Rhenium in PDB 6f9p: Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II)

The structure of Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II), PDB code: 6f9p was solved by T.Isabet, E.Stura, P.Legrand, A.Zaparucha, K.Bastard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.43 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.200, 98.870, 165.960, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 21.3

The structure of Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II) also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Rhenium atom in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II) (pdb code 6f9p). This binding sites where shown within 5.0 Angstroms radius around Rhenium atom.
In total 4 binding sites of Rhenium where determined in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II), PDB code: 6f9p:
Jump to Rhenium binding site number: 1; 2; 3; 4;

Rhenium binding site 1 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II)


Mono view


Stereo pair view

A full contact list of Rhenium with other atoms in the Re binding site number 1 of Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Re402 b:76.5 occ:0.41 NE2 A:HIS312 2.1 60.3 1.0 NE2 A:HIS176 2.1 66.1 1.0 OE2 A:GLU178 2.2 62.5 1.0 CL A:CL401 2.8 92.9 1.0 CE1 A:HIS176 2.8 66.3 1.0 O A:HOH555 2.9 81.2 1.0 CE1 A:HIS312 3.0 59.2 1.0 CD2 A:HIS312 3.2 60.2 1.0 CD A:GLU178 3.2 80.8 1.0 CD2 A:HIS176 3.3 65.4 1.0 OE1 A:GLU178 3.5 92.8 1.0 ND1 A:HIS176 4.0 66.8 1.0 ND1 A:HIS312 4.2 60.1 1.0 CG A:HIS312 4.2 59.2 1.0 CG A:HIS176 4.2 63.6 1.0 CG A:GLU178 4.5 62.7 1.0 O A:HOH538 4.7 82.6 1.0 CB A:GLU178 4.8 54.2 1.0 CA A:GLU178 4.8 54.3 1.0 CZ A:PHE191 4.9 62.7 1.0 CD2 A:LEU173 4.9 0.4 1.0

Rhenium binding site 2 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II)


Mono view


Stereo pair view

A full contact list of Rhenium with other atoms in the Re binding site number 2 of Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Re402 b:0.4 occ:0.52 NE2 B:HIS312 2.1 72.0 1.0 NE2 B:HIS176 2.2 88.9 1.0 OE2 B:GLU178 2.4 93.1 1.0 CL B:CL401 2.8 92.7 0.5 CE1 B:HIS176 3.0 88.9 1.0 CD2 B:HIS312 3.1 73.3 1.0 CE1 B:HIS312 3.1 69.8 1.0 CD2 B:HIS176 3.3 89.4 1.0 CD B:GLU178 3.4 0.8 1.0 OE1 B:GLU178 3.7 0.0 1.0 ND1 B:HIS176 4.2 90.1 1.0 CG B:HIS312 4.2 71.8 1.0 ND1 B:HIS312 4.2 70.6 1.0 CG B:HIS176 4.3 87.8 1.0 CG B:GLU178 4.7 78.4 1.0 CB B:ARG314 4.8 0.9 1.0 CZ B:PHE191 4.9 80.0 1.0 CA B:GLU178 4.9 69.7 1.0 CB B:GLU178 4.9 70.2 1.0 O B:GLY313 4.9 94.8 1.0 CD B:ARG314 5.0 0.1 1.0

Rhenium binding site 3 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II)


Mono view


Stereo pair view

A full contact list of Rhenium with other atoms in the Re binding site number 3 of Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II) within 5.0Å range: probe atom residue distance (Å) B Occ C:Re402 b:0.1 occ:0.59 NE2 C:HIS312 2.2 80.8 1.0 NE2 C:HIS176 2.2 94.7 1.0 OE2 C:GLU178 2.4 0.9 1.0 CL C:CL401 2.8 0.5 0.6 CE1 C:HIS176 2.8 96.4 1.0 CE1 C:HIS312 3.2 79.0 1.0 CD2 C:HIS312 3.2 81.7 1.0 CD C:GLU178 3.3 0.2 1.0 CD2 C:HIS176 3.4 94.5 1.0 OE1 C:GLU178 3.6 0.7 1.0 ND1 C:HIS176 4.1 98.3 1.0 CG C:HIS312 4.3 79.6 1.0 ND1 C:HIS312 4.3 79.5 1.0 CG C:HIS176 4.4 94.7 1.0 CG C:GLU178 4.7 79.4 1.0 CD2 C:LEU173 4.8 0.0 1.0 CZ C:PHE191 4.9 83.8 1.0 CB C:GLU178 4.9 75.3 1.0 CA C:GLU178 4.9 76.8 1.0

Rhenium binding site 4 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II)


Mono view


Stereo pair view

A full contact list of Rhenium with other atoms in the Re binding site number 4 of Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Re(II) within 5.0Å range: probe atom residue distance (Å) B Occ D:Re402 b:0.9 occ:0.58 NE2 D:HIS312 2.2 76.3 1.0 NE2 D:HIS176 2.2 78.8 1.0 OE2 D:GLU178 2.3 87.1 1.0 CL D:CL401 2.8 0.4 0.6 CE1 D:HIS176 2.9 79.5 1.0 CD2 D:HIS312 3.2 76.8 1.0 CE1 D:HIS312 3.2 74.6 1.0 CD D:GLU178 3.3 94.6 1.0 CD2 D:HIS176 3.5 78.1 1.0 OE1 D:GLU178 3.5 95.2 1.0 ND1 D:HIS176 4.1 79.6 1.0 CG D:HIS312 4.3 74.7 1.0 ND1 D:HIS312 4.3 74.9 1.0 CG D:HIS176 4.4 76.4 1.0 CG D:GLU178 4.6 77.6 1.0 CD2 D:LEU173 4.8 0.2 1.0 CA D:GLU178 4.9 70.7 1.0 CB D:GLU178 5.0 71.3 1.0 CZ D:PHE191 5.0 75.2 1.0

K.Bastard, T.Isabet, E.A.Stura, P.Legrand, A.Zaparucha. Structural Studies Based on Two Lysine Dioxygenases with Distinct Regioselectivity Brings Insights Into Enzyme Specificity Within the Clavaminate Synthase-Like Family. Sci Rep V. 8 16587 2018.
ISSN: ESSN 2045-2322
PubMed: 30410048
DOI: 10.1038/S41598-018-34795-9