Magnesium in PDB 6gk4: Human NBD1 of Cftr in Complex with Nanobodies D12 and T8

All present enzymatic activity of Human NBD1 of Cftr in Complex with Nanobodies D12 and T8:
3.6.3.49;

The structure of Human NBD1 of Cftr in Complex with Nanobodies D12 and T8, PDB code: 6gk4 was solved by M.Sigoillot, M.Overtus, M.Grodecka, D.Scholl, A.Garcia-Pino, T.Laeremans, L.He, E.Pardon, E.Hildebrandt, I.Urbatsch, J.Steyaert, J.R.Riordan, C.Govaerts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.16 / 2.91
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.940, 55.190, 114.990, 90.00, 103.96, 90.00
R / Rfree (%)	24.6 / 29.5

The binding sites of Magnesium atom in the Human NBD1 of Cftr in Complex with Nanobodies D12 and T8 (pdb code 6gk4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human NBD1 of Cftr in Complex with Nanobodies D12 and T8, PDB code: 6gk4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human NBD1 of Cftr in Complex with Nanobodies D12 and T8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human NBD1 of Cftr in Complex with Nanobodies D12 and T8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:56.8 occ:1.00 O1G A:ATP703 1.7 63.7 1.0 OG1 A:THR465 1.9 46.0 1.0 OE1 A:GLN493 2.0 79.3 1.0 O1B A:ATP703 2.4 61.9 1.0 CD A:GLN493 2.9 82.1 1.0 CB A:THR465 2.9 49.9 1.0 PG A:ATP703 3.1 63.7 1.0 NE2 A:GLN493 3.2 75.5 1.0 CG2 A:THR465 3.2 48.4 1.0 PB A:ATP703 3.6 62.6 1.0 O3B A:ATP703 3.7 64.0 1.0 O3G A:ATP703 3.9 63.4 1.0 OD1 A:ASP572 4.1 54.4 1.0 O2G A:ATP703 4.2 62.6 1.0 CG A:GLN493 4.2 59.2 1.0 CA A:THR465 4.3 45.1 1.0 O2A A:ATP703 4.4 67.8 1.0 OD2 A:ASP572 4.4 61.1 1.0 CB A:GLN493 4.5 45.5 1.0 N A:THR465 4.6 45.4 1.0 O3A A:ATP703 4.6 64.0 1.0 CG A:ASP572 4.6 53.0 1.0 O2B A:ATP703 4.7 63.0 1.0 CE2 A:PHE494 4.8 61.4 1.0 CZ A:PHE494 4.9 59.9 1.0 PA A:ATP703 5.0 67.1 1.0

Magnesium binding site 2 out of 2 in the Human NBD1 of Cftr in Complex with Nanobodies D12 and T8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human NBD1 of Cftr in Complex with Nanobodies D12 and T8 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg702 b:34.8 occ:1.00 OD1 D:ASP572 2.5 38.5 1.0 OG1 D:THR465 2.8 22.2 1.0 O D:HOH806 3.0 20.7 1.0 CG1 D:VAL603 3.1 32.6 1.0 OE1 D:GLN493 3.2 77.5 1.0 OG D:SER573 3.4 52.1 1.0 O1G D:ATP701 3.6 82.8 1.0 CG D:ASP572 3.6 38.8 1.0 O1B D:ATP701 3.7 83.6 1.0 CD D:GLN493 3.8 79.9 1.0 CE D:LYS464 4.0 87.8 1.0 CB D:THR465 4.1 30.8 1.0 OD2 D:ASP572 4.1 45.4 1.0 N D:THR465 4.2 32.4 1.0 O2G D:ATP701 4.2 81.8 1.0 CB D:VAL603 4.2 32.6 1.0 CB D:LYS464 4.3 36.0 1.0 CA D:THR465 4.4 32.0 1.0 PG D:ATP701 4.5 82.1 1.0 NE2 D:GLN493 4.5 67.6 1.0 CG D:GLN493 4.5 62.0 1.0 O2B D:ATP701 4.5 82.5 1.0 PB D:ATP701 4.5 83.4 1.0 NZ D:LYS464 4.5 0.6 1.0 CG2 D:VAL603 4.6 32.3 1.0 CB D:SER573 4.7 39.3 1.0 CB D:ASP572 4.8 30.3 1.0 C D:LYS464 4.9 34.9 1.0 CB D:GLN493 5.0 49.3 1.0 CG2 D:THR465 5.0 27.5 1.0 C D:ASP572 5.0 35.9 1.0

M.Sigoillot, M.Overtus, M.Grodecka, D.Scholl, A.Garcia-Pino, T.Laeremans, L.He, E.Pardon, E.Hildebrandt, I.Urbatsch, J.Steyaert, J.R.Riordan, C.Govaerts. Domain-Interface Dynamics of Cftr Revealed By Stabilizing Nanobodies. Nat Commun V. 10 2636 2019.
ISSN: ESSN 2041-1723
PubMed: 31201318
DOI: 10.1038/S41467-019-10714-Y