Manganese 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
Calcium	(Ca)	6 atoms

The binding sites of Manganese 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 Manganese atom.
In total 6 binding sites of Manganese where determined in the Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn, PDB code: 6h6v:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese 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 Manganese with other atoms in the Mn 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:Mn503 b:46.0 occ:1.00 ND1 A:HIS169 2.1 44.6 1.0 OD1 A:ASN147 2.2 48.8 1.0 OE2 A:GLU210 2.2 43.4 1.0 O3P A:FMN501 2.2 39.8 1.0 O A:HOH619 2.3 30.1 1.0 CE1 A:HIS169 2.8 44.0 1.0 CD A:GLU210 3.3 47.8 1.0 CG A:ASN147 3.3 45.4 1.0 CG A:HIS169 3.3 44.7 1.0 P A:FMN501 3.5 41.9 1.0 K A:K502 3.6 56.2 1.0 OE1 A:GLU210 3.6 50.8 1.0 O2P A:FMN501 3.6 41.3 1.0 CB A:HIS169 3.9 44.6 1.0 ND2 A:ASN147 3.9 51.4 1.0 NE2 A:HIS169 4.1 41.2 1.0 OG1 A:THR204 4.2 78.9 1.0 CD2 A:HIS169 4.3 43.1 1.0 O A:VAL208 4.4 48.8 1.0 O5' A:FMN501 4.5 34.5 1.0 CB A:ASN147 4.5 44.5 1.0 CG A:GLU210 4.6 46.0 1.0 O1P A:FMN501 4.6 36.3 1.0 O A:VAL148 4.7 37.8 1.0 O A:ARG205 4.9 82.1 1.0 O A:ALA202 4.9 49.4 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn503 b:35.6 occ:1.00 O B:HOH625 2.0 48.1 1.0 O3P B:FMN501 2.0 40.2 1.0 ND1 B:HIS169 2.2 38.2 1.0 OE2 B:GLU210 2.2 27.4 1.0 OD1 B:ASN147 2.2 28.4 1.0 O B:HOH624 2.5 42.2 1.0 CE1 B:HIS169 2.9 39.7 1.0 CD B:GLU210 3.2 36.0 1.0 P B:FMN501 3.3 40.6 1.0 CG B:ASN147 3.3 33.2 1.0 CG B:HIS169 3.3 38.5 1.0 K B:K502 3.6 44.1 1.0 OE1 B:GLU210 3.7 38.7 1.0 O2P B:FMN501 3.7 41.8 1.0 ND2 B:ASN147 3.8 33.5 1.0 CB B:HIS169 3.9 36.9 1.0 NE2 B:HIS169 4.1 37.3 1.0 O1P B:FMN501 4.2 42.4 1.0 O5' B:FMN501 4.3 38.8 1.0 OG1 B:THR204 4.3 67.5 1.0 CD2 B:HIS169 4.3 38.4 1.0 O B:VAL208 4.5 56.1 1.0 CG B:GLU210 4.5 39.4 1.0 O B:HOH612 4.6 43.0 1.0 CB B:ASN147 4.6 37.1 1.0 O B:VAL148 4.6 37.5 1.0 O B:ALA202 4.8 47.6 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn503 b:42.1 occ:1.00 O3P C:FMN501 2.0 43.6 1.0 OE2 C:GLU210 2.0 41.5 1.0 OD1 C:ASN147 2.3 30.3 1.0 ND1 C:HIS169 2.3 41.9 1.0 O C:HOH621 2.5 24.4 1.0 CE1 C:HIS169 3.0 41.4 1.0 CD C:GLU210 3.1 48.6 1.0 P C:FMN501 3.3 45.1 1.0 CG C:ASN147 3.4 37.5 1.0 K C:K502 3.5 53.6 1.0 CG C:HIS169 3.5 45.8 1.0 OE1 C:GLU210 3.5 45.9 1.0 O2P C:FMN501 3.6 39.9 1.0 ND2 C:ASN147 4.0 41.1 1.0 CB C:HIS169 4.0 49.2 1.0 OG1 C:THR204 4.2 72.8 1.0 NE2 C:HIS169 4.2 38.9 1.0 O5' C:FMN501 4.4 44.7 1.0 O1P C:FMN501 4.4 45.4 1.0 CG C:GLU210 4.4 50.8 1.0 O C:VAL208 4.4 48.5 1.0 CD2 C:HIS169 4.5 43.6 1.0 O C:VAL148 4.6 46.8 1.0 CB C:ASN147 4.6 40.0 1.0 O C:ALA202 4.7 50.7 1.0 O C:ARG205 4.9 72.5 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn503 b:40.5 occ:1.00 ND1 D:HIS169 2.1 52.0 1.0 OD1 D:ASN147 2.2 41.1 1.0 O3P D:FMN501 2.2 41.1 1.0 OE2 D:GLU210 2.2 48.1 1.0 O D:HOH629 2.2 33.4 1.0 O D:HOH610 2.3 48.0 1.0 CE1 D:HIS169 2.9 53.3 1.0 CD D:GLU210 3.3 50.4 1.0 CG D:ASN147 3.3 43.2 1.0 CG D:HIS169 3.3 53.5 1.0 K D:K502 3.5 58.1 1.0 P D:FMN501 3.5 42.7 1.0 OE1 D:GLU210 3.6 53.2 1.0 O2P D:FMN501 3.7 38.7 1.0 ND2 D:ASN147 3.8 46.9 1.0 CB D:HIS169 3.8 47.8 1.0 NE2 D:HIS169 4.1 55.4 1.0 OG1 D:THR204 4.3 65.7 1.0 CD2 D:HIS169 4.3 54.5 1.0 O5' D:FMN501 4.5 34.8 1.0 O D:VAL208 4.5 52.7 1.0 CB D:ASN147 4.5 42.8 1.0 O1P D:FMN501 4.5 39.4 1.0 CG D:GLU210 4.6 50.1 1.0 O D:VAL148 4.6 33.6 1.0 O D:ALA202 4.9 55.5 1.0 O D:ARG205 5.0 82.6 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn503 b:47.2 occ:1.00 O E:HOH618 2.0 50.4 1.0 OD1 E:ASN147 2.1 52.6 1.0 ND1 E:HIS169 2.2 49.9 1.0 OE2 E:GLU210 2.2 57.6 1.0 O3P E:FMN501 2.2 45.3 1.0 O E:HOH627 2.4 45.4 1.0 CE1 E:HIS169 2.9 47.9 1.0 CG E:ASN147 3.2 52.5 1.0 CD E:GLU210 3.2 58.4 1.0 CG E:HIS169 3.3 49.4 1.0 P E:FMN501 3.4 46.5 1.0 OE1 E:GLU210 3.6 54.8 1.0 ND2 E:ASN147 3.7 43.5 1.0 O2P E:FMN501 3.7 43.0 1.0 K E:K502 3.7 46.7 1.0 CB E:HIS169 3.8 47.6 1.0 NE2 E:HIS169 4.1 42.7 1.0 CD2 E:HIS169 4.3 46.4 1.0 O5' E:FMN501 4.4 42.5 1.0 OG1 E:THR204 4.4 70.7 1.0 CB E:ASN147 4.4 52.8 1.0 O1P E:FMN501 4.5 42.9 1.0 O E:VAL208 4.5 58.4 1.0 O E:VAL148 4.5 44.2 1.0 CG E:GLU210 4.6 56.4 1.0 O E:ALA202 4.9 59.2 1.0 CA E:ASN147 4.9 53.5 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn503 b:63.0 occ:1.00 OE2 F:GLU210 2.1 75.4 1.0 OD1 F:ASN147 2.2 90.5 1.0 ND1 F:HIS169 2.2 74.3 1.0 O F:HOH608 2.4 57.4 1.0 O2P F:FMN501 2.7 58.8 1.0 CE1 F:HIS169 2.9 75.5 1.0 O3P F:FMN501 3.1 78.0 1.0 CD F:GLU210 3.2 76.9 1.0 CG F:ASN147 3.3 82.5 1.0 K F:K502 3.4 85.5 1.0 CG F:HIS169 3.4 72.8 1.0 P F:FMN501 3.4 66.5 1.0 OE1 F:GLU210 3.6 82.7 1.0 ND2 F:ASN147 3.9 71.3 1.0 CB F:HIS169 3.9 73.1 1.0 NE2 F:HIS169 4.2 72.9 1.0 OG1 F:THR204 4.2 90.8 1.0 CD2 F:HIS169 4.4 71.0 1.0 O F:VAL208 4.4 86.9 1.0 CG F:GLU210 4.5 79.8 1.0 O1P F:FMN501 4.5 59.6 1.0 CB F:ASN147 4.6 90.0 1.0 O F:VAL148 4.6 73.3 1.0 O5' F:FMN501 4.7 68.8 1.0 O F:ALA202 4.8 79.8 1.0 O F:ARG205 5.0 0.6 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