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Magnesium in PDB 3mle: Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp

Enzymatic activity of Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp

All present enzymatic activity of Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp:
6.3.3.3;

Protein crystallography data

The structure of Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp, PDB code: 3mle was solved by R.Nicholls, P.J.Porebski, M.M.Klimecka, M.Chruszcz, K.Murzyn, A.Joachimiak, G.Murshudov, W.Minor, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.773, 131.905, 133.099, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24.6

Other elements in 3mle:

The structure of Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp (pdb code 3mle). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp, PDB code: 3mle:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3mle

Go back to Magnesium Binding Sites List in 3mle
Magnesium binding site 1 out of 6 in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp


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 Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg222

b:30.0
occ:1.00
 O2 A:PO4221 2.0 22.1 1.0
O2B A:ADP226 2.0 34.4 1.0
OG1 A:THR14 2.1 39.2 1.0
OD2 A:ASP50 2.1 42.1 1.0
OE2 A:GLU116 2.2 35.0 1.0
O1A A:ADP226 2.8 63.8 1.0
PB A:ADP226 3.0 35.3 1.0
CG A:ASP50 3.1 35.8 1.0
O3B A:ADP226 3.1 20.4 1.0
CD A:GLU116 3.3 38.4 1.0
P A:PO4221 3.4 26.9 1.0
CB A:THR14 3.4 40.2 1.0
OD1 A:ASP50 3.5 38.7 1.0
O1 A:PO4221 3.5 22.1 1.0
OE1 A:GLU116 3.7 38.0 1.0
NZ A:LYS35 3.8 41.5 1.0
N A:THR14 3.9 41.7 1.0
O3A A:ADP226 4.0 34.7 1.0
PA A:ADP226 4.0 66.9 1.0
O1B A:ADP226 4.2 32.1 1.0
CA A:THR14 4.2 40.4 1.0
O4 A:PO4221 4.2 31.6 1.0
CB A:ASP50 4.3 37.5 1.0
CE A:LYS13 4.4 42.9 1.0
CB A:LYS13 4.4 42.7 1.0
CG2 A:THR14 4.5 38.4 1.0
O3 A:PO4221 4.5 28.6 1.0
NZ A:LYS13 4.6 40.0 1.0
CG A:GLU116 4.6 37.3 1.0
CE A:LYS35 4.8 42.4 1.0
O2A A:ADP226 4.9 47.6 1.0
C A:LYS13 4.9 42.4 1.0

Magnesium binding site 2 out of 6 in 3mle

Go back to Magnesium Binding Sites List in 3mle
Magnesium binding site 2 out of 6 in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp


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 Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg222

b:24.0
occ:1.00
 O2B B:ADP226 2.0 27.5 0.5
O2 B:PO4221 2.0 30.1 1.0
OD2 B:ASP50 2.1 44.4 1.0
OG1 B:THR14 2.1 38.5 1.0
O3 B:PO4224 2.2 34.4 0.5
OE2 B:GLU116 2.2 37.7 1.0
O1A B:ADP226 2.8 32.2 0.5
CG B:ASP50 2.9 38.7 1.0
PB B:ADP226 3.1 33.1 0.5
O3B B:ADP226 3.1 29.7 0.5
P B:PO4224 3.2 35.5 0.5
O1 B:PO4224 3.2 34.6 0.5
CD B:GLU116 3.2 41.6 1.0
OD1 B:ASP50 3.3 36.9 1.0
P B:PO4221 3.4 36.0 1.0
CB B:THR14 3.4 39.6 1.0
OE1 B:GLU116 3.6 40.7 1.0
O1 B:PO4221 3.6 28.6 1.0
NZ B:LYS35 3.7 42.0 1.0
PA B:ADP226 3.9 40.6 0.5
N B:THR14 3.9 41.1 1.0
O3A B:ADP226 4.0 31.1 0.5
O4 B:PO4224 4.1 28.6 0.5
CA B:THR14 4.2 40.0 1.0
CB B:ASP50 4.2 39.4 1.0
O4 B:PO4221 4.2 27.7 1.0
O1B B:ADP226 4.3 27.9 0.5
O2 B:PO4224 4.3 33.3 0.5
CG2 B:THR14 4.4 38.2 1.0
O3 B:PO4221 4.4 29.2 1.0
CE B:LYS13 4.5 43.4 1.0
CB B:LYS13 4.6 42.7 1.0
CG B:GLU116 4.6 40.7 1.0
CE B:LYS35 4.7 42.9 1.0
NZ B:LYS13 4.7 40.2 1.0
O2A B:ADP226 4.8 29.4 0.5
C B:LYS13 5.0 42.0 1.0

Magnesium binding site 3 out of 6 in 3mle

Go back to Magnesium Binding Sites List in 3mle
Magnesium binding site 3 out of 6 in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp


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 Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg222

b:32.5
occ:1.00
 O2 C:PO4221 2.0 31.7 1.0
O2B C:ADP225 2.0 39.5 1.0
OG1 C:THR14 2.1 41.9 1.0
OD2 C:ASP50 2.1 49.1 1.0
OE2 C:GLU116 2.2 38.5 1.0
O1A C:ADP225 3.0 68.1 1.0
CG C:ASP50 3.0 43.9 1.0
CD C:GLU116 3.2 41.8 1.0
PB C:ADP225 3.2 37.7 1.0
O3B C:ADP225 3.2 27.9 1.0
CB C:THR14 3.3 42.8 1.0
OD1 C:ASP50 3.4 44.3 1.0
P C:PO4221 3.5 37.1 1.0
OE1 C:GLU116 3.6 41.4 1.0
NZ C:LYS35 3.7 44.0 1.0
N C:THR14 3.8 44.6 1.0
O1 C:PO4221 4.0 32.3 1.0
PA C:ADP225 4.1 77.8 1.0
O3A C:ADP225 4.1 43.5 1.0
CA C:THR14 4.1 43.3 1.0
O4 C:PO4221 4.2 41.5 1.0
CB C:ASP50 4.3 44.7 1.0
CG2 C:THR14 4.4 41.2 1.0
O1B C:ADP225 4.4 33.2 1.0
O3 C:PO4221 4.4 39.9 1.0
CE C:LYS13 4.4 45.3 1.0
CB C:LYS13 4.4 45.5 1.0
CG C:GLU116 4.5 41.0 1.0
NZ C:LYS13 4.7 42.7 1.0
CE C:LYS35 4.8 45.0 1.0
C C:LYS13 4.9 45.4 1.0
O2A C:ADP225 5.0 55.0 1.0

Magnesium binding site 4 out of 6 in 3mle

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Magnesium binding site 4 out of 6 in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg222

b:31.9
occ:1.00
 O2B D:ADP225 2.0 39.6 0.5
O2 D:PO4223 2.0 39.5 0.5
O2 D:PO4221 2.1 35.2 1.0
OG1 D:THR14 2.1 43.5 1.0
OD2 D:ASP50 2.1 53.7 1.0
OE2 D:GLU116 2.2 37.1 1.0
CG D:ASP50 2.9 47.4 1.0
PB D:ADP225 3.2 42.0 0.5
CD D:GLU116 3.2 40.4 1.0
P D:PO4223 3.3 39.0 0.5
OD1 D:ASP50 3.3 49.7 1.0
O1A D:ADP225 3.3 44.1 0.5
O4 D:PO4223 3.4 39.0 0.5
O3B D:ADP225 3.4 41.8 0.5
CB D:THR14 3.4 44.1 1.0
P D:PO4221 3.5 41.7 1.0
OE1 D:GLU116 3.6 39.7 1.0
NZ D:LYS35 3.7 46.5 1.0
O1 D:PO4221 3.8 37.4 1.0
N D:THR14 4.0 45.8 1.0
O3A D:ADP225 4.1 43.6 0.5
CB D:ASP50 4.2 47.1 1.0
PA D:ADP225 4.2 47.9 0.5
CA D:THR14 4.2 44.5 1.0
O1 D:PO4223 4.3 37.0 0.5
O3 D:PO4223 4.3 39.9 0.5
O1B D:ADP225 4.3 41.1 0.5
O4 D:PO4221 4.4 35.2 1.0
CG2 D:THR14 4.4 42.1 1.0
CE D:LYS13 4.5 47.4 1.0
O3 D:PO4221 4.5 43.9 1.0
CB D:LYS13 4.6 47.1 1.0
CG D:GLU116 4.6 39.8 1.0
CE D:LYS35 4.6 47.6 1.0
NZ D:LYS13 4.8 44.4 1.0

Magnesium binding site 5 out of 6 in 3mle

Go back to Magnesium Binding Sites List in 3mle
Magnesium binding site 5 out of 6 in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg222

b:30.6
occ:1.00
 O E:HOH236 1.9 37.1 1.0
O2B E:ADP223 2.0 31.8 1.0
O2 E:PO4221 2.0 29.5 1.0
OG1 E:THR14 2.1 43.4 1.0
OE2 E:GLU116 2.1 38.9 1.0
OD2 E:ASP50 2.1 53.5 1.0
CG E:ASP50 3.0 51.6 1.0
O1A E:ADP223 3.1 60.5 1.0
O1 E:PO4221 3.2 35.1 1.0
CD E:GLU116 3.2 41.7 1.0
P E:PO4221 3.2 46.0 1.0
PB E:ADP223 3.2 36.3 1.0
O3B E:ADP223 3.3 21.1 1.0
OD1 E:ASP50 3.3 46.2 1.0
CB E:THR14 3.4 44.6 1.0
OE1 E:GLU116 3.6 41.0 1.0
NZ E:LYS35 3.6 46.1 1.0
N E:THR14 3.9 45.9 1.0
O4 E:PO4221 4.0 41.1 1.0
O3A E:ADP223 4.1 35.4 1.0
PA E:ADP223 4.1 63.7 1.0
CA E:THR14 4.2 44.8 1.0
CB E:ASP50 4.3 52.6 1.0
CE E:LYS13 4.3 46.9 1.0
CB E:LYS13 4.4 47.0 1.0
O1B E:ADP223 4.4 21.1 1.0
CG E:GLU116 4.5 41.0 1.0
CG2 E:THR14 4.5 43.0 1.0
O3 E:PO4221 4.5 42.9 1.0
NZ E:LYS13 4.6 44.4 1.0
CE E:LYS35 4.6 47.5 1.0
C E:LYS13 4.9 46.7 1.0

Magnesium binding site 6 out of 6 in 3mle

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Magnesium binding site 6 out of 6 in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg222

b:31.3
occ:1.00
 O2 F:PO4221 2.0 44.5 1.0
O2B F:ADP226 2.0 32.3 0.8
OG1 F:THR14 2.1 40.9 1.0
OD2 F:ASP50 2.1 53.6 1.0
OE2 F:GLU116 2.1 37.2 1.0
O1A F:ADP226 2.7 56.7 0.8
PB F:ADP226 3.1 34.2 0.8
CG F:ASP50 3.2 51.1 1.0
O3B F:ADP226 3.2 24.3 0.8
CD F:GLU116 3.2 39.7 1.0
P F:PO4221 3.3 46.2 1.0
CB F:THR14 3.3 41.8 1.0
O1 F:PO4221 3.5 41.0 1.0
OE1 F:GLU116 3.6 39.7 1.0
OD1 F:ASP50 3.7 53.1 1.0
NZ F:LYS35 3.8 43.0 1.0
N F:THR14 3.8 43.4 1.0
PA F:ADP226 3.9 61.5 0.8
O3A F:ADP226 4.0 39.0 0.8
CA F:THR14 4.1 42.4 1.0
O4 F:PO4221 4.2 45.4 1.0
O1B F:ADP226 4.3 29.0 0.8
O3 F:PO4221 4.3 50.5 1.0
CB F:ASP50 4.4 49.4 1.0
CB F:LYS13 4.4 44.2 1.0
CE F:LYS13 4.4 43.8 1.0
CG2 F:THR14 4.4 40.3 1.0
CG F:GLU116 4.6 38.9 1.0
NZ F:LYS13 4.7 41.3 1.0
O2A F:ADP226 4.7 52.8 0.8
CE F:LYS35 4.8 43.6 1.0
C F:LYS13 4.8 44.2 1.0

Reference:

P.J.Porebski, M.Klimecka, M.Chruszcz, R.A.Nicholls, K.Murzyn, M.E.Cuff, X.Xu, M.Cymborowski, G.N.Murshudov, A.Savchenko, A.Edwards, W.Minor. Structural Characterization of Helicobacter Pylori Dethiobiotin Synthetase Reveals Differences Between Family Members. Febs J. V. 279 1093 2012.
ISSN: ISSN 1742-464X
PubMed: 22284390
DOI: 10.1111/J.1742-4658.2012.08506.X
Page generated: Wed Aug 14 19:21:47 2024

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