Manganese in PDB 8p5y: Artificial Transfer Hydrogenase with A Mn-12 Cofactor and Streptavidin S112Y-K121M Mutant

The structure of Artificial Transfer Hydrogenase with A Mn-12 Cofactor and Streptavidin S112Y-K121M Mutant, PDB code: 8p5y 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)	45.89 / 1.88
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.437, 51.198, 92.535, 90, 117.46, 90
R / Rfree (%)	19.6 / 26.5

The structure of Artificial Transfer Hydrogenase with A Mn-12 Cofactor and Streptavidin S112Y-K121M Mutant also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Bromine	(Br)	4 atoms

The binding sites of Manganese atom in the Artificial Transfer Hydrogenase with A Mn-12 Cofactor and Streptavidin S112Y-K121M Mutant (pdb code 8p5y). 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-12 Cofactor and Streptavidin S112Y-K121M Mutant, PDB code: 8p5y:
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-12 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-12 Cofactor and Streptavidin S112Y-K121M Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:70.3 occ:1.00 H011 A:WZQ201 2.2 77.9 1.0 N01 A:WZQ201 2.4 64.8 1.0 N08 A:WZQ201 2.6 76.5 1.0 H131 A:WZQ201 3.0 56.5 1.0 H071 A:WZQ201 3.2 89.5 1.0 C13 A:WZQ201 3.3 46.9 1.0 C07 A:WZQ201 3.3 74.5 1.0 C03 A:WZQ201 3.5 68.5 1.0 C02 A:WZQ201 3.5 59.9 1.0 HE3 D:MET121 3.8 62.1 1.0 H142 A:WZQ201 3.8 55.8 1.0 BR A:BR204 3.9 112.6 1.0 H132 A:WZQ201 4.1 56.5 1.0 C14 A:WZQ201 4.1 46.4 1.0 H022 A:WZQ201 4.1 72.0 1.0 HD13 A:LEU124 4.1 58.4 1.0 H021 A:WZQ201 4.3 72.0 1.0 HD22 A:LEU124 4.3 61.9 1.0 HD11 A:LEU124 4.3 58.4 1.0 HE1 D:MET121 4.4 62.1 1.0 HD21 A:LEU124 4.5 61.9 1.0 CE D:MET121 4.5 51.6 1.0 H141 A:WZQ201 4.5 55.8 1.0 HB2 D:MET121 4.7 49.6 1.0 CD1 A:LEU124 4.7 48.6 1.0 C06 A:WZQ201 4.7 79.1 1.0 C04 A:WZQ201 4.8 72.9 1.0 HD1 A:TYR112 4.8 53.8 1.0 CD2 A:LEU124 4.8 51.5 1.0 HE1 A:TYR112 4.9 51.1 1.0 HD21 A:LEU110 4.9 43.6 1.0 HD22 A:LEU110 4.9 43.6 1.0 CD1 A:TYR112 5.0 44.7 1.0

Manganese binding site 2 out of 4 in the Artificial Transfer Hydrogenase with A Mn-12 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-12 Cofactor and Streptavidin S112Y-K121M Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:101.1 occ:1.00 H071 D:WZQ201 2.5 96.9 1.0 N08 D:WZQ201 2.6 78.1 1.0 C07 D:WZQ201 2.9 80.6 1.0 HE2 A:MET121 3.0 55.8 1.0 HE1 A:MET121 3.2 55.8 1.0 CE A:MET121 3.4 46.4 1.0 BR D:BR202 3.4 110.6 1.0 N01 D:WZQ201 3.5 62.9 1.0 HE3 A:MET121 3.5 55.8 1.0 H142 D:WZQ201 3.5 58.0 1.0 H011 D:WZQ201 3.6 75.6 1.0 C03 D:WZQ201 3.7 72.0 1.0 HD21 D:LEU124 3.7 54.9 1.0 C02 D:WZQ201 4.1 69.7 1.0 C06 D:WZQ201 4.3 72.6 1.0 C14 D:WZQ201 4.4 48.2 1.0 H022 D:WZQ201 4.4 83.7 1.0 HD22 D:LEU124 4.5 54.9 1.0 CD2 D:LEU124 4.5 45.7 1.0 C13 D:WZQ201 4.5 68.5 1.0 H141 D:WZQ201 4.6 58.0 1.0 HB2 A:MET121 4.6 45.0 1.0 H101 A:WZQ201 4.8 85.2 1.0 HD11 D:LEU124 4.9 57.4 1.0 C04 D:WZQ201 4.9 75.2 1.0 HD23 D:LEU124 4.9 54.9 1.0 HH2 A:TRP120 4.9 52.1 1.0 H131 D:WZQ201 4.9 82.3 1.0

Manganese binding site 3 out of 4 in the Artificial Transfer Hydrogenase with A Mn-12 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-12 Cofactor and Streptavidin S112Y-K121M Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn202 b:66.8 occ:1.00 N08 B:WZQ201 2.1 63.3 1.0 H011 B:WZQ201 2.4 69.1 1.0 N01 B:WZQ201 2.4 57.5 1.0 H071 B:WZQ201 2.7 73.2 1.0 C07 B:WZQ201 2.8 60.9 1.0 HE2 C:MET121 3.0 90.0 1.0 C03 B:WZQ201 3.2 52.6 1.0 BR C:BR202 3.3 107.9 1.0 H132 B:WZQ201 3.4 66.5 1.0 HE1 C:MET121 3.4 90.0 1.0 C02 B:WZQ201 3.4 54.0 1.0 C13 B:WZQ201 3.5 55.3 1.0 CE C:MET121 3.5 74.9 1.0 H101 C:WZQ201 3.7 80.1 1.0 HE3 C:MET121 3.8 90.0 1.0 H021 B:WZQ201 4.0 65.0 1.0 HD22 B:LEU124 4.0 62.1 1.0 HD21 B:LEU124 4.1 62.1 1.0 H131 B:WZQ201 4.1 66.5 1.0 C06 B:WZQ201 4.2 65.8 1.0 H022 B:WZQ201 4.2 65.0 1.0 HD13 B:LEU124 4.2 70.1 1.0 HD11 B:LEU124 4.2 70.1 1.0 H102 C:WZQ201 4.3 80.1 1.0 H141 B:WZQ201 4.3 62.2 1.0 C10 C:WZQ201 4.4 66.7 1.0 C04 B:WZQ201 4.4 56.5 1.0 C14 B:WZQ201 4.5 51.7 1.0 CD2 B:LEU124 4.5 51.6 1.0 HB2 C:MET121 4.6 60.0 1.0 CD1 B:LEU124 4.7 58.3 1.0 C05 B:WZQ201 4.8 65.7 1.0 O09 C:WZQ201 4.9 71.3 1.0

Manganese binding site 4 out of 4 in the Artificial Transfer Hydrogenase with A Mn-12 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-12 Cofactor and Streptavidin S112Y-K121M Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn203 b:101.4 occ:1.00 H011 C:WZQ201 2.3 84.9 1.0 N08 C:WZQ201 2.4 81.3 1.0 H071 C:WZQ201 2.7 92.8 1.0 N01 C:WZQ201 2.8 70.6 1.0 H141 C:WZQ201 2.9 72.0 1.0 C07 C:WZQ201 3.0 77.2 1.0 C03 C:WZQ201 3.5 72.6 1.0 H142 C:WZQ201 3.5 72.0 1.0 C14 C:WZQ201 3.5 59.9 1.0 BR C:BR203 3.7 132.1 1.0 C02 C:WZQ201 3.8 78.7 1.0 C13 C:WZQ201 3.8 75.4 1.0 H132 C:WZQ201 4.4 90.7 1.0 C06 C:WZQ201 4.4 76.7 1.0 H022 C:WZQ201 4.4 94.5 1.0 H021 C:WZQ201 4.5 94.5 1.0 H131 C:WZQ201 4.6 90.7 1.0 HD11 C:LEU124 4.6 57.7 1.0 H101 B:WZQ201 4.6 69.8 1.0 C04 C:WZQ201 4.7 74.8 1.0 HH2 B:TRP120 4.8 71.0 1.0 O17 C:WZQ201 4.9 50.0 1.0 N15 C:WZQ201 4.9 42.4 1.0 HD21 C:LEU124 4.9 66.0 1.0 SD B:MET121 5.0 76.7 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