Magnesium in PDB 6qv0: Structure of Atp-Bound Outward-Facing TM287/288 in Complex with Sybody SB_TM35
Protein crystallography data
The structure of Structure of Atp-Bound Outward-Facing TM287/288 in Complex with Sybody SB_TM35, PDB code: 6qv0
was solved by
C.A.J.Hutter,
L.M.Huerlimann,
I.Zimmermann,
P.Egloff,
M.A.Seeger,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.19 /
3.12
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
166.280,
77.290,
207.180,
90.00,
112.55,
90.00
|
R / Rfree (%)
|
24.4 /
26.4
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of Atp-Bound Outward-Facing TM287/288 in Complex with Sybody SB_TM35
(pdb code 6qv0). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Structure of Atp-Bound Outward-Facing TM287/288 in Complex with Sybody SB_TM35, PDB code: 6qv0:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6qv0
Go back to
Magnesium Binding Sites List in 6qv0
Magnesium binding site 1 out
of 4 in the Structure of Atp-Bound Outward-Facing TM287/288 in Complex with Sybody SB_TM35
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of Atp-Bound Outward-Facing TM287/288 in Complex with Sybody SB_TM35 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:13.2
occ:1.00
|
OG
|
A:SER373
|
1.9
|
37.2
|
1.0
|
O2G
|
A:ATP600
|
1.9
|
37.0
|
1.0
|
OE1
|
A:GLN414
|
1.9
|
45.6
|
1.0
|
O2B
|
A:ATP600
|
2.2
|
36.0
|
1.0
|
CD
|
A:GLN414
|
2.7
|
51.1
|
1.0
|
NE2
|
A:GLN414
|
2.9
|
44.5
|
1.0
|
PG
|
A:ATP600
|
3.1
|
36.9
|
1.0
|
CB
|
A:SER373
|
3.1
|
28.7
|
1.0
|
PB
|
A:ATP600
|
3.4
|
35.8
|
1.0
|
O1G
|
A:ATP600
|
3.4
|
37.0
|
1.0
|
O3B
|
A:ATP600
|
3.5
|
36.3
|
1.0
|
OD1
|
A:ASP494
|
3.7
|
45.4
|
1.0
|
N
|
A:SER373
|
4.0
|
25.8
|
1.0
|
CA
|
A:SER373
|
4.1
|
25.3
|
1.0
|
OD2
|
A:ASP494
|
4.1
|
51.2
|
1.0
|
CG
|
A:GLN414
|
4.2
|
35.4
|
1.0
|
O1A
|
A:ATP600
|
4.2
|
32.0
|
1.0
|
O3A
|
A:ATP600
|
4.2
|
34.5
|
1.0
|
CG
|
A:ASP494
|
4.3
|
45.1
|
1.0
|
O3G
|
A:ATP600
|
4.3
|
36.5
|
1.0
|
O1B
|
A:ATP600
|
4.5
|
36.1
|
1.0
|
CB
|
A:GLN414
|
4.6
|
28.7
|
1.0
|
PA
|
A:ATP600
|
4.7
|
32.7
|
1.0
|
N
|
B:GLN494
|
4.7
|
30.6
|
1.0
|
O2A
|
A:ATP600
|
4.7
|
32.4
|
1.0
|
CB
|
B:GLN494
|
4.8
|
31.9
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6qv0
Go back to
Magnesium Binding Sites List in 6qv0
Magnesium binding site 2 out
of 4 in the Structure of Atp-Bound Outward-Facing TM287/288 in Complex with Sybody SB_TM35
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of Atp-Bound Outward-Facing TM287/288 in Complex with Sybody SB_TM35 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:34.6
occ:1.00
|
OG1
|
B:THR395
|
1.9
|
47.5
|
1.0
|
OE1
|
B:GLN436
|
1.9
|
65.5
|
1.0
|
CD
|
B:GLN436
|
2.4
|
71.6
|
1.0
|
O1G
|
B:ATP600
|
2.4
|
48.7
|
1.0
|
NE2
|
B:GLN436
|
2.5
|
61.6
|
1.0
|
O1B
|
B:ATP600
|
2.7
|
48.7
|
1.0
|
CB
|
B:THR395
|
3.3
|
49.1
|
1.0
|
PG
|
B:ATP600
|
3.5
|
48.6
|
1.0
|
CG
|
B:GLN436
|
3.7
|
59.9
|
1.0
|
O3G
|
B:ATP600
|
3.8
|
49.0
|
1.0
|
O1A
|
B:ATP600
|
3.8
|
48.6
|
1.0
|
OD1
|
B:ASP516
|
3.8
|
59.8
|
1.0
|
PB
|
B:ATP600
|
3.9
|
48.6
|
1.0
|
CG2
|
B:THR395
|
3.9
|
47.9
|
1.0
|
O3B
|
B:ATP600
|
4.0
|
48.7
|
1.0
|
OD2
|
B:ASP516
|
4.0
|
64.0
|
1.0
|
CB
|
B:GLN436
|
4.2
|
50.0
|
1.0
|
N
|
A:GLY472
|
4.2
|
36.7
|
1.0
|
CA
|
B:THR395
|
4.3
|
43.0
|
1.0
|
N
|
B:THR395
|
4.4
|
43.1
|
1.0
|
CG
|
B:ASP516
|
4.4
|
59.4
|
1.0
|
O3A
|
B:ATP600
|
4.6
|
48.5
|
1.0
|
CA
|
A:GLY472
|
4.7
|
35.8
|
1.0
|
PA
|
B:ATP600
|
4.7
|
49.2
|
1.0
|
O2G
|
B:ATP600
|
4.8
|
47.8
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6qv0
Go back to
Magnesium Binding Sites List in 6qv0
Magnesium binding site 3 out
of 4 in the Structure of Atp-Bound Outward-Facing TM287/288 in Complex with Sybody SB_TM35
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of Atp-Bound Outward-Facing TM287/288 in Complex with Sybody SB_TM35 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg601
b:43.4
occ:1.00
|
OG
|
C:SER373
|
1.9
|
59.9
|
1.0
|
O2G
|
C:ATP600
|
1.9
|
70.2
|
1.0
|
OE1
|
C:GLN414
|
1.9
|
65.2
|
1.0
|
O2B
|
C:ATP600
|
2.2
|
68.8
|
1.0
|
CD
|
C:GLN414
|
3.0
|
69.1
|
1.0
|
CB
|
C:SER373
|
3.0
|
50.6
|
1.0
|
PG
|
C:ATP600
|
3.3
|
70.1
|
1.0
|
PB
|
C:ATP600
|
3.3
|
68.8
|
1.0
|
NE2
|
C:GLN414
|
3.3
|
59.1
|
1.0
|
O1A
|
C:ATP600
|
3.4
|
65.7
|
1.0
|
O3B
|
C:ATP600
|
3.5
|
69.7
|
1.0
|
OD1
|
C:ASP494
|
3.8
|
61.0
|
1.0
|
O3A
|
C:ATP600
|
3.8
|
67.6
|
1.0
|
O3G
|
C:ATP600
|
4.0
|
69.5
|
1.0
|
N
|
C:SER373
|
4.1
|
47.2
|
1.0
|
CA
|
C:SER373
|
4.1
|
46.8
|
1.0
|
PA
|
C:ATP600
|
4.1
|
65.9
|
1.0
|
CG
|
C:GLN414
|
4.3
|
53.8
|
1.0
|
O1G
|
C:ATP600
|
4.4
|
70.3
|
1.0
|
N
|
D:GLN494
|
4.4
|
51.1
|
1.0
|
O2A
|
C:ATP600
|
4.5
|
66.4
|
1.0
|
O1B
|
C:ATP600
|
4.5
|
68.5
|
1.0
|
CB
|
D:GLN494
|
4.6
|
51.7
|
1.0
|
CB
|
C:GLN414
|
4.7
|
44.5
|
1.0
|
CB
|
D:SER493
|
4.7
|
56.8
|
1.0
|
CG
|
C:ASP494
|
4.8
|
61.2
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6qv0
Go back to
Magnesium Binding Sites List in 6qv0
Magnesium binding site 4 out
of 4 in the Structure of Atp-Bound Outward-Facing TM287/288 in Complex with Sybody SB_TM35
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of Atp-Bound Outward-Facing TM287/288 in Complex with Sybody SB_TM35 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg601
b:20.0
occ:1.00
|
OE1
|
D:GLN436
|
1.9
|
64.0
|
1.0
|
OG1
|
D:THR395
|
1.9
|
46.6
|
1.0
|
CD
|
D:GLN436
|
2.3
|
70.5
|
1.0
|
O1G
|
D:ATP600
|
2.3
|
52.9
|
1.0
|
NE2
|
D:GLN436
|
2.4
|
60.2
|
1.0
|
O2B
|
D:ATP600
|
2.7
|
45.5
|
1.0
|
CB
|
D:THR395
|
3.3
|
45.2
|
1.0
|
PG
|
D:ATP600
|
3.6
|
52.6
|
1.0
|
CG
|
D:GLN436
|
3.6
|
59.8
|
1.0
|
OD1
|
D:ASP516
|
3.7
|
66.6
|
1.0
|
OD2
|
D:ASP516
|
3.9
|
72.1
|
1.0
|
CG2
|
D:THR395
|
3.9
|
44.0
|
1.0
|
PB
|
D:ATP600
|
4.0
|
46.2
|
1.0
|
O1A
|
D:ATP600
|
4.0
|
43.5
|
1.0
|
CB
|
D:GLN436
|
4.1
|
54.2
|
1.0
|
O3G
|
D:ATP600
|
4.1
|
53.3
|
1.0
|
O3B
|
D:ATP600
|
4.2
|
49.7
|
1.0
|
CG
|
D:ASP516
|
4.2
|
66.4
|
1.0
|
N
|
C:GLY472
|
4.3
|
34.9
|
1.0
|
CA
|
D:THR395
|
4.4
|
35.5
|
1.0
|
N
|
D:THR395
|
4.4
|
35.6
|
1.0
|
CA
|
C:GLY472
|
4.7
|
34.3
|
1.0
|
O3A
|
D:ATP600
|
4.8
|
44.4
|
1.0
|
O2G
|
D:ATP600
|
4.9
|
52.8
|
1.0
|
PA
|
D:ATP600
|
4.9
|
44.0
|
1.0
|
|
Reference:
C.A.J.Hutter,
M.H.Timachi,
L.M.Hurlimann,
I.Zimmermann,
P.Egloff,
H.Goddeke,
S.Kucher,
S.Stefanic,
M.Karttunen,
L.V.Schafer,
E.Bordignon,
M.A.Seeger.
The Extracellular Gate Shapes the Energy Profile of An Abc Exporter. Nat Commun V. 10 2260 2019.
ISSN: ESSN 2041-1723
PubMed: 31113958
DOI: 10.1038/S41467-019-09892-6
Page generated: Tue Oct 1 16:26:44 2024
|