Manganese in PDB 8p5z: Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant

The structure of Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant, PDB code: 8p5z was solved by K.Lau, W.Wang, F.Pojer, A.Larabi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.14 / 1.56
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.95, 51.892, 93.367, 90, 117.42, 90
R / Rfree (%)	18 / 21.8

The structure of Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant also contains other interesting chemical elements:

Bromine

(Br)

4 atoms

The binding sites of Manganese atom in the Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant (pdb code 8p5z). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant, PDB code: 8p5z:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:30.1 occ:0.47 H011 A:X08201 1.3 51.8 1.0 N01 A:X08201 2.1 43.2 1.0 N08 A:X08201 2.3 43.9 1.0 C03 A:X08201 3.0 38.0 1.0 H101 A:X08201 3.0 42.2 1.0 C10 A:X08201 3.1 35.1 1.0 C02 A:X08201 3.1 39.8 1.0 HE3 D:MET121 3.2 56.2 1.0 C07 A:X08201 3.2 42.9 1.0 HD11 A:LEU124 3.3 42.9 1.0 H071 A:X08201 3.3 51.5 1.0 BR A:BR203 3.5 74.4 0.7 H102 A:X08201 3.5 42.2 1.0 H022 A:X08201 3.7 47.8 1.0 HD12 A:LEU124 3.8 42.9 1.0 H021 A:X08201 3.9 47.8 1.0 HE1 D:MET121 4.0 56.2 1.0 H091 D:X08201 4.0 55.5 1.0 CD1 A:LEU124 4.0 35.8 1.0 CE D:MET121 4.0 46.8 1.0 H092 D:X08201 4.4 55.5 1.0 C04 A:X08201 4.4 43.3 1.0 C11 A:X08201 4.4 29.8 1.0 H112 A:X08201 4.4 35.8 1.0 HE2 D:MET121 4.5 56.2 1.0 C06 A:X08201 4.5 44.8 1.0 HG A:LEU124 4.6 37.9 1.0 HB2 D:MET121 4.6 35.5 1.0 C09 D:X08201 4.7 46.2 1.0 HD13 A:LEU124 4.7 42.9 1.0 H111 A:X08201 4.8 35.8 1.0 HD21 A:LEU110 4.8 41.3 1.0 HD2 A:TYR112 4.8 35.8 1.0 CG A:LEU124 4.9 31.6 1.0 HE2 A:TYR112 4.9 34.0 1.0

Manganese binding site 2 out of 4 in the Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn203 b:41.4 occ:0.53 H011 B:X08201 1.3 63.5 1.0 N01 B:X08201 2.1 52.9 1.0 N08 B:X08201 2.6 46.9 1.0 H101 B:X08201 2.8 50.1 1.0 C10 B:X08201 3.0 41.7 1.0 C02 B:X08201 3.2 43.4 1.0 BR C:BR203 3.2 97.9 1.0 C03 B:X08201 3.2 42.5 1.0 HE2 C:MET121 3.3 76.0 1.0 HE1 C:MET121 3.3 76.0 1.0 HE3 C:MET121 3.3 76.0 1.0 H102 B:X08201 3.5 50.1 1.0 CE C:MET121 3.5 63.3 1.0 HD11 B:LEU124 3.6 48.9 1.0 C07 B:X08201 3.6 48.4 1.0 H022 B:X08201 3.7 52.0 1.0 H071 B:X08201 3.7 58.1 1.0 H093 C:X08201 3.8 67.8 1.0 H021 B:X08201 4.0 52.0 1.0 H112 B:X08201 4.2 49.9 1.0 HD12 B:LEU124 4.2 48.9 1.0 C11 B:X08201 4.2 41.5 1.0 CD1 B:LEU124 4.3 40.7 1.0 HG B:LEU124 4.4 40.4 1.0 HB2 C:MET121 4.5 51.1 1.0 H091 C:X08201 4.6 67.8 1.0 C04 B:X08201 4.6 49.3 1.0 C09 C:X08201 4.7 56.5 1.0 H111 B:X08201 4.7 49.9 1.0 CG B:LEU124 4.9 33.6 1.0 C06 B:X08201 4.9 54.2 1.0 HD21 B:LEU124 4.9 45.0 1.0 HD21 B:LEU110 5.0 46.0 1.0

Manganese binding site 3 out of 4 in the Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn202 b:43.8 occ:0.45 H011 C:X08201 2.2 55.8 1.0 N08 C:X08201 2.6 56.9 1.0 N01 C:X08201 2.8 46.5 1.0 H112 C:X08201 3.2 54.1 1.0 H071 C:X08201 3.2 68.7 1.0 C07 C:X08201 3.3 57.3 1.0 BR C:BR204 3.4 104.1 1.0 HE3 B:MET121 3.5 65.1 1.0 C03 C:X08201 3.5 57.8 1.0 C02 C:X08201 3.7 56.5 1.0 HD11 C:LEU124 3.9 52.3 1.0 C10 C:X08201 3.9 55.6 1.0 C11 C:X08201 4.0 45.0 1.0 HE1 B:MET121 4.1 65.1 1.0 H111 C:X08201 4.1 54.1 1.0 CE B:MET121 4.2 54.2 1.0 HG C:LEU124 4.3 41.6 1.0 H021 C:X08201 4.3 67.8 1.0 H022 C:X08201 4.4 67.8 1.0 H101 C:X08201 4.5 66.7 1.0 CD1 C:LEU124 4.6 43.5 1.0 HD12 C:LEU124 4.6 52.3 1.0 HB2 B:MET121 4.6 62.0 1.0 C06 C:X08201 4.7 59.0 1.0 H102 C:X08201 4.7 66.7 1.0 HD21 C:LEU124 4.7 52.2 1.0 HE1 C:TYR112 4.8 50.7 1.0 HD1 C:TYR112 4.8 49.4 1.0 HE2 B:MET121 4.8 65.1 1.0 C04 C:X08201 4.8 60.6 1.0 H093 B:X08201 4.8 56.1 1.0 CG C:LEU124 4.9 34.6 1.0 H071 B:X08201 4.9 58.1 1.0 CE1 C:TYR112 4.9 44.9 1.0 CD1 C:TYR112 4.9 48.0 1.0

Manganese binding site 4 out of 4 in the Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn202 b:34.7 occ:0.49 H011 D:X08201 2.3 51.2 1.0 N08 D:X08201 2.4 45.4 1.0 N01 D:X08201 2.4 42.7 1.0 H071 D:X08201 3.2 63.5 1.0 C07 D:X08201 3.3 52.9 1.0 C03 D:X08201 3.3 44.4 1.0 HD11 D:LEU124 3.3 45.2 1.0 C02 D:X08201 3.4 49.7 1.0 C10 D:X08201 3.6 50.6 1.0 H101 D:X08201 3.6 60.7 1.0 BR D:BR203 3.6 81.5 0.7 H111 D:X08201 3.7 40.3 1.0 HD12 D:LEU124 3.9 45.2 1.0 O D:HOH342 4.0 43.5 1.0 CD1 D:LEU124 4.0 37.6 1.0 H021 D:X08201 4.1 59.6 1.0 H022 D:X08201 4.1 59.6 1.0 H092 A:X08201 4.2 46.0 1.0 C11 D:X08201 4.2 33.6 1.0 H102 D:X08201 4.4 60.7 1.0 HG D:LEU124 4.4 41.1 1.0 HB2 A:MET121 4.5 33.4 1.0 C04 D:X08201 4.6 47.1 1.0 C06 D:X08201 4.6 47.9 1.0 H112 D:X08201 4.8 40.3 1.0 HD13 D:LEU124 4.8 45.2 1.0 CG D:LEU124 4.8 34.3 1.0 HD21 D:LEU110 4.9 38.2 1.0 SD A:MET121 4.9 39.0 1.0

W.Wang, R.Tachibana, Z.Zou, D.Chen, X.Zhang, K.Lau, F.Pojer, T.Ward, X.Hu. Manganese Transfer Hydrogenases Based on the Biotin-Streptavidin Technology. Angew.Chem.Int.Ed.Engl. 11896 2023.
ISSN: ESSN 1521-3773
PubMed: 37671593
DOI: 10.1002/ANIE.202311896