O2A
|
C:ATP301
|
2.1
|
28.8
|
1.0
|
O
|
C:HOH413
|
2.1
|
25.9
|
1.0
|
O
|
C:PRO227
|
2.1
|
28.8
|
1.0
|
OE2
|
C:GLU190
|
2.1
|
31.8
|
1.0
|
CD
|
C:GLU190
|
3.1
|
32.7
|
1.0
|
PB
|
C:ATP301
|
3.3
|
25.4
|
1.0
|
PA
|
C:ATP301
|
3.3
|
30.7
|
1.0
|
C
|
C:PRO227
|
3.3
|
26.2
|
1.0
|
OE1
|
C:GLU190
|
3.4
|
30.8
|
1.0
|
O3A
|
C:ATP301
|
3.6
|
30.8
|
1.0
|
OD2
|
C:ASP171
|
3.9
|
30.2
|
1.0
|
O
|
C:HOH466
|
3.9
|
26.1
|
1.0
|
NZ
|
C:LYS45
|
4.0
|
23.5
|
1.0
|
O
|
C:HOH474
|
4.0
|
27.9
|
1.0
|
O3G
|
C:ATP301
|
4.1
|
24.2
|
1.0
|
CA
|
C:PRO227
|
4.2
|
28.9
|
1.0
|
OD1
|
C:ASP171
|
4.2
|
26.9
|
1.0
|
N
|
C:VAL228
|
4.2
|
27.3
|
1.0
|
O
|
C:HOH504
|
4.3
|
30.9
|
1.0
|
O3B
|
C:ATP301
|
4.3
|
28.1
|
1.0
|
CA
|
C:VAL228
|
4.4
|
26.6
|
1.0
|
O5'
|
C:ATP301
|
4.4
|
34.9
|
1.0
|
O2B
|
C:ATP301
|
4.4
|
26.4
|
1.0
|
O1A
|
C:ATP301
|
4.4
|
32.0
|
1.0
|
C5'
|
C:ATP301
|
4.5
|
30.4
|
1.0
|
CG
|
C:ASP171
|
4.5
|
27.0
|
1.0
|
CG
|
C:GLU190
|
4.5
|
30.8
|
1.0
|
CB
|
C:PRO227
|
4.5
|
32.2
|
1.0
|
PG
|
C:ATP301
|
4.7
|
25.6
|
1.0
|
CG1
|
C:VAL228
|
4.9
|
23.6
|
1.0
|
O
|
C:HOH408
|
4.9
|
33.5
|
1.0
|
O2G
|
C:ATP301
|
4.9
|
27.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6rj4
Go back to
Magnesium Binding Sites List in 6rj4
Magnesium binding site 4 out
of 4 in the Molybdenum Storage Protein - P6422, Adp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Molybdenum Storage Protein - P6422, Adp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg302
b:27.7
occ:1.00
|
O1B
|
E:ATP301
|
2.0
|
30.1
|
1.0
|
O
|
E:HOH403
|
2.0
|
25.6
|
1.0
|
O
|
E:HOH417
|
2.0
|
25.5
|
1.0
|
O2A
|
E:ATP301
|
2.1
|
32.5
|
1.0
|
OE2
|
E:GLU190
|
2.1
|
39.1
|
1.0
|
O
|
E:PRO227
|
2.1
|
37.6
|
1.0
|
CD
|
E:GLU190
|
3.0
|
38.3
|
1.0
|
PB
|
E:ATP301
|
3.3
|
29.9
|
1.0
|
OE1
|
E:GLU190
|
3.3
|
35.3
|
1.0
|
C
|
E:PRO227
|
3.3
|
34.4
|
1.0
|
PA
|
E:ATP301
|
3.4
|
34.2
|
1.0
|
O3A
|
E:ATP301
|
3.6
|
30.4
|
1.0
|
OD2
|
E:ASP171
|
3.8
|
32.8
|
1.0
|
NZ
|
E:LYS45
|
3.9
|
26.7
|
1.0
|
O
|
F:HOH453
|
3.9
|
35.7
|
1.0
|
O
|
E:HOH466
|
4.0
|
29.1
|
1.0
|
OD1
|
E:ASP171
|
4.1
|
31.3
|
1.0
|
O3G
|
E:ATP301
|
4.2
|
27.9
|
1.0
|
CA
|
E:PRO227
|
4.2
|
34.9
|
1.0
|
O
|
E:HOH475
|
4.2
|
27.2
|
1.0
|
O3B
|
E:ATP301
|
4.3
|
30.9
|
1.0
|
N
|
E:VAL228
|
4.3
|
30.9
|
1.0
|
O2B
|
E:ATP301
|
4.4
|
27.1
|
1.0
|
CA
|
E:VAL228
|
4.4
|
27.4
|
1.0
|
O1A
|
E:ATP301
|
4.4
|
34.9
|
1.0
|
CG
|
E:ASP171
|
4.4
|
29.7
|
1.0
|
O5'
|
E:ATP301
|
4.4
|
34.8
|
1.0
|
CG
|
E:GLU190
|
4.4
|
34.2
|
1.0
|
C5'
|
E:ATP301
|
4.5
|
31.9
|
1.0
|
CB
|
E:PRO227
|
4.5
|
31.9
|
1.0
|
PG
|
E:ATP301
|
4.7
|
29.7
|
1.0
|
CG1
|
E:VAL228
|
4.9
|
35.0
|
1.0
|
O2G
|
E:ATP301
|
4.9
|
27.0
|
1.0
|
O
|
E:HOH419
|
5.0
|
32.4
|
1.0
|
|
Reference:
S.Brunle,
M.L.Eisinger,
J.Poppe,
D.J.Mills,
J.D.Langer,
J.Vonck,
U.Ermler.
Molybdate Pumping Into the Molybdenum Storage Protein Via An Atp-Powered Piercing Mechanism. Proc.Natl.Acad.Sci.Usa 2019.
ISSN: ESSN 1091-6490
PubMed: 31811022
DOI: 10.1073/PNAS.1913031116
Page generated: Tue Oct 1 17:01:35 2024
|