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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

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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

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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

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