Iron in PDB 6zmb: Structure of the Native Trna-Monooxygenase Enzyme Miae

The structure of Structure of the Native Trna-Monooxygenase Enzyme Miae, PDB code: 6zmb 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)	46.75 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.797, 50.929, 76.258, 90.00, 91.00, 90.00
R / Rfree (%)	18.8 / 21.7

The structure of Structure of the Native Trna-Monooxygenase Enzyme Miae also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	1 atom

The binding sites of Iron atom in the Structure of the Native Trna-Monooxygenase Enzyme Miae (pdb code 6zmb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of the Native Trna-Monooxygenase Enzyme Miae, PDB code: 6zmb:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of the Native Trna-Monooxygenase Enzyme Miae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Native Trna-Monooxygenase Enzyme Miae within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:31.3 occ:1.00 O3 B:TRS306 2.0 40.2 1.0 OE1 B:GLU69 2.0 27.1 1.0 OE1 B:GLU38 2.0 25.5 1.0 O B:HOH451 2.2 39.3 1.0 O B:HOH412 2.2 28.7 1.0 ND1 B:HIS72 2.5 30.2 1.0 CD B:GLU38 3.0 32.2 1.0 CD B:GLU69 3.1 37.9 1.0 C3 B:TRS306 3.1 36.4 1.0 FE B:FE302 3.2 35.8 1.0 OE2 B:GLU38 3.2 30.2 1.0 CE1 B:HIS72 3.3 34.6 1.0 OE2 B:GLU69 3.5 30.5 1.0 CG B:HIS72 3.6 23.3 1.0 OE1 B:GLU151 3.8 37.6 1.0 CB B:HIS72 3.9 22.0 1.0 O2 B:TRS306 4.0 42.5 1.0 C B:TRS306 4.2 38.7 1.0 N B:TRS306 4.2 42.8 1.0 CD B:GLU151 4.2 38.6 1.0 OE2 B:GLU151 4.3 42.6 1.0 CG B:GLU38 4.4 25.1 1.0 CG B:GLU69 4.4 25.1 1.0 CE1 B:HIS154 4.4 40.4 1.0 NE2 B:HIS72 4.5 32.2 1.0 CA B:GLU69 4.5 22.5 1.0 ND1 B:HIS154 4.6 31.5 1.0 CB B:GLU69 4.7 19.6 1.0 CD2 B:HIS72 4.7 28.0 1.0 OG B:SER150 4.7 46.3 1.0 C2 B:TRS306 4.7 30.8 1.0 CB B:GLU38 4.8 22.2 1.0

Iron binding site 2 out of 4 in the Structure of the Native Trna-Monooxygenase Enzyme Miae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Native Trna-Monooxygenase Enzyme Miae within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:35.8 occ:1.00 OE1 B:GLU122 2.2 38.2 1.0 OE2 B:GLU69 2.2 30.5 1.0 ND1 B:HIS154 2.3 31.5 1.0 O B:HOH451 2.3 39.3 1.0 O3 B:TRS306 2.4 40.2 1.0 O2 B:TRS306 2.5 42.5 1.0 OE2 B:GLU151 2.6 42.6 1.0 CE1 B:HIS154 3.1 40.4 1.0 CD B:GLU69 3.1 37.9 1.0 FE B:FE301 3.2 31.3 1.0 OE1 B:GLU69 3.2 27.1 1.0 CD B:GLU122 3.3 35.5 1.0 CG B:HIS154 3.4 35.1 1.0 C3 B:TRS306 3.4 36.4 1.0 CD B:GLU151 3.5 38.6 1.0 O B:HOH419 3.6 36.7 1.0 OE2 B:GLU122 3.8 46.0 1.0 CB B:HIS154 3.8 27.9 1.0 OE1 B:GLU151 3.9 37.6 1.0 C2 B:TRS306 3.9 30.8 1.0 NE2 B:HIS154 4.3 34.4 1.0 O B:HOH412 4.3 28.7 1.0 C B:TRS306 4.3 38.7 1.0 CD2 B:HIS154 4.4 31.6 1.0 CG B:GLU122 4.5 25.6 1.0 CG B:GLU69 4.5 25.1 1.0 CA B:GLU151 4.5 29.2 1.0 CG B:GLU151 4.6 36.3 1.0 OE1 B:GLU38 4.8 25.5 1.0 CD1 B:LEU65 4.9 36.3 1.0 CB B:GLU151 5.0 32.2 1.0 OG B:SER150 5.0 46.3 1.0 O B:SER150 5.0 31.4 1.0

Iron binding site 3 out of 4 in the Structure of the Native Trna-Monooxygenase Enzyme Miae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Native Trna-Monooxygenase Enzyme Miae within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:29.1 occ:1.00 O C:HOH439 2.0 29.0 1.0 OE1 C:GLU69 2.0 23.6 1.0 OE1 C:GLU38 2.1 25.8 1.0 O C:HOH412 2.1 24.6 1.0 O1 C:TRS303 2.2 35.8 1.0 ND1 C:HIS72 2.4 25.6 1.0 CD C:GLU38 3.1 28.8 1.0 CD C:GLU69 3.1 33.8 1.0 C1 C:TRS303 3.2 31.9 1.0 CE1 C:HIS72 3.2 28.6 1.0 FE C:FE302 3.2 31.9 1.0 OE2 C:GLU38 3.4 30.3 1.0 CG C:HIS72 3.4 22.5 1.0 OE2 C:GLU69 3.5 28.8 1.0 CB C:HIS72 3.8 22.5 1.0 OE1 C:GLU151 3.9 34.6 1.0 O3 C:TRS303 4.3 51.4 1.0 OE2 C:GLU151 4.3 35.4 1.0 CD C:GLU151 4.3 32.3 1.0 NE2 C:HIS72 4.4 27.5 1.0 C C:TRS303 4.4 47.3 1.0 CG C:GLU69 4.4 22.3 1.0 CG C:GLU38 4.5 26.2 1.0 CA C:GLU69 4.5 24.0 1.0 N C:TRS303 4.5 45.9 1.0 CD2 C:HIS72 4.5 27.9 1.0 CE1 C:HIS154 4.6 29.9 1.0 OG C:SER150 4.6 40.3 1.0 CB C:GLU69 4.6 22.4 1.0 ND1 C:HIS154 4.7 30.7 1.0 CB C:GLU38 4.8 23.1 1.0 C3 C:TRS303 4.9 48.2 1.0

Iron binding site 4 out of 4 in the Structure of the Native Trna-Monooxygenase Enzyme Miae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Native Trna-Monooxygenase Enzyme Miae within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe302 b:31.9 occ:1.00 O C:HOH439 2.1 29.0 1.0 OE1 C:GLU122 2.1 33.0 1.0 OE2 C:GLU69 2.2 28.8 1.0 OE2 C:GLU151 2.4 35.4 1.0 O1 C:TRS303 2.4 35.8 1.0 ND1 C:HIS154 2.4 30.7 1.0 O3 C:TRS303 2.7 51.4 1.0 CD C:GLU69 3.1 33.8 1.0 CE1 C:HIS154 3.2 29.9 1.0 FE C:FE301 3.2 29.1 1.0 OE1 C:GLU69 3.3 23.6 1.0 CD C:GLU122 3.3 34.6 1.0 CD C:GLU151 3.3 32.3 1.0 C1 C:TRS303 3.4 31.9 1.0 CG C:HIS154 3.5 26.5 1.0 O C:HOH414 3.6 36.7 1.0 OE1 C:GLU151 3.7 34.6 1.0 OE2 C:GLU122 3.8 44.6 1.0 CB C:HIS154 4.0 25.3 1.0 C3 C:TRS303 4.0 48.2 1.0 O C:HOH412 4.2 24.6 1.0 C C:TRS303 4.4 47.3 1.0 NE2 C:HIS154 4.4 30.9 1.0 CG C:GLU122 4.5 24.4 1.0 CG C:GLU69 4.5 22.3 1.0 CG C:GLU151 4.5 30.9 1.0 CA C:GLU151 4.5 25.7 1.0 CD2 C:HIS154 4.6 28.2 1.0 N C:GLU151 4.9 27.2 1.0 CB C:GLU151 4.9 25.6 1.0 OE1 C:GLU38 4.9 25.8 1.0 OG C:SER150 4.9 40.3 1.0 ND1 C:HIS72 5.0 25.6 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