Magnesium in PDB 6f5d: Trypanosoma Brucei F1-Atpase

All present enzymatic activity of Trypanosoma Brucei F1-Atpase:
3.6.3.14;

The structure of Trypanosoma Brucei F1-Atpase, PDB code: 6f5d was solved by M.G.Montgomery, O.Gahura, A.G.W.Leslie, A.Zikova, J.E.Walker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.51 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	124.218, 206.350, 130.210, 90.00, 104.85, 90.00
R / Rfree (%)	27.2 / 29.7

The binding sites of Magnesium atom in the Trypanosoma Brucei F1-Atpase (pdb code 6f5d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Trypanosoma Brucei F1-Atpase, PDB code: 6f5d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Trypanosoma Brucei F1-Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Trypanosoma Brucei F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:64.5 occ:1.00 OG1 A:THR189 2.2 66.5 1.0 O A:HOH701 2.2 65.0 1.0 O A:HOH702 2.2 63.3 1.0 O2B A:ADP600 2.2 65.3 1.0 O A:HOH704 2.2 64.1 1.0 O A:HOH703 2.2 64.7 1.0 PB A:ADP600 3.3 65.8 1.0 CB A:THR189 3.4 68.6 1.0 O3B A:ADP600 3.5 65.5 1.0 OD2 A:ASP282 3.8 73.2 1.0 OD1 A:ASP282 3.9 75.9 1.0 N A:THR189 4.0 70.2 1.0 O2A A:ADP600 4.1 65.1 1.0 CA A:THR189 4.2 69.4 1.0 CG A:ASP282 4.3 74.1 1.0 O1B A:ADP600 4.3 66.2 1.0 O3A A:ADP600 4.4 66.2 1.0 CG2 A:THR189 4.4 68.7 1.0 PA A:ADP600 4.6 65.7 1.0 O1A A:ADP600 4.8 65.1 1.0 OE1 A:GLN221 4.9 82.2 1.0 CB A:LYS188 4.9 70.6 1.0 NZ A:LYS188 5.0 70.4 1.0

Magnesium binding site 2 out of 5 in the Trypanosoma Brucei F1-Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Trypanosoma Brucei F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:52.1 occ:1.00 O B:HOH703 2.2 52.9 1.0 O B:HOH702 2.2 53.9 1.0 OG1 B:THR189 2.2 53.1 1.0 O B:HOH701 2.2 52.7 1.0 O B:HOH704 2.2 52.5 1.0 O2B B:ADP600 2.2 52.9 1.0 PB B:ADP600 3.1 54.6 1.0 O3B B:ADP600 3.2 53.6 1.0 CB B:THR189 3.4 53.6 1.0 OD1 B:ASP282 3.7 68.6 1.0 OD2 B:ASP282 3.8 69.2 1.0 N B:THR189 3.9 55.8 1.0 O1B B:ADP600 4.1 53.5 1.0 CA B:THR189 4.2 54.6 1.0 CG B:ASP282 4.2 67.5 1.0 O2A B:ADP600 4.3 55.1 1.0 O3A B:ADP600 4.4 55.3 1.0 CG2 B:THR189 4.5 53.0 1.0 NE2 B:GLN221 4.5 79.3 1.0 PA B:ADP600 4.7 54.0 1.0 CB B:LYS188 4.7 59.4 1.0 O1A B:ADP600 4.8 54.4 1.0 NZ B:LYS188 4.8 60.1 1.0 C B:LYS188 4.9 57.6 1.0

Magnesium binding site 3 out of 5 in the Trypanosoma Brucei F1-Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Trypanosoma Brucei F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:54.2 occ:1.00 O C:HOH703 2.2 53.4 1.0 O C:HOH702 2.2 53.7 1.0 OG1 C:THR189 2.2 55.5 1.0 O C:HOH701 2.2 54.0 1.0 O C:HOH704 2.2 54.6 1.0 O2B C:ADP600 2.2 55.5 1.0 PB C:ADP600 3.2 55.8 1.0 O3B C:ADP600 3.4 57.1 1.0 CB C:THR189 3.4 57.2 1.0 OD1 C:ASP282 3.9 66.6 1.0 OD2 C:ASP282 3.9 66.6 1.0 O2A C:ADP600 4.0 57.1 1.0 N C:THR189 4.0 58.4 1.0 CA C:THR189 4.2 57.8 1.0 O1B C:ADP600 4.3 54.9 1.0 CG C:ASP282 4.3 67.8 1.0 O3A C:ADP600 4.4 57.3 1.0 CG2 C:THR189 4.5 57.8 1.0 PA C:ADP600 4.6 58.6 1.0 CB C:LYS188 4.8 64.8 1.0 NZ C:LYS188 4.9 66.5 1.0 O1A C:ADP600 4.9 58.3 1.0 C C:LYS188 5.0 61.4 1.0 OE1 C:GLN221 5.0 82.9 1.0

Magnesium binding site 4 out of 5 in the Trypanosoma Brucei F1-Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Trypanosoma Brucei F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:65.6 occ:1.00 O D:HOH704 2.2 67.4 1.0 O2B D:ADP600 2.2 66.5 1.0 O D:HOH701 2.2 66.6 1.0 O D:HOH702 2.2 67.4 1.0 O D:HOH703 2.2 63.1 1.0 OG1 D:THR169 2.2 66.5 1.0 PB D:ADP600 3.3 67.2 1.0 CB D:THR169 3.4 69.0 1.0 O3B D:ADP600 3.5 66.0 1.0 NH1 D:ARG195 3.8 98.1 1.0 O3A D:ADP600 3.9 66.7 1.0 NH1 C:ARG386 4.1 79.8 1.0 N D:THR169 4.1 70.7 1.0 OE2 D:GLU198 4.2 93.0 1.0 OE1 D:GLU194 4.2 0.6 1.0 OE1 D:GLU198 4.3 92.1 1.0 OE2 D:GLU194 4.3 0.2 1.0 CA D:THR169 4.3 69.9 1.0 O2A D:ADP600 4.3 65.4 1.0 CG2 D:THR169 4.4 69.5 1.0 OD1 D:ASP261 4.4 83.1 1.0 CD D:GLU194 4.4 1.0 1.0 OD2 D:ASP261 4.4 79.4 1.0 PA D:ADP600 4.4 65.0 1.0 CE D:LYS168 4.5 70.8 1.0 O1A D:ADP600 4.5 63.9 1.0 O1B D:ADP600 4.6 67.8 1.0 CD D:GLU198 4.7 92.8 1.0 CG D:ASP261 4.9 79.8 1.0 CB D:LYS168 4.9 72.4 1.0 CZ D:ARG195 5.0 98.0 1.0

Magnesium binding site 5 out of 5 in the Trypanosoma Brucei F1-Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Trypanosoma Brucei F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg601 b:73.1 occ:1.00 O2B F:ADP600 2.2 68.3 1.0 O F:HOH701 2.2 74.2 1.0 O F:HOH703 2.2 71.9 1.0 O F:HOH704 2.2 72.8 1.0 O F:HOH702 2.2 72.0 1.0 OG1 F:THR169 2.2 73.2 1.0 PB F:ADP600 3.4 63.9 1.0 CB F:THR169 3.4 74.7 1.0 OE2 F:GLU194 3.8 77.3 1.0 O3B F:ADP600 3.8 64.3 1.0 NH1 F:ARG195 3.9 57.5 1.0 O3A F:ADP600 3.9 65.1 1.0 N F:THR169 4.1 73.4 1.0 OE1 F:GLU198 4.2 88.3 1.0 OD2 F:ASP261 4.2 69.6 1.0 OD1 F:ASP261 4.3 71.0 1.0 CD F:GLU194 4.3 76.7 1.0 CA F:THR169 4.3 74.6 1.0 OE2 F:GLU198 4.4 88.1 1.0 CG2 F:THR169 4.4 75.2 1.0 O2A F:ADP600 4.5 63.6 1.0 OE1 F:GLU194 4.5 78.7 1.0 PA F:ADP600 4.6 64.0 1.0 CE F:LYS168 4.7 73.5 1.0 O1A F:ADP600 4.7 64.5 1.0 O1B F:ADP600 4.7 63.2 1.0 CG F:ASP261 4.7 69.3 1.0 CD F:GLU198 4.8 87.0 1.0 CB F:LYS168 4.9 71.1 1.0

M.G.Montgomery, O.Gahura, A.G.W.Leslie, A.Zikova, J.E.Walker. Atp Synthase Fromtrypanosoma Bruceihas An Elaborated Canonical F1-Domain and Conventional Catalytic Sites. Proc. Natl. Acad. Sci. V. 115 2102 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29440423
DOI: 10.1073/PNAS.1720940115