Magnesium in PDB 6qv2: Structure of Atpgs-Bound Outward-Facing TM287/288 in Complex with Nanobody NB_TM#2

The structure of Structure of Atpgs-Bound Outward-Facing TM287/288 in Complex with Nanobody NB_TM#2, PDB code: 6qv2 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)	32.59 / 4.23
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	88.600, 113.070, 126.890, 83.18, 73.00, 67.37
R / Rfree (%)	30.6 / 33

The binding sites of Magnesium atom in the Structure of Atpgs-Bound Outward-Facing TM287/288 in Complex with Nanobody NB_TM#2 (pdb code 6qv2). 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_TM#2, PDB code: 6qv2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Atpgs-Bound Outward-Facing TM287/288 in Complex with Nanobody NB_TM#2


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_TM#2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:0.2 occ:1.00 OG A:SER373 1.9 0.8 1.0 OE1 A:GLN414 1.9 0.6 1.0 NE2 A:GLN414 2.2 0.0 1.0 CD A:GLN414 2.3 0.1 1.0 O2B A:AGS600 2.3 1.0 1.0 O2G A:AGS600 2.5 0.4 1.0 CB A:SER373 3.2 0.7 1.0 OD1 A:ASP494 3.4 0.5 1.0 OD2 A:ASP494 3.6 0.2 1.0 CG A:GLN414 3.7 0.2 1.0 PB A:AGS600 3.7 0.5 1.0 PG A:AGS600 3.9 0.7 1.0 CG A:ASP494 3.9 0.9 1.0 O3B A:AGS600 4.1 0.8 1.0 CB A:GLN414 4.2 0.6 1.0 CA A:SER373 4.3 0.0 1.0 N A:SER373 4.3 0.3 1.0 O2A A:AGS600 4.4 0.9 1.0 O3A A:AGS600 4.4 0.2 1.0 O1B A:AGS600 4.8 0.2 1.0 O3G A:AGS600 4.8 0.7 1.0 CB B:SER493 4.9 0.8 1.0 S1G A:AGS600 4.9 99.7 1.0 PA A:AGS600 4.9 0.3 1.0

Magnesium binding site 2 out of 4 in the Structure of Atpgs-Bound Outward-Facing TM287/288 in Complex with Nanobody NB_TM#2


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_TM#2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:70.6 occ:1.00 O2B B:AGS600 1.9 76.3 1.0 OG1 B:THR395 1.9 62.1 1.0 NE2 B:GLN436 2.2 68.6 1.0 O3G B:AGS600 2.6 75.0 1.0 O3A B:AGS600 2.7 72.0 1.0 PB B:AGS600 2.8 76.0 1.0 CB B:THR395 3.0 19.1 1.0 CD B:GLN436 3.3 49.0 1.0 O3B B:AGS600 3.4 77.5 1.0 PG B:AGS600 3.5 78.4 1.0 OE1 B:GLN436 3.6 13.4 1.0 CG2 B:THR395 3.8 11.9 1.0 PA B:AGS600 4.0 60.8 1.0 O1B B:AGS600 4.1 77.3 1.0 O2A B:AGS600 4.2 15.9 1.0 OD1 B:ASP516 4.2 71.1 1.0 N B:THR395 4.2 72.4 1.0 CA B:THR395 4.2 54.9 1.0 S1G B:AGS600 4.4 82.1 1.0 O1A B:AGS600 4.5 63.9 1.0 CG B:GLN436 4.5 62.9 1.0 O2G B:AGS600 4.7 79.0 1.0 CB A:SER471 4.8 0.9 1.0 N A:GLY472 4.8 0.6 1.0 OD2 B:ASP516 4.9 14.1 1.0 CG B:ASP516 5.0 61.0 1.0

Magnesium binding site 3 out of 4 in the Structure of Atpgs-Bound Outward-Facing TM287/288 in Complex with Nanobody NB_TM#2


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_TM#2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:0.1 occ:1.00 O2G C:AGS600 1.9 0.2 1.0 OE1 C:GLN414 2.0 0.5 1.0 OG C:SER373 2.2 0.2 1.0 NE2 C:GLN414 2.2 1.0 1.0 CD C:GLN414 2.3 0.9 1.0 O2B C:AGS600 2.5 0.9 1.0 PG C:AGS600 3.3 0.7 1.0 CB C:SER373 3.5 0.7 1.0 OD1 C:ASP494 3.6 0.3 1.0 PB C:AGS600 3.7 0.4 1.0 O3B C:AGS600 3.7 0.4 1.0 CG C:GLN414 3.8 0.5 1.0 OD2 C:ASP494 3.9 0.5 1.0 CG C:ASP494 4.2 0.0 1.0 O3G C:AGS600 4.3 0.0 1.0 N C:SER373 4.3 0.5 1.0 S1G C:AGS600 4.4 0.8 1.0 CB C:GLN414 4.4 0.1 1.0 O3A C:AGS600 4.4 0.2 1.0 O2A C:AGS600 4.4 0.6 1.0 CA C:SER373 4.4 0.6 1.0 CB D:SER493 4.6 0.4 1.0 O1B C:AGS600 4.9 0.1 1.0 PA C:AGS600 4.9 0.3 1.0

Magnesium binding site 4 out of 4 in the Structure of Atpgs-Bound Outward-Facing TM287/288 in Complex with Nanobody NB_TM#2


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_TM#2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:0.2 occ:1.00 OG1 D:THR395 1.9 0.9 1.0 O3A D:AGS600 1.9 0.2 1.0 O2B D:AGS600 2.0 0.4 1.0 PB D:AGS600 2.2 0.6 1.0 CB D:THR395 2.2 0.6 1.0 N D:THR395 2.2 0.1 1.0 O1A D:AGS600 2.4 0.5 1.0 PA D:AGS600 2.6 0.3 1.0 CA D:THR395 2.7 0.3 1.0 O1B D:AGS600 2.8 0.9 1.0 O2A D:AGS600 3.3 0.7 1.0 C D:LYS394 3.4 0.8 1.0 N D:LYS394 3.6 0.7 1.0 O3B D:AGS600 3.7 0.1 1.0 CG2 D:THR395 3.7 0.1 1.0 C D:THR395 3.8 0.8 1.0 CA D:LYS394 3.9 0.1 1.0 N D:THR396 3.9 0.3 1.0 O5' D:AGS600 4.0 0.6 1.0 CB D:LYS394 4.1 0.8 1.0 O3G D:AGS600 4.3 0.3 1.0 C D:GLY393 4.4 0.8 1.0 NE2 D:GLN436 4.5 0.3 1.0 O D:LYS394 4.5 0.7 1.0 PG D:AGS600 4.6 0.9 1.0 CA D:GLY393 4.8 0.3 1.0 C5' D:AGS600 4.8 0.8 1.0 O D:THR395 4.8 0.4 1.0 N D:GLY393 4.9 0.6 1.0 OG1 D:THR396 5.0 0.1 1.0

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