Magnesium in PDB 6qv1: Structure of Atpgs-Bound Outward-Facing TM287/288 in Complex with Nanobody NB_TM1
Protein crystallography data
The structure of Structure of Atpgs-Bound Outward-Facing TM287/288 in Complex with Nanobody NB_TM1, PDB code: 6qv1
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)
|
34.64 /
3.48
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
90.750,
199.260,
113.160,
90.00,
91.26,
90.00
|
R / Rfree (%)
|
26.7 /
30.3
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of Atpgs-Bound Outward-Facing TM287/288 in Complex with Nanobody NB_TM1
(pdb code 6qv1). 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 Atpgs-Bound Outward-Facing TM287/288 in Complex with Nanobody NB_TM1, PDB code: 6qv1:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6qv1
Go back to
Magnesium Binding Sites List in 6qv1
Magnesium binding site 1 out
of 4 in the Structure of Atpgs-Bound Outward-Facing TM287/288 in Complex with Nanobody NB_TM1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of Atpgs-Bound Outward-Facing TM287/288 in Complex with Nanobody NB_TM1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:87.4
occ:1.00
|
O2G
|
A:AGS600
|
1.9
|
0.2
|
1.0
|
O2B
|
A:AGS600
|
1.9
|
0.8
|
1.0
|
OE1
|
A:GLN414
|
2.0
|
0.9
|
1.0
|
OG
|
A:SER373
|
2.3
|
0.3
|
1.0
|
CD
|
A:GLN414
|
2.9
|
0.3
|
1.0
|
PG
|
A:AGS600
|
3.1
|
0.5
|
1.0
|
NE2
|
A:GLN414
|
3.1
|
0.9
|
1.0
|
PB
|
A:AGS600
|
3.1
|
0.6
|
1.0
|
O2A
|
A:AGS600
|
3.2
|
0.7
|
1.0
|
CB
|
A:SER373
|
3.3
|
0.9
|
1.0
|
O3B
|
A:AGS600
|
3.4
|
0.8
|
1.0
|
O3A
|
A:AGS600
|
3.6
|
0.9
|
1.0
|
PA
|
A:AGS600
|
3.9
|
0.7
|
1.0
|
S1G
|
A:AGS600
|
3.9
|
0.5
|
1.0
|
N
|
A:SER373
|
4.2
|
0.4
|
1.0
|
O1A
|
A:AGS600
|
4.2
|
0.1
|
1.0
|
O3G
|
A:AGS600
|
4.2
|
0.9
|
1.0
|
OD1
|
A:ASP494
|
4.2
|
0.7
|
1.0
|
N
|
B:GLN494
|
4.3
|
0.8
|
1.0
|
CA
|
A:SER373
|
4.3
|
0.6
|
1.0
|
CG
|
A:GLN414
|
4.4
|
0.6
|
1.0
|
O1B
|
A:AGS600
|
4.4
|
0.5
|
1.0
|
OD2
|
A:ASP494
|
4.5
|
0.3
|
1.0
|
CB
|
B:SER493
|
4.6
|
0.8
|
1.0
|
CB
|
B:GLN494
|
4.7
|
0.8
|
1.0
|
CG
|
A:ASP494
|
4.8
|
0.3
|
1.0
|
CB
|
A:GLN414
|
4.9
|
1.0
|
1.0
|
CA
|
B:SER493
|
4.9
|
0.9
|
1.0
|
CG
|
B:GLN494
|
5.0
|
1.0
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6qv1
Go back to
Magnesium Binding Sites List in 6qv1
Magnesium binding site 2 out
of 4 in the Structure of Atpgs-Bound Outward-Facing TM287/288 in Complex with Nanobody NB_TM1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of Atpgs-Bound Outward-Facing TM287/288 in Complex with Nanobody NB_TM1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:76.8
occ:1.00
|
OG1
|
B:THR395
|
1.9
|
75.6
|
1.0
|
O2B
|
B:AGS600
|
2.1
|
99.2
|
1.0
|
OE1
|
B:GLN436
|
2.2
|
0.8
|
1.0
|
NE2
|
B:GLN436
|
2.3
|
0.7
|
1.0
|
CD
|
B:GLN436
|
2.5
|
0.5
|
1.0
|
O3G
|
B:AGS600
|
2.6
|
0.1
|
1.0
|
CB
|
B:THR395
|
3.1
|
79.0
|
1.0
|
PB
|
B:AGS600
|
3.5
|
99.3
|
1.0
|
PG
|
B:AGS600
|
3.7
|
0.6
|
1.0
|
OD1
|
B:ASP516
|
3.7
|
0.3
|
1.0
|
CG2
|
B:THR395
|
3.9
|
79.0
|
1.0
|
O3B
|
B:AGS600
|
3.9
|
99.8
|
1.0
|
CG
|
B:GLN436
|
4.0
|
0.8
|
1.0
|
O2A
|
B:AGS600
|
4.0
|
97.5
|
1.0
|
CA
|
B:THR395
|
4.2
|
74.3
|
1.0
|
N
|
B:THR395
|
4.2
|
75.3
|
1.0
|
O3A
|
B:AGS600
|
4.3
|
97.7
|
1.0
|
S1G
|
B:AGS600
|
4.4
|
0.2
|
1.0
|
CB
|
B:GLN436
|
4.6
|
0.1
|
1.0
|
O1B
|
B:AGS600
|
4.6
|
0.3
|
1.0
|
CG
|
B:ASP516
|
4.6
|
0.3
|
1.0
|
N
|
A:GLY472
|
4.6
|
77.5
|
1.0
|
PA
|
B:AGS600
|
4.6
|
96.8
|
1.0
|
OD2
|
B:ASP516
|
4.7
|
0.6
|
1.0
|
O2G
|
B:AGS600
|
4.9
|
0.3
|
1.0
|
O1A
|
B:AGS600
|
5.0
|
97.3
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6qv1
Go back to
Magnesium Binding Sites List in 6qv1
Magnesium binding site 3 out
of 4 in the Structure of Atpgs-Bound Outward-Facing TM287/288 in Complex with Nanobody NB_TM1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of Atpgs-Bound Outward-Facing TM287/288 in Complex with Nanobody NB_TM1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg601
b:0.9
occ:1.00
|
OE1
|
C:GLN414
|
1.9
|
0.7
|
1.0
|
OG
|
C:SER373
|
1.9
|
0.7
|
1.0
|
O2B
|
C:AGS600
|
2.1
|
0.8
|
1.0
|
O2G
|
C:AGS600
|
2.2
|
0.2
|
1.0
|
NE2
|
C:GLN414
|
2.4
|
0.9
|
1.0
|
CD
|
C:GLN414
|
2.4
|
0.0
|
1.0
|
CB
|
C:SER373
|
3.1
|
0.6
|
1.0
|
PG
|
C:AGS600
|
3.3
|
0.2
|
1.0
|
PB
|
C:AGS600
|
3.4
|
0.7
|
1.0
|
O2A
|
C:AGS600
|
3.5
|
0.3
|
1.0
|
O3B
|
C:AGS600
|
3.6
|
0.0
|
1.0
|
CG
|
C:GLN414
|
3.9
|
0.9
|
1.0
|
O3A
|
C:AGS600
|
3.9
|
0.5
|
1.0
|
OD1
|
C:ASP494
|
4.0
|
0.7
|
1.0
|
S1G
|
C:AGS600
|
4.0
|
0.1
|
1.0
|
N
|
C:SER373
|
4.1
|
0.9
|
1.0
|
PA
|
C:AGS600
|
4.1
|
0.4
|
1.0
|
CA
|
C:SER373
|
4.2
|
0.3
|
1.0
|
OD2
|
C:ASP494
|
4.2
|
0.2
|
1.0
|
O1A
|
C:AGS600
|
4.4
|
0.9
|
1.0
|
O3G
|
C:AGS600
|
4.5
|
0.0
|
1.0
|
CG
|
C:ASP494
|
4.5
|
0.1
|
1.0
|
CB
|
C:GLN414
|
4.5
|
0.2
|
1.0
|
O1B
|
C:AGS600
|
4.6
|
0.3
|
1.0
|
N
|
D:GLN494
|
4.7
|
0.6
|
1.0
|
CB
|
D:GLN494
|
4.8
|
0.4
|
1.0
|
CB
|
D:SER493
|
5.0
|
0.5
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6qv1
Go back to
Magnesium Binding Sites List in 6qv1
Magnesium binding site 4 out
of 4 in the Structure of Atpgs-Bound Outward-Facing TM287/288 in Complex with Nanobody NB_TM1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of Atpgs-Bound Outward-Facing TM287/288 in Complex with Nanobody NB_TM1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg601
b:0.4
occ:1.00
|
O2B
|
D:AGS600
|
1.9
|
0.5
|
1.0
|
OG1
|
D:THR395
|
1.9
|
0.5
|
1.0
|
O3G
|
D:AGS600
|
2.2
|
0.2
|
1.0
|
OE1
|
D:GLN436
|
2.3
|
0.7
|
1.0
|
NE2
|
D:GLN436
|
2.8
|
0.1
|
1.0
|
CD
|
D:GLN436
|
2.9
|
0.9
|
1.0
|
PG
|
D:AGS600
|
3.1
|
0.9
|
1.0
|
PB
|
D:AGS600
|
3.2
|
0.3
|
1.0
|
CB
|
D:THR395
|
3.2
|
0.0
|
1.0
|
O3B
|
D:AGS600
|
3.4
|
0.5
|
1.0
|
O2A
|
D:AGS600
|
3.7
|
0.0
|
1.0
|
O3A
|
D:AGS600
|
3.7
|
0.7
|
1.0
|
S1G
|
D:AGS600
|
3.8
|
0.5
|
1.0
|
N
|
D:THR395
|
4.0
|
0.9
|
1.0
|
OD1
|
D:ASP516
|
4.1
|
0.8
|
1.0
|
CA
|
D:THR395
|
4.1
|
0.7
|
1.0
|
CG2
|
D:THR395
|
4.1
|
0.5
|
1.0
|
PA
|
D:AGS600
|
4.2
|
0.4
|
1.0
|
N
|
C:GLY472
|
4.3
|
0.1
|
1.0
|
O2G
|
D:AGS600
|
4.4
|
0.7
|
1.0
|
O1B
|
D:AGS600
|
4.4
|
0.8
|
1.0
|
CG
|
D:GLN436
|
4.4
|
0.2
|
1.0
|
OD2
|
D:ASP516
|
4.6
|
0.1
|
1.0
|
O1A
|
D:AGS600
|
4.7
|
0.8
|
1.0
|
CA
|
C:GLY472
|
4.7
|
0.3
|
1.0
|
CG
|
D:ASP516
|
4.8
|
0.6
|
1.0
|
CB
|
D:LYS394
|
5.0
|
0.7
|
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
|