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Chlorine 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:

Magnesium (Mg) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Cocrystallized with Atp, PDB code: 3mle:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 3mle

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl224

b:64.8
occ:1.00
 NE2 A:GLN22 3.1 47.2 1.0
NE2 B:GLN22 3.3 47.0 1.0
O B:HOH232 3.5 28.9 1.0
CG B:GLN22 3.8 46.6 1.0
CB B:GLN22 3.9 46.4 1.0
OD2 B:ASP57 3.9 47.0 1.0
CD B:GLN22 4.0 47.3 1.0
CG A:GLN22 4.0 46.6 1.0
CD A:GLN22 4.0 47.6 1.0
CG B:ASP57 4.2 46.4 1.0
O A:HOH241 4.3 25.5 1.0
OD1 B:ASP57 4.3 49.0 1.0
CB A:GLN22 4.4 46.4 1.0
CA B:GLN22 4.4 47.0 1.0
OD2 A:ASP57 4.6 42.3 1.0
OD1 A:ASP57 4.6 45.2 1.0
CG A:ASP57 4.7 39.1 1.0
CD1 A:LEU60 4.7 46.3 1.0
NH2 B:ARG18 4.9 47.1 1.0
CA A:GLN22 5.0 46.9 1.0
CB B:ASP57 5.0 43.1 1.0

Chlorine binding site 2 out of 3 in 3mle

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
C:Cl223

b:67.9
occ:1.00
 NE2 E:GLN22 3.3 52.0 1.0
NE2 C:GLN22 3.4 51.4 1.0
OD2 E:ASP57 3.7 52.5 1.0
CG E:ASP57 4.0 54.5 1.0
OD1 E:ASP57 4.0 59.0 1.0
CG E:GLN22 4.1 51.9 1.0
CD E:GLN22 4.1 52.7 1.0
CB E:GLN22 4.2 51.9 1.0
CG C:GLN22 4.2 51.3 1.0
CD C:GLN22 4.3 52.2 1.0
OD2 C:ASP57 4.3 50.1 1.0
CG C:ASP57 4.4 48.9 1.0
NH2 E:ARG18 4.5 51.5 1.0
OD1 C:ASP57 4.5 48.9 1.0
CB C:GLN22 4.5 51.0 1.0
CD1 C:LEU60 4.7 50.1 1.0
CA E:GLN22 4.8 52.8 1.0
NH2 C:ARG18 4.8 49.9 1.0
CB E:ASP57 4.9 52.6 1.0

Chlorine binding site 3 out of 3 in 3mle

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
F:Cl224

b:58.6
occ:1.00
 NE2 F:GLN22 3.2 52.0 1.0
OD2 F:ASP57 3.9 61.6 1.0
CG F:GLN22 4.0 51.7 1.0
CB F:GLN22 4.1 51.2 1.0
CD F:GLN22 4.1 52.5 1.0
CG F:ASP57 4.1 60.5 1.0
OD1 F:ASP57 4.2 64.4 1.0
CA F:GLN22 4.6 52.0 1.0
NH2 F:ARG18 4.7 50.2 1.0
CB F:ASP57 4.9 58.1 1.0
CD1 F:LEU60 4.9 51.9 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: Sun Jul 21 00:14:55 2024

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