Magnesium in PDB 6foc: F1-Atpase From Mycobacterium Smegmatis

Enzymatic activity of F1-Atpase From Mycobacterium Smegmatis

All present enzymatic activity of F1-Atpase From Mycobacterium Smegmatis:
3.6.3.14;

Protein crystallography data

The structure of F1-Atpase From Mycobacterium Smegmatis, PDB code: 6foc was solved by T.Zhang, M.G.Montgomery, A.G.W.Leslie, G.M.Cook, J.E.Walker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.59 / 4.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.189, 105.189, 628.624, 90.00, 90.00, 120.00
R / Rfree (%) 33.1 / 36.7

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 5 in 6foc

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Magnesium binding site 1 out of 5 in the F1-Atpase From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of F1-Atpase From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:0.1
occ:1.00
O A:HOH1702 2.2 0.6 1.0
O2B A:ADP1600 2.2 0.7 1.0
O A:HOH1704 2.2 0.2 1.0
O A:HOH1701 2.2 0.9 1.0
O A:HOH1703 2.2 0.6 1.0
OG1 A:THR179 2.2 1.0 1.0
CB A:THR179 3.2 0.3 1.0
PB A:ADP1600 3.4 0.9 1.0
O2A A:ADP1600 3.5 0.4 1.0
O3B A:ADP1600 3.6 0.5 1.0
OD2 A:ASP272 4.0 0.3 1.0
CG2 A:THR179 4.1 0.8 1.0
N A:THR179 4.2 0.8 1.0
PA A:ADP1600 4.2 0.0 1.0
OD1 A:ASP272 4.2 0.7 1.0
CA A:THR179 4.3 0.9 1.0
O3A A:ADP1600 4.3 0.1 1.0
O1A A:ADP1600 4.5 0.8 1.0
O1B A:ADP1600 4.5 0.3 1.0
NE2 A:GLN211 4.5 0.8 1.0
CG A:ASP272 4.6 0.9 1.0

Magnesium binding site 2 out of 5 in 6foc

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Magnesium binding site 2 out of 5 in the F1-Atpase From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of F1-Atpase From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:0.1
occ:1.00
O2B B:ADP600 2.2 0.8 1.0
O B:HOH702 2.2 0.5 1.0
O B:HOH703 2.2 0.4 1.0
O B:HOH701 2.2 0.3 1.0
OG1 B:THR179 2.2 0.7 1.0
O B:HOH704 2.2 0.2 1.0
PB B:ADP600 3.2 0.9 1.0
O1B B:ADP600 3.2 0.2 1.0
CB B:THR179 3.4 0.6 1.0
OD1 B:ASP272 3.8 0.9 1.0
OD2 B:ASP272 3.9 0.8 1.0
N B:THR179 4.0 0.4 1.0
O1A B:ADP600 4.1 0.0 1.0
O3B B:ADP600 4.2 0.1 1.0
CA B:THR179 4.3 0.1 1.0
CG B:ASP272 4.3 0.5 1.0
O3A B:ADP600 4.3 0.5 1.0
CG2 B:THR179 4.4 0.9 1.0
PA B:ADP600 4.5 0.6 1.0
NE2 B:GLN211 4.6 0.3 1.0
O2A B:ADP600 4.7 0.6 1.0
CB B:LYS178 4.7 0.9 1.0

Magnesium binding site 3 out of 5 in 6foc

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Magnesium binding site 3 out of 5 in the F1-Atpase From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of F1-Atpase From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:0.0
occ:1.00
O C:HOH702 2.2 0.4 1.0
O2B C:ADP600 2.2 0.1 1.0
O C:HOH701 2.2 0.8 1.0
OG1 C:THR179 2.2 0.4 1.0
O C:HOH703 2.2 0.4 1.0
O C:HOH704 2.2 0.6 1.0
PB C:ADP600 3.2 0.5 1.0
CB C:THR179 3.3 0.9 1.0
O3B C:ADP600 3.4 1.0 1.0
OD1 C:ASP272 3.9 98.1 1.0
OD2 C:ASP272 3.9 99.6 1.0
N C:THR179 4.1 0.6 1.0
O1A C:ADP600 4.2 0.4 1.0
O1B C:ADP600 4.2 0.6 1.0
CA C:THR179 4.3 0.3 1.0
CG C:ASP272 4.3 99.0 1.0
CG2 C:THR179 4.3 0.6 1.0
O3A C:ADP600 4.4 0.3 1.0
PA C:ADP600 4.6 0.3 1.0
O2A C:ADP600 4.6 0.4 1.0
NE2 C:GLN211 4.6 0.8 1.0
CB C:LYS178 4.9 0.2 1.0

Magnesium binding site 4 out of 5 in 6foc

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Magnesium binding site 4 out of 5 in the F1-Atpase From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of F1-Atpase From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:0.7
occ:1.00
OG1 D:THR167 2.2 0.5 1.0
O D:HOH701 2.2 0.0 1.0
O D:HOH702 2.2 0.9 1.0
O D:HOH703 2.2 0.3 1.0
O D:HOH704 2.2 0.6 1.0
O2B D:ADP600 2.2 0.7 1.0
OE1 D:GLU192 3.4 0.8 1.0
CB D:THR167 3.5 0.1 1.0
PB D:ADP600 3.5 0.6 1.0
NH1 D:ARG193 3.5 0.2 1.0
O2A D:ADP600 3.9 0.1 1.0
OE1 D:GLU196 3.9 0.3 1.0
O3B D:ADP600 4.0 0.5 1.0
OD2 D:ASP254 4.1 0.0 1.0
NH1 C:ARG376 4.2 0.7 1.0
O3A D:ADP600 4.2 0.3 1.0
N D:THR167 4.3 0.3 1.0
OD1 D:ASP254 4.3 0.2 1.0
PA D:ADP600 4.3 0.7 1.0
O1A D:ADP600 4.3 0.9 1.0
OE2 D:GLU196 4.3 0.5 1.0
CG2 D:THR167 4.3 0.2 1.0
CD D:GLU192 4.3 0.2 1.0
CA D:THR167 4.4 0.6 1.0
CD D:GLU196 4.6 0.0 1.0
CG D:ASP254 4.6 0.5 1.0
O1B D:ADP600 4.7 1.0 1.0
CZ D:ARG193 4.8 0.0 1.0
CB D:LYS166 4.9 0.8 1.0
CE D:LYS166 5.0 0.5 1.0
CG D:GLU192 5.0 0.9 1.0

Magnesium binding site 5 out of 5 in 6foc

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Magnesium binding site 5 out of 5 in the F1-Atpase From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of F1-Atpase From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:0.2
occ:1.00
OG1 F:THR167 2.2 0.7 1.0
O F:HOH701 2.2 0.3 1.0
O F:HOH702 2.2 0.9 1.0
O F:HOH704 2.2 0.4 1.0
O F:HOH703 2.2 0.0 1.0
O2B F:ADP600 2.2 0.3 1.0
PB F:ADP600 3.3 0.7 1.0
CB F:THR167 3.4 0.5 1.0
O1B F:ADP600 3.5 0.9 1.0
NH1 F:ARG193 3.6 0.2 1.0
OE1 F:GLU192 3.7 0.5 1.0
OE1 F:GLU196 4.0 0.7 1.0
O1A F:ADP600 4.0 0.3 1.0
N F:THR167 4.1 0.9 1.0
OE2 F:GLU196 4.3 0.0 1.0
CG2 F:THR167 4.3 0.3 1.0
CA F:THR167 4.3 0.4 1.0
OD2 F:ASP254 4.4 0.8 1.0
O3B F:ADP600 4.4 0.5 1.0
O3A F:ADP600 4.4 0.7 1.0
PA F:ADP600 4.5 0.3 1.0
O2A F:ADP600 4.5 0.5 1.0
CD F:GLU196 4.6 0.5 1.0
OD1 F:ASP254 4.6 0.1 1.0
CD F:GLU192 4.7 0.5 1.0
CZ F:ARG193 4.8 0.7 1.0
CB F:LYS166 4.8 0.4 1.0
CG F:ASP254 4.9 0.7 1.0
CE F:LYS166 5.0 0.8 1.0

Reference:

A.T.Zhang, M.G.Montgomery, A.G.W.Leslie, G.M.Cook, J.E.Walker. The Structure of the Catalytic Domain of the Atp Synthase Frommycobacterium Smegmatisis A Target For Developing Antitubercular Drugs. Proc.Natl.Acad.Sci.Usa V. 116 4206 2019.
ISSN: ESSN 1091-6490
PubMed: 30683723
DOI: 10.1073/PNAS.1817615116
Page generated: Mon Dec 14 22:42:36 2020

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