Calcium in PDB 6h6v: Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn

The structure of Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn, PDB code: 6h6v was solved by K.A.P.Payne, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.20 / 2.66
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.910, 139.250, 136.880, 90.00, 93.74, 90.00
R / Rfree (%)	19.9 / 23.6

The structure of Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn also contains other interesting chemical elements:

Potassium	(K)	6 atoms
Manganese	(Mn)	6 atoms

The binding sites of Calcium atom in the Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn (pdb code 6h6v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn, PDB code: 6h6v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn


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 Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:56.2 occ:1.00 O A:THR420 2.6 40.2 1.0 OD2 A:ASP391 2.9 43.6 1.0 O A:ASP418 2.9 33.1 1.0 O A:ARG385 3.0 38.3 1.0 CG A:ASP391 3.1 41.7 1.0 OD1 A:ASP391 3.1 45.0 1.0 O A:HOH633 3.2 47.2 1.0 C A:THR420 3.8 35.2 1.0 N A:THR420 3.8 32.8 1.0 C A:ASP418 3.8 34.1 1.0 OD1 A:ASP418 3.8 36.9 1.0 CG A:ASP418 3.9 44.2 1.0 OD2 A:ASP418 4.0 53.0 1.0 CB A:ASP391 4.1 38.8 1.0 C A:ARG385 4.2 34.5 1.0 C A:ALA419 4.3 33.0 1.0 CA A:ALA419 4.3 34.3 1.0 CA A:THR420 4.4 34.6 1.0 OG1 A:THR420 4.4 33.1 1.0 N A:ALA419 4.4 33.2 1.0 CB A:ASP418 4.5 40.6 1.0 CA A:CYS386 4.7 40.5 1.0 CA A:ASP418 4.8 36.1 1.0 N A:ILE421 4.9 39.5 1.0 CD A:PRO422 4.9 52.5 1.0 N A:CYS386 5.0 38.1 1.0

Calcium binding site 2 out of 6 in the Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn


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 Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:49.2 occ:1.00 O B:ASP418 2.8 34.8 1.0 O B:ARG385 2.8 38.2 1.0 OD2 B:ASP391 2.8 52.8 1.0 O B:THR420 2.8 44.1 1.0 CG B:ASP391 3.0 46.0 1.0 OD1 B:ASP391 3.1 55.2 1.0 O B:HOH648 3.1 36.3 1.0 O B:HOH645 3.2 39.4 1.0 C B:ASP418 3.7 33.0 1.0 N B:THR420 3.8 34.9 1.0 C B:THR420 3.9 40.0 1.0 CB B:ASP391 3.9 41.7 1.0 OD1 B:ASP418 3.9 38.1 1.0 CG B:ASP418 3.9 36.4 1.0 C B:ARG385 4.0 34.4 1.0 CA B:ALA419 4.1 32.2 1.0 OD2 B:ASP418 4.2 34.7 1.0 C B:ALA419 4.2 34.2 1.0 N B:ALA419 4.3 33.8 1.0 CA B:CYS386 4.4 35.6 1.0 CA B:THR420 4.5 36.5 1.0 CB B:ASP418 4.5 34.9 1.0 OG1 B:THR420 4.6 39.5 1.0 N B:CYS386 4.7 36.0 1.0 CA B:ASP418 4.7 33.7 1.0

Calcium binding site 3 out of 6 in the Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca504 b:43.1 occ:1.00 O C:ASP418 2.7 30.9 1.0 O C:THR420 2.7 44.7 1.0 O C:ARG385 2.8 43.4 1.0 OD2 C:ASP391 2.9 50.5 1.0 O C:HOH602 3.0 40.9 1.0 CG C:ASP391 3.1 44.9 1.0 O C:HOH629 3.2 39.2 1.0 OD1 C:ASP391 3.2 51.3 1.0 C C:ASP418 3.6 32.3 1.0 N C:THR420 3.7 35.1 1.0 C C:THR420 3.8 38.5 1.0 OD1 C:ASP418 3.8 42.1 1.0 CG C:ASP418 3.9 38.3 1.0 C C:ARG385 3.9 40.6 1.0 CB C:ASP391 4.0 41.0 1.0 CA C:ALA419 4.0 34.9 1.0 C C:ALA419 4.1 36.6 1.0 OD2 C:ASP418 4.2 43.3 1.0 N C:ALA419 4.2 34.0 1.0 CA C:THR420 4.4 35.8 1.0 CA C:CYS386 4.4 39.5 1.0 CB C:ASP418 4.5 34.5 1.0 OG1 C:THR420 4.6 30.9 1.0 N C:CYS386 4.6 39.9 1.0 CA C:ASP418 4.7 31.1 1.0 N C:ILE421 5.0 39.1 1.0 O C:ALA419 5.0 35.8 1.0

Calcium binding site 4 out of 6 in the Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca504 b:64.1 occ:1.00 O D:THR420 2.5 44.5 1.0 OD2 D:ASP391 3.0 43.7 1.0 O D:ASP418 3.0 35.2 1.0 O D:ARG385 3.0 39.4 1.0 O D:HOH624 3.0 42.0 1.0 CG D:ASP391 3.1 46.1 1.0 OD1 D:ASP391 3.1 45.0 1.0 O D:HOH636 3.3 42.8 1.0 C D:THR420 3.7 40.1 1.0 N D:THR420 3.8 35.9 1.0 OD1 D:ASP418 3.9 42.9 1.0 C D:ASP418 3.9 35.1 1.0 CG D:ASP418 3.9 44.1 1.0 OD2 D:ASP418 4.1 49.5 1.0 CB D:ASP391 4.1 45.8 1.0 C D:ARG385 4.2 38.5 1.0 C D:ALA419 4.3 33.3 1.0 CA D:ALA419 4.3 33.4 1.0 CA D:THR420 4.3 37.6 1.0 OG1 D:THR420 4.4 35.2 1.0 N D:ALA419 4.4 33.4 1.0 CB D:ASP418 4.6 39.0 1.0 CA D:CYS386 4.7 39.0 1.0 N D:ILE421 4.8 45.8 1.0 CD D:PRO422 4.8 56.3 1.0 CA D:ASP418 4.9 36.4 1.0 N D:CYS386 4.9 39.7 1.0

Calcium binding site 5 out of 6 in the Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca504 b:45.0 occ:1.00 O E:HOH612 2.5 34.6 1.0 O E:THR420 2.7 35.5 1.0 O E:ARG385 2.7 46.5 1.0 O E:ASP418 2.8 41.4 1.0 OD2 E:ASP391 2.9 48.6 1.0 CG E:ASP391 3.1 46.4 1.0 OD1 E:ASP391 3.2 53.7 1.0 C E:ASP418 3.7 38.8 1.0 N E:THR420 3.7 41.0 1.0 C E:THR420 3.8 39.8 1.0 C E:ARG385 3.9 43.3 1.0 OD1 E:ASP418 4.0 41.1 1.0 CG E:ASP418 4.0 44.6 1.0 CB E:ASP391 4.0 42.5 1.0 CA E:ALA419 4.1 38.3 1.0 C E:ALA419 4.1 38.6 1.0 OD2 E:ASP418 4.3 44.8 1.0 N E:ALA419 4.3 36.6 1.0 CA E:THR420 4.4 40.6 1.0 CA E:CYS386 4.4 43.8 1.0 CB E:ASP418 4.6 42.0 1.0 OG1 E:THR420 4.6 45.5 1.0 N E:CYS386 4.6 45.1 1.0 CA E:ASP418 4.8 38.9 1.0 N E:ILE421 4.9 44.9 1.0 O E:ALA419 5.0 40.3 1.0 CA E:ARG385 5.0 39.0 1.0 CB E:ARG385 5.0 36.9 1.0

Calcium binding site 6 out of 6 in the Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca504 b:52.0 occ:1.00 O F:THR420 2.7 42.9 1.0 O F:ARG385 2.7 40.0 1.0 O F:ASP418 2.7 40.3 1.0 OD2 F:ASP391 2.9 50.6 1.0 CG F:ASP391 3.1 51.5 1.0 O F:HOH630 3.1 50.3 1.0 O F:HOH633 3.1 33.1 1.0 OD1 F:ASP391 3.2 56.5 1.0 C F:ASP418 3.7 38.3 1.0 N F:THR420 3.7 36.5 1.0 C F:THR420 3.8 41.1 1.0 OD1 F:ASP418 3.9 37.6 1.0 C F:ARG385 3.9 36.4 1.0 CG F:ASP418 4.0 38.4 1.0 CB F:ASP391 4.0 46.9 1.0 CA F:ALA419 4.0 33.9 1.0 C F:ALA419 4.1 32.0 1.0 OD2 F:ASP418 4.2 40.6 1.0 N F:ALA419 4.2 36.0 1.0 CA F:THR420 4.4 39.9 1.0 CA F:CYS386 4.4 37.0 1.0 CB F:ASP418 4.5 36.3 1.0 OG1 F:THR420 4.6 39.8 1.0 N F:CYS386 4.6 35.2 1.0 CA F:ASP418 4.7 36.6 1.0 N F:ILE421 4.9 50.6 1.0 O F:ALA419 5.0 32.6 1.0

K.A.P.Payne, S.A.Marshall, K.Fisher, M.J.Cliff, D.M.Cannas, C.Yan, D.J.Heyes, D.A.Parker, I.Larrosa, D.Leys. Enzymatic Carboxylation of 2-Furoic Acid Yields 2,5-Furandicarboxylic Acid (Fdca). Acs Catalysis V. 9 2854 2019.
ISSN: ESSN 2155-5435
PubMed: 31057985
DOI: 10.1021/ACSCATAL.8B04862