Manganese in PDB 6bwq: LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Mnctp

The structure of LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Mnctp, PDB code: 6bwq was solved by M.Fellner, R.P.Hausinger, J.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.61 / 1.85
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	97.215, 97.215, 97.215, 90.00, 90.00, 90.00
R / Rfree (%)	14.4 / 19.2

The structure of LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Mnctp also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Manganese atom in the LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Mnctp (pdb code 6bwq). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Mnctp, PDB code: 6bwq:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Mnctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Mnctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:26.5 occ:1.00 O2B A:CTP504 1.9 27.4 1.0 O A:HOH648 2.1 29.9 1.0 O3G A:CTP504 2.1 22.5 1.0 OE1 A:GLU387 2.1 33.7 1.0 O A:HOH621 2.1 33.4 1.0 O2A A:CTP504 2.4 29.8 1.0 CD A:GLU387 3.0 28.5 1.0 PB A:CTP504 3.1 27.7 1.0 OE2 A:GLU387 3.3 28.2 1.0 PG A:CTP504 3.3 21.5 1.0 PA A:CTP504 3.5 30.4 1.0 O3B A:CTP504 3.6 27.3 1.0 O3A A:CTP504 3.7 27.6 1.0 O A:HOH665 3.8 33.7 1.0 O A:HOH618 3.8 27.6 1.0 O A:HOH637 3.9 25.6 1.0 O A:HOH649 4.1 28.4 1.0 NZ A:LYS374 4.2 33.2 1.0 O A:HOH664 4.2 33.4 1.0 O1G A:CTP504 4.3 23.1 1.0 O2G A:CTP504 4.3 26.1 1.0 O1B A:CTP504 4.4 25.6 1.0 CG A:GLU387 4.4 29.8 1.0 O1A A:CTP504 4.4 28.7 1.0 O5' A:CTP504 4.7 33.7 1.0 CE A:LYS374 4.8 31.7 1.0 MN B:MN501 4.9 27.6 1.0

Manganese binding site 2 out of 6 in the LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Mnctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Mnctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:19.0 occ:0.33 O A:HOH626 2.1 22.9 1.0 OD1 A:ASP370 2.2 34.2 1.0 CG A:ASP370 3.2 27.8 1.0 OD2 A:ASP370 3.7 27.6 1.0 CB A:ASP370 4.5 24.8 1.0

Manganese binding site 3 out of 6 in the LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Mnctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Mnctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:34.1 occ:1.00 O B:HOH628 1.8 30.6 1.0 O B:HOH667 2.1 38.6 1.0 O1G B:CTP504 2.1 35.1 1.0 O B:HOH640 2.2 40.8 1.0 O2A B:CTP504 2.8 46.9 1.0 O1A B:CTP504 3.0 50.8 1.0 PG B:CTP504 3.4 30.4 1.0 PA B:CTP504 3.4 46.4 1.0 O3G B:CTP504 3.8 30.3 1.0 O3B B:CTP504 3.8 34.0 1.0 O3A B:CTP504 4.4 44.5 1.0 O B:HOH637 4.4 28.4 1.0 OE2 A:GLU289 4.5 29.1 1.0 O2G B:CTP504 4.5 28.8 1.0 O B:HOH668 4.6 39.8 1.0 PB B:CTP504 4.6 39.6 1.0 O B:HOH632 4.7 47.6 1.0 O1B B:CTP504 4.7 42.0 1.0 O5' B:CTP504 4.8 43.2 1.0 MN B:MN502 4.9 44.6 1.0

Manganese binding site 4 out of 6 in the LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Mnctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Mnctp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:27.6 occ:1.00 O A:HOH649 1.9 28.4 1.0 O1A A:CTP504 2.0 28.7 1.0 O A:HOH628 2.1 32.1 1.0 O1G A:CTP504 2.2 23.1 1.0 PA A:CTP504 3.3 30.4 1.0 PG A:CTP504 3.4 21.5 1.0 O2A A:CTP504 3.5 29.8 1.0 O3G A:CTP504 3.7 22.5 1.0 OE2 B:GLU289 4.2 22.3 1.0 O3B A:CTP504 4.2 27.3 1.0 O3A A:CTP504 4.3 27.6 1.0 O A:HOH637 4.4 25.6 1.0 O5' A:CTP504 4.4 33.7 1.0 O2G A:CTP504 4.6 26.1 1.0 O A:HOH621 4.6 33.4 1.0 MN A:MN501 4.9 26.5 1.0 PB A:CTP504 4.9 27.7 1.0 O A:HOH643 5.0 34.8 1.0

Manganese binding site 5 out of 6 in the LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Mnctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Mnctp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:44.6 occ:1.00 O1B B:CTP504 1.8 42.0 1.0 O B:HOH654 2.0 43.4 1.0 OE1 B:GLU387 2.1 65.9 1.0 O3G B:CTP504 2.6 30.3 1.0 O1A B:CTP504 3.2 50.8 1.0 CD B:GLU387 3.2 59.7 1.0 PB B:CTP504 3.3 39.6 1.0 OE2 B:GLU387 3.7 60.8 1.0 PG B:CTP504 3.7 30.4 1.0 O B:HOH643 3.8 46.1 1.0 NZ B:LYS374 3.9 38.0 1.0 O3B B:CTP504 3.9 34.0 1.0 O B:HOH640 3.9 40.8 1.0 O3A B:CTP504 4.1 44.5 1.0 PA B:CTP504 4.2 46.4 1.0 O B:HOH637 4.2 28.4 1.0 O2B B:CTP504 4.3 37.6 1.0 O B:HOH659 4.4 48.0 1.0 CG B:GLU387 4.4 51.0 1.0 O1G B:CTP504 4.5 35.1 1.0 CE B:LYS374 4.5 36.6 1.0 O2G B:CTP504 4.9 28.8 1.0 MN A:MN503 4.9 34.1 1.0

Manganese binding site 6 out of 6 in the LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Mnctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of LARC2, the C-Terminal Domain of A Cyclometallase Involved in the Synthesis of the Npn Cofactor of Lactate Racemase, in Complex with Mnctp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn503 b:44.8 occ:0.90 O B:HOH663 2.0 46.4 1.0 NE2 B:HIS399 2.5 27.1 1.0 CE1 B:HIS399 3.2 26.9 1.0 CD2 B:HIS399 3.6 26.0 1.0 O B:GLN397 4.3 29.9 1.0 ND1 B:HIS399 4.4 26.6 1.0 CG B:HIS399 4.6 28.8 1.0 O B:GLN396 4.6 26.6 1.0

B.Desguin, M.Fellner, O.Riant, J.Hu, R.P.Hausinger, P.Hols, P.Soumillion. Biosynthesis of the Nickel-Pincer Nucleotide Cofactor of Lactate Racemase Requires A Ctp-Dependent Cyclometallase. J. Biol. Chem. V. 293 12303 2018.
ISSN: ESSN 1083-351X
PubMed: 29887527
DOI: 10.1074/JBC.RA118.003741