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

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

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:

Iron	(Fe)	4 atoms
Calcium	(Ca)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Krypton 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 Krypton atom.
In total 6 binding sites of Krypton 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 Krypton binding site number: 1; 2; 3; 4; 5; 6;

Krypton binding site 1 out of 6 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 Krypton with other atoms in the Kr 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:Kr311 b:50.6 occ:0.21 N B:TRS306 3.1 59.4 1.0 CD2 B:PHE195 3.1 53.9 1.0 CE2 B:PHE195 3.3 53.7 1.0 CG B:PHE195 3.3 47.3 1.0 CD2 B:HIS34 3.4 38.6 1.0 CZ B:PHE195 3.6 53.9 1.0 CZ B:PHE129 3.7 46.0 1.0 CD1 B:PHE195 3.7 54.5 1.0 CE1 B:PHE195 3.9 58.7 1.0 CG B:HIS34 3.9 37.1 1.0 CB B:CYS37 4.0 36.1 1.0 CB B:PHE195 4.1 43.9 1.0 CE1 B:HIS196 4.1 49.8 1.0 NE2 B:HIS34 4.2 40.2 1.0 CA B:HIS34 4.2 36.1 1.0 CB B:HIS34 4.3 36.0 1.0 CE1 B:PHE129 4.3 50.1 1.0 O1 B:TRS306 4.3 60.4 1.0 CE2 B:PHE129 4.3 45.5 1.0 SG B:CYS37 4.4 38.8 1.0 C B:TRS306 4.5 58.1 1.0 OG B:SER125 4.5 33.6 1.0 NE2 B:HIS196 4.6 46.2 1.0 O B:HIS34 4.6 35.8 1.0 CB B:SER125 4.8 34.1 1.0 OE2 B:GLU38 4.9 39.1 1.0 ND1 B:HIS34 4.9 40.9 1.0 C2 B:TRS306 4.9 59.1 1.0 C B:HIS34 4.9 35.3 1.0 CE1 B:HIS34 5.0 40.6 1.0 ND1 B:HIS196 5.0 48.6 1.0

Krypton binding site 2 out of 6 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 Krypton with other atoms in the Kr 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:Kr312 b:35.9 occ:0.19 CD1 B:LEU30 3.6 57.0 1.0 OH B:TYR144 3.6 47.6 1.0 O B:GLN27 3.8 36.0 1.0 CB B:LEU30 4.0 42.2 1.0 CD1 B:LEU140 4.0 66.0 1.0 CE2 B:TYR144 4.0 51.5 1.0 CG B:LEU30 4.0 46.7 1.0 CB B:GLN27 4.1 41.1 1.0 CZ B:TYR144 4.1 50.8 1.0 CG B:LEU31 4.2 46.8 1.0 CA B:GLN27 4.3 41.3 1.0 CG B:GLN27 4.3 42.8 1.0 N B:LEU31 4.3 36.2 1.0 CD2 B:LEU140 4.4 65.5 1.0 CD2 B:LEU136 4.5 50.0 1.0 OE1 B:GLN27 4.5 41.4 1.0 C B:GLN27 4.5 38.5 1.0 CD2 B:LEU31 4.5 48.4 1.0 C B:LEU30 4.8 37.8 1.0 CD B:GLN27 4.8 41.2 1.0 CA B:LEU31 4.8 38.4 1.0 CG B:LEU140 4.8 63.3 1.0 CA B:LEU30 5.0 39.3 1.0 CB B:LEU31 5.0 40.0 1.0

Krypton binding site 3 out of 6 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 Krypton with other atoms in the Kr binding site number 3 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 C:Kr308 b:48.7 occ:0.28 N C:TRS303 2.8 60.5 1.0 C3 C:TRS303 3.2 59.4 1.0 KR C:KR309 3.3 43.2 0.1 CE2 C:PHE195 3.6 55.2 1.0 C C:TRS303 3.6 54.5 1.0 CD2 C:HIS34 3.7 36.4 1.0 CD2 C:PHE195 3.7 52.9 1.0 CZ C:PHE129 3.8 45.3 1.0 OG C:SER125 3.9 36.8 1.0 CZ C:PHE195 4.0 51.7 1.0 OE1 C:GLU151 4.0 45.1 1.0 CE2 C:PHE129 4.1 44.7 1.0 O2 C:TRS303 4.1 61.3 1.0 CB C:CYS37 4.2 40.2 1.0 OE2 C:GLU38 4.2 36.1 1.0 CG C:PHE195 4.2 46.6 1.0 CB C:SER125 4.2 37.4 1.0 NE2 C:HIS34 4.2 38.7 1.0 CE1 C:HIS196 4.2 45.8 1.0 C2 C:TRS303 4.5 58.1 1.0 CE1 C:PHE195 4.5 60.2 1.0 O3 C:TRS303 4.5 71.6 1.0 CG C:HIS34 4.6 36.0 1.0 NE2 C:HIS196 4.6 42.4 1.0 CD1 C:PHE195 4.6 55.5 1.0 O1 C:TRS303 4.7 39.8 1.0 C1 C:TRS303 4.8 46.5 1.0 CE1 C:PHE129 4.8 47.4 1.0 CD C:GLU38 4.9 36.4 1.0 O C:HOH421 4.9 38.9 1.0 O C:HIS34 5.0 31.5 1.0

Krypton binding site 4 out of 6 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 Krypton with other atoms in the Kr binding site number 4 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 C:Kr309 b:43.2 occ:0.05 CD1 C:PHE195 2.3 55.5 1.0 CE1 C:PHE195 2.5 60.2 1.0 CG C:PHE195 2.9 46.6 1.0 CG C:HIS34 2.9 36.0 1.0 CB C:HIS34 3.1 36.5 1.0 CD2 C:HIS34 3.2 36.4 1.0 CZ C:PHE195 3.2 51.7 1.0 KR C:KR308 3.3 48.7 0.3 KR C:KR310 3.4 49.5 0.1 ND1 C:HIS34 3.5 39.0 1.0 CD2 C:PHE195 3.5 52.9 1.0 CE2 C:PHE195 3.6 55.2 1.0 CE1 C:PHE129 3.7 47.4 1.0 CZ C:PHE129 3.7 45.3 1.0 CB C:PHE195 3.8 40.6 1.0 CA C:HIS34 3.8 34.7 1.0 NE2 C:HIS34 3.8 38.7 1.0 CE1 C:HIS34 4.0 38.3 1.0 OH C:TYR144 4.5 43.8 1.0 CD1 C:PHE129 4.7 43.5 1.0 N C:HIS34 4.7 34.4 1.0 CE2 C:PHE129 4.7 44.7 1.0 CZ C:TYR144 4.8 44.1 1.0 O C:LEU30 4.9 36.1 1.0 C C:HIS34 4.9 32.8 1.0 CD1 C:LEU30 4.9 47.2 1.0

Krypton binding site 5 out of 6 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 Krypton with other atoms in the Kr binding site number 5 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 C:Kr310 b:49.5 occ:0.05 OH C:TYR144 1.3 43.8 1.0 CZ C:TYR144 1.9 44.1 1.0 CE2 C:TYR144 2.5 44.4 1.0 CE1 C:TYR144 3.1 43.6 1.0 ND1 C:HIS34 3.1 39.0 1.0 KR C:KR309 3.4 43.2 0.1 CG C:HIS34 3.7 36.0 1.0 CD2 C:TYR144 3.7 43.6 1.0 CB C:HIS34 3.8 36.5 1.0 KR C:KR311 3.8 49.9 0.3 CG C:LEU30 3.9 43.8 1.0 CE1 C:HIS34 3.9 38.3 1.0 CD2 C:LEU30 4.0 48.9 1.0 CE1 C:PHE129 4.1 47.4 1.0 CD1 C:TYR144 4.2 40.6 1.0 CE1 C:PHE195 4.2 60.2 1.0 CD1 C:PHE195 4.3 55.5 1.0 CG C:TYR144 4.4 40.5 1.0 O C:LEU30 4.5 36.1 1.0 CD1 C:LEU30 4.6 47.2 1.0 CD2 C:LEU31 4.6 55.0 1.0 CD2 C:HIS34 4.7 36.4 1.0 C C:LEU30 4.8 37.0 1.0 NE2 C:HIS34 4.8 38.7 1.0 CD1 C:PHE129 4.8 43.5 1.0 N C:LEU31 4.9 38.0 1.0 CA C:LEU31 4.9 39.1 1.0 CD1 C:LEU132 4.9 43.9 1.0

Krypton binding site 6 out of 6 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 Krypton with other atoms in the Kr binding site number 6 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 C:Kr311 b:49.9 occ:0.30 OH C:TYR144 3.3 43.8 1.0 CD2 C:LEU30 3.4 48.9 1.0 CD1 C:LEU140 3.6 45.8 1.0 CE2 C:TYR144 3.8 44.4 1.0 KR C:KR310 3.8 49.5 0.1 CZ C:TYR144 3.9 44.1 1.0 O C:GLN27 3.9 39.6 1.0 CB C:GLN27 3.9 36.8 1.0 CG C:LEU30 4.0 43.8 1.0 CG C:GLN27 4.1 40.6 1.0 CG C:LEU31 4.2 51.5 1.0 CB C:LEU30 4.3 40.2 1.0 OE1 C:GLN27 4.3 41.3 1.0 CA C:GLN27 4.3 39.6 1.0 CD2 C:LEU31 4.3 55.0 1.0 CD2 C:LEU140 4.5 45.4 1.0 CD2 C:LEU136 4.5 38.0 1.0 C C:GLN27 4.6 39.4 1.0 CD C:GLN27 4.6 39.5 1.0 N C:LEU31 4.7 38.0 1.0 CG C:LEU140 4.7 45.8 1.0 CD2 C:TYR144 4.9 43.6 1.0 CE1 C:TYR144 5.0 43.6 1.0

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