Magnesium in PDB 5knb: Crystal Structure of the 2 Adp-Bound V1 Complex

All present enzymatic activity of Crystal Structure of the 2 Adp-Bound V1 Complex:
3.6.3.15;

The structure of Crystal Structure of the 2 Adp-Bound V1 Complex, PDB code: 5knb 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)	44.55 / 3.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	127.350, 129.620, 237.210, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 24.5

The binding sites of Magnesium atom in the Crystal Structure of the 2 Adp-Bound V1 Complex (pdb code 5knb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the 2 Adp-Bound V1 Complex, PDB code: 5knb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the 2 Adp-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 2 Adp-Bound V1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:15.0 occ:1.00 O B:HOH702 2.0 36.8 1.0 O B:HOH701 2.0 69.7 1.0 OG1 B:THR239 2.1 32.6 1.0 O2B B:ADP602 2.4 40.1 1.0 O B:HOH709 2.6 76.5 1.0 OE2 B:GLU265 3.2 52.2 1.0 NH1 B:ARG262 3.3 55.6 1.0 CB B:THR239 3.3 33.0 1.0 PB B:ADP602 3.4 40.1 1.0 O3B B:ADP602 3.5 40.1 1.0 OE1 B:GLU261 3.5 60.4 1.0 OE1 B:GLU265 3.6 48.1 1.0 O2A B:ADP602 3.8 50.6 1.0 CD B:GLU265 3.8 49.2 1.0 OD2 B:ASP329 4.2 35.8 1.0 CG2 B:THR239 4.2 32.2 1.0 N B:THR239 4.2 35.1 1.0 CA B:THR239 4.3 35.2 1.0 O3A B:ADP602 4.3 68.2 1.0 CD B:GLU261 4.4 58.2 1.0 PA B:ADP602 4.4 46.0 1.0 OD1 B:ASP329 4.5 37.3 1.0 CZ B:ARG262 4.6 53.7 1.0 O1B B:ADP602 4.6 40.1 1.0 O1A B:ADP602 4.6 45.9 1.0 CG B:ASP329 4.8 36.6 1.0 NH1 E:ARG350 4.8 74.1 1.0 O B:HOH704 4.9 63.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the 2 Adp-Bound V1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the 2 Adp-Bound V1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:52.2 occ:1.00 O C:HOH701 2.0 44.3 1.0 OG1 C:THR239 2.0 68.3 1.0 O C:HOH704 2.1 44.8 1.0 O C:HOH705 2.2 75.0 1.0 O1B C:ADP602 2.4 62.0 1.0 O3B C:ADP602 3.1 64.3 1.0 CB C:THR239 3.2 70.2 1.0 PB C:ADP602 3.2 62.4 1.0 O2A C:ADP602 3.4 0.7 1.0 OE2 C:GLU265 3.6 83.0 1.0 N C:THR239 3.9 77.3 1.0 NH1 C:ARG262 3.9 76.7 1.0 PA C:ADP602 4.0 0.2 1.0 CA C:THR239 4.1 71.6 1.0 O3A C:ADP602 4.1 55.8 1.0 OD2 C:ASP329 4.1 75.0 1.0 O1A C:ADP602 4.2 0.2 1.0 OE1 C:GLU265 4.2 84.9 1.0 CG2 C:THR239 4.3 70.4 1.0 CD C:GLU265 4.3 84.7 1.0 OD1 C:ASP329 4.4 73.9 1.0 OE1 C:GLU261 4.5 77.2 1.0 O2B C:ADP602 4.5 61.4 1.0 NH1 F:ARG350 4.5 75.9 1.0 CD C:GLU261 4.6 76.4 1.0 NZ C:LYS238 4.7 72.1 1.0 CG C:ASP329 4.7 74.2 1.0 OE2 C:GLU261 4.7 76.6 1.0 CB C:LYS238 4.9 70.5 1.0 C C:LYS238 4.9 78.4 1.0 CE C:LYS238 5.0 72.0 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