Magnesium in PDB 5knd: Crystal Structure of the Pi-Bound V1 Complex

All present enzymatic activity of Crystal Structure of the Pi-Bound V1 Complex:
3.6.3.15;

The structure of Crystal Structure of the Pi-Bound V1 Complex, PDB code: 5knd was solved by K.Suzuki, K.Mizutani, S.Maruyama, K.Shimono, F.L.Imai, E.Muneyuki, Y.Kakinuma, Y.Ishizuka-Katsura, M.Shirouzu, S.Yokoyama, I.Yamato, T.Murata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.04 / 2.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	128.220, 128.352, 228.033, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 25.1

The binding sites of Magnesium atom in the Crystal Structure of the Pi-Bound V1 Complex (pdb code 5knd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the Pi-Bound V1 Complex, PDB code: 5knd:

Magnesium binding site 1 out of 1 in the Crystal Structure of the Pi-Bound V1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Pi-Bound V1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:46.5 occ:1.00 OG1 C:THR239 2.0 56.0 1.0 O C:HOH702 2.0 65.2 1.0 O C:HOH701 2.0 67.3 1.0 O4 C:PO4603 2.0 56.8 1.0 O C:HOH712 2.6 38.1 1.0 P C:PO4603 3.2 56.2 1.0 O2 C:PO4603 3.4 55.8 1.0 CB C:THR239 3.4 56.8 1.0 O C:HOH708 3.7 67.2 1.0 N C:THR239 3.8 56.2 1.0 O3 C:PO4603 3.9 55.8 1.0 OD1 C:ASP329 3.9 47.8 1.0 OE1 C:GLU261 3.9 53.6 1.0 OD2 C:ASP329 4.0 49.5 1.0 CA C:THR239 4.1 55.9 1.0 NH1 C:ARG262 4.2 49.8 1.0 CG2 C:THR239 4.3 57.2 1.0 OE2 C:GLU265 4.4 58.4 1.0 O1 C:PO4603 4.4 56.2 1.0 CG C:ASP329 4.4 48.3 1.0 CB C:LYS238 4.5 53.2 1.0 O C:HOH717 4.5 43.4 1.0 NZ C:LYS238 4.5 51.1 1.0 CE C:LYS238 4.5 51.2 1.0 NH1 F:ARG350 4.6 53.7 1.0 OE1 C:GLU265 4.7 57.0 1.0 C C:LYS238 4.7 55.5 1.0 CD C:GLU261 4.8 52.2 1.0 O C:HOH710 4.8 57.3 1.0 CD C:GLU265 4.9 57.5 1.0 N C:LYS238 5.0 54.4 1.0 CA C:LYS238 5.0 54.3 1.0

K.Suzuki, K.Mizutani, S.Maruyama, K.Shimono, F.L.Imai, E.Muneyuki, Y.Kakinuma, Y.Ishizuka-Katsura, M.Shirouzu, S.Yokoyama, I.Yamato, T.Murata. Crystal Structures of the Atp-Binding and Adp-Release Dwells of the V1 Rotary Motor Nat Commun V. 7 13235 2016.
ISSN: ESSN 2041-1723
PubMed: 27807367
DOI: 10.1038/NCOMMS13235