Calcium in PDB 6zma: Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 140 Bar of Krypton Using the Soak and Freeze Methodology

Protein crystallography data

The structure of Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 140 Bar of Krypton Using the Soak and Freeze Methodology, PDB code: 6zma was solved by P.Carpentier, M.Atta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.40 / 2.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.622, 52.300, 79.407, 90.00, 90.74, 90.00
R / Rfree (%) 18 / 24.4

Other elements in 6zma:

The structure of Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 140 Bar of Krypton Using the Soak and Freeze Methodology also contains other interesting chemical elements:

Krypton (Kr) 6 atoms
Iron (Fe) 4 atoms
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 140 Bar of Krypton Using the Soak and Freeze Methodology (pdb code 6zma). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 140 Bar of Krypton Using the Soak and Freeze Methodology, PDB code: 6zma:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6zma

Go back to Calcium Binding Sites List in 6zma
Calcium binding site 1 out of 2 in the Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 140 Bar of Krypton Using the Soak and Freeze Methodology


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 140 Bar of Krypton Using the Soak and Freeze Methodology within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:42.6
occ:1.00
O B:ASP8 2.3 43.7 1.0
O B:LEU11 2.3 42.9 1.0
O B:HOH432 2.4 41.3 1.0
C B:ASP8 3.5 44.4 1.0
C B:LEU11 3.5 42.3 1.0
O B:ALA9 4.2 38.0 1.0
CA B:ALA9 4.3 44.7 1.0
N B:ALA9 4.4 43.4 1.0
O B:HOH446 4.4 40.5 1.0
C B:ALA9 4.4 43.0 1.0
C B:GLY12 4.4 46.0 1.0
N B:GLY12 4.4 44.2 1.0
N B:CYS13 4.5 45.2 1.0
CA B:LEU11 4.5 41.3 1.0
CA B:GLY12 4.5 45.1 1.0
CA B:ASP8 4.5 46.4 1.0
N B:LEU11 4.6 40.0 1.0
CB B:LEU11 4.9 41.1 1.0
O B:GLY12 4.9 48.3 1.0
CA B:CYS13 5.0 42.2 1.0

Calcium binding site 2 out of 2 in 6zma

Go back to Calcium Binding Sites List in 6zma
Calcium binding site 2 out of 2 in the Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 140 Bar of Krypton Using the Soak and Freeze Methodology


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Trna-Monooxygenase Enzyme Miae Frozen Under 140 Bar of Krypton Using the Soak and Freeze Methodology within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:0.0
occ:0.50
O B:HOH403 1.5 0.1 1.0
O B:HOH444 2.4 86.5 0.5
O B:HOH422 2.6 81.2 1.0
O B:GLY84 3.2 59.5 1.0
C B:GLY84 4.4 53.6 1.0
OE2 B:GLU28 4.5 53.4 1.0
CD B:PRO86 4.8 57.6 1.0
OE1 B:GLU28 4.8 51.0 1.0
CA B:GLY84 5.0 51.0 1.0

Reference:

P.Carpentier, C.Lepretre, C.Basset, T.Douki, S.Torelli, V.Duarte, D.Hamdane, M.Fontecave, M.Atta. Structural, Biochemical and Functional Analyses of Trna-Monooxygenase Enzyme Miae From Pseudomonas Putida Provide Insights Into Trna/Miae Interaction. Nucleic Acids Res. V. 48 9918 2020.
ISSN: ESSN 1362-4962
PubMed: 32785618
DOI: 10.1093/NAR/GKAA667
Page generated: Sat Dec 12 07:59:12 2020

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