Magnesium in PDB 5knc: Crystal Structure of the 3 Adp-Bound V1 Complex

All present enzymatic activity of Crystal Structure of the 3 Adp-Bound V1 Complex:
3.6.3.15;

The structure of Crystal Structure of the 3 Adp-Bound V1 Complex, PDB code: 5knc 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)	48.37 / 3.02
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	121.680, 126.490, 225.260, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 25.3

The binding sites of Magnesium atom in the Crystal Structure of the 3 Adp-Bound V1 Complex (pdb code 5knc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the 3 Adp-Bound V1 Complex, PDB code: 5knc:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the 3 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 3 Adp-Bound V1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:50.5 occ:1.00 O4 A:SO4702 2.2 72.6 1.0 OG1 A:THR239 2.3 34.7 1.0 O A:HOH804 2.3 61.7 1.0 O A:HOH801 2.4 41.6 1.0 O3B A:ADP703 2.4 46.1 1.0 O1B A:ADP703 2.6 48.6 1.0 PB A:ADP703 3.0 48.2 1.0 O1A A:ADP703 3.1 36.9 1.0 CB A:THR239 3.4 34.9 1.0 NH1 D:ARG350 3.5 35.2 1.0 S A:SO4702 3.5 72.7 1.0 O A:HOH802 3.6 56.2 1.0 OE1 A:GLU265 3.8 52.2 1.0 O2 A:SO4702 3.9 72.8 1.0 OE2 A:GLU265 3.9 52.7 1.0 PA A:ADP703 4.0 36.2 1.0 O3A A:ADP703 4.0 42.0 1.0 O1 A:SO4702 4.1 72.9 1.0 O2B A:ADP703 4.3 46.2 1.0 CD A:GLU265 4.3 53.4 1.0 CG2 A:THR239 4.3 35.7 1.0 O2A A:ADP703 4.4 36.9 1.0 N A:THR239 4.4 34.9 1.0 CA A:THR239 4.5 35.0 1.0 CZ D:ARG350 4.5 34.5 1.0 NH2 A:ARG333 4.6 40.8 1.0 O3 A:SO4702 4.6 72.6 1.0 NH2 D:ARG350 4.8 34.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the 3 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 3 Adp-Bound V1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:65.4 occ:1.00 O B:HOH703 2.0 42.8 1.0 O B:HOH702 2.1 39.8 1.0 O B:HOH708 2.1 0.8 1.0 O2B B:ADP602 2.7 36.4 1.0 O B:HOH707 2.8 47.6 1.0 O3B B:ADP602 2.9 36.5 1.0 OG1 B:THR239 2.9 17.7 1.0 NH1 B:ARG262 3.1 40.3 1.0 PB B:ADP602 3.3 35.7 1.0 OE1 B:GLU261 3.6 45.9 1.0 OE2 B:GLU265 4.2 30.6 1.0 CD B:GLU261 4.2 45.7 1.0 CZ B:ARG262 4.2 40.4 1.0 CB B:THR239 4.3 18.5 1.0 O2A B:ADP602 4.3 41.9 1.0 O3A B:ADP602 4.4 38.7 1.0 NH2 B:ARG262 4.5 41.1 1.0 OE2 B:GLU261 4.5 46.2 1.0 O1B B:ADP602 4.5 33.7 1.0 CE B:LYS238 4.6 22.9 1.0 OE1 B:GLU265 4.7 30.4 1.0 OD1 B:ASP329 4.7 38.4 1.0 NH1 E:ARG350 4.8 31.2 1.0 N B:THR239 4.8 22.8 1.0 OD2 B:ASP329 4.8 38.5 1.0 PA B:ADP602 4.8 41.1 1.0 NZ B:LYS238 4.8 23.1 1.0 CD B:GLU265 4.9 30.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the 3 Adp-Bound V1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the 3 Adp-Bound V1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:26.9 occ:1.00 O C:HOH703 2.0 43.6 1.0 O C:HOH701 2.1 75.9 1.0 O1B C:ADP602 2.1 37.3 1.0 OG1 C:THR239 2.1 44.9 1.0 O C:HOH709 2.2 58.0 1.0 PB C:ADP602 3.1 37.9 1.0 O3B C:ADP602 3.2 36.2 1.0 CB C:THR239 3.5 45.7 1.0 OE1 C:GLU261 3.6 57.1 1.0 O C:HOH707 3.8 64.0 1.0 NH1 C:ARG262 3.8 40.0 1.0 O2A C:ADP602 3.8 62.5 1.0 N C:THR239 4.1 45.4 1.0 O3A C:ADP602 4.2 50.7 1.0 OD2 C:ASP329 4.2 39.8 1.0 NH1 F:ARG350 4.3 45.2 1.0 O2B C:ADP602 4.3 36.5 1.0 OE2 C:GLU265 4.3 49.9 1.0 CA C:THR239 4.3 45.9 1.0 OD1 C:ASP329 4.3 39.5 1.0 PA C:ADP602 4.3 61.9 1.0 O C:HOH702 4.4 55.2 1.0 CG2 C:THR239 4.4 46.4 1.0 O1A C:ADP602 4.5 61.5 1.0 CD C:GLU261 4.5 56.6 1.0 CE C:LYS238 4.6 37.5 1.0 CG C:ASP329 4.7 39.3 1.0 NZ C:LYS238 4.8 37.2 1.0 OE1 C:GLU265 4.8 51.1 1.0 CB C:LYS238 4.9 39.3 1.0 CD C:GLU265 5.0 50.8 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