Manganese in PDB 8ro4: The Crystal Structure of 2-Hydroxy-3-Keto-Glucal Hydratase Athyd From A. Tumefaciens

The structure of The Crystal Structure of 2-Hydroxy-3-Keto-Glucal Hydratase Athyd From A. Tumefaciens, PDB code: 8ro4 was solved by C.Grininger, J.Bitter, M.Pfeiffer, B.Nidetzky, T.Pavkov-Keller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.04 / 2.51
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.32, 165.55, 93.38, 90, 113.34, 90
R / Rfree (%)	18.1 / 21.7

The binding sites of Manganese atom in the The Crystal Structure of 2-Hydroxy-3-Keto-Glucal Hydratase Athyd From A. Tumefaciens (pdb code 8ro4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the The Crystal Structure of 2-Hydroxy-3-Keto-Glucal Hydratase Athyd From A. Tumefaciens, PDB code: 8ro4:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the The Crystal Structure of 2-Hydroxy-3-Keto-Glucal Hydratase Athyd From A. Tumefaciens


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of 2-Hydroxy-3-Keto-Glucal Hydratase Athyd From A. Tumefaciens within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:45.6 occ:1.00 OE2 A:GLU185 2.0 57.0 1.0 OD2 A:ASP216 2.1 48.3 1.0 OE1 A:GLU299 2.1 64.8 1.0 ND1 A:HIS242 2.1 54.1 1.0 CD A:GLU185 2.9 56.7 1.0 CD A:GLU299 3.1 56.1 1.0 CE1 A:HIS242 3.1 55.3 1.0 OE1 A:GLU185 3.1 55.5 1.0 CG A:HIS242 3.2 54.6 1.0 CG A:ASP216 3.2 53.3 1.0 OE2 A:GLU299 3.5 78.7 1.0 CB A:HIS242 3.5 45.5 1.0 CB A:ASP216 3.7 41.0 1.0 CE1 A:HIS219 3.9 44.8 1.0 NE2 A:HIS242 4.2 47.7 1.0 CG A:GLU185 4.2 53.1 1.0 OD1 A:ASP216 4.3 50.1 1.0 CD2 A:HIS242 4.3 45.5 1.0 CG A:GLU299 4.3 49.2 1.0 CB A:GLU299 4.4 43.1 1.0 CD A:LYS244 4.6 47.4 1.0 CD2 A:LEU214 4.7 39.7 1.0 ND1 A:HIS219 4.7 50.5 1.0 NE2 A:HIS219 4.7 44.8 1.0 NZ A:LYS244 5.0 73.0 1.0

Manganese binding site 2 out of 6 in the The Crystal Structure of 2-Hydroxy-3-Keto-Glucal Hydratase Athyd From A. Tumefaciens


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of 2-Hydroxy-3-Keto-Glucal Hydratase Athyd From A. Tumefaciens within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:45.8 occ:1.00 OE2 C:GLU185 1.9 49.6 1.0 ND1 C:HIS242 2.1 55.2 1.0 OD2 C:ASP216 2.1 52.2 1.0 OE1 C:GLU299 2.1 54.8 1.0 CD C:GLU185 2.8 55.1 1.0 CD C:GLU299 3.0 60.7 1.0 CE1 C:HIS242 3.0 42.5 1.0 OE1 C:GLU185 3.1 51.4 1.0 CG C:HIS242 3.1 46.1 1.0 CG C:ASP216 3.2 53.5 1.0 OE2 C:GLU299 3.3 77.1 1.0 CB C:HIS242 3.5 41.2 1.0 CB C:ASP216 3.7 46.0 1.0 CE1 C:HIS219 3.9 50.6 1.0 NE2 C:HIS242 4.1 56.1 1.0 CG C:GLU185 4.2 55.9 1.0 CG C:GLU299 4.2 49.6 1.0 CD2 C:HIS242 4.2 43.5 1.0 OD1 C:ASP216 4.3 49.9 1.0 CB C:GLU299 4.3 42.6 1.0 CD2 C:LEU214 4.6 58.9 1.0 NE2 C:HIS219 4.7 53.8 1.0 ND1 C:HIS219 4.7 49.0 1.0 CD C:LYS244 4.8 46.4 1.0

Manganese binding site 3 out of 6 in the The Crystal Structure of 2-Hydroxy-3-Keto-Glucal Hydratase Athyd From A. Tumefaciens


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of 2-Hydroxy-3-Keto-Glucal Hydratase Athyd From A. Tumefaciens within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn401 b:43.2 occ:1.00 OE2 D:GLU185 2.0 55.5 1.0 OD2 D:ASP216 2.0 48.6 1.0 OE1 D:GLU299 2.1 57.2 1.0 ND1 D:HIS242 2.2 53.6 1.0 CD D:GLU185 3.0 52.6 1.0 CG D:ASP216 3.1 46.1 1.0 CE1 D:HIS242 3.2 55.1 1.0 CD D:GLU299 3.2 61.4 1.0 CG D:HIS242 3.2 48.8 1.0 OE1 D:GLU185 3.3 48.7 1.0 CB D:HIS242 3.4 49.0 1.0 CB D:ASP216 3.6 35.5 1.0 OE2 D:GLU299 3.7 68.6 1.0 CE1 D:HIS219 3.8 50.6 1.0 OD1 D:ASP216 4.2 52.7 1.0 CG D:GLU185 4.3 60.8 1.0 NE2 D:HIS242 4.3 60.1 1.0 CD2 D:HIS242 4.3 48.9 1.0 CG D:GLU299 4.3 51.0 1.0 CB D:GLU299 4.4 45.6 1.0 ND1 D:HIS219 4.6 50.3 1.0 CD D:LYS244 4.7 50.1 1.0 CD2 D:LEU214 4.7 56.9 1.0 NE2 D:HIS219 4.7 53.8 1.0 CA D:HIS242 5.0 42.4 1.0

Manganese binding site 4 out of 6 in the The Crystal Structure of 2-Hydroxy-3-Keto-Glucal Hydratase Athyd From A. Tumefaciens


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Crystal Structure of 2-Hydroxy-3-Keto-Glucal Hydratase Athyd From A. Tumefaciens within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:46.2 occ:1.00 OE2 B:GLU185 2.0 56.4 1.0 OD2 B:ASP216 2.1 57.0 1.0 OE1 B:GLU299 2.1 69.6 1.0 ND1 B:HIS242 2.2 62.3 1.0 CD B:GLU185 2.9 53.8 1.0 CD B:GLU299 3.0 62.5 1.0 CE1 B:HIS242 3.1 62.8 1.0 CG B:ASP216 3.1 44.8 1.0 OE1 B:GLU185 3.2 60.1 1.0 CG B:HIS242 3.2 58.6 1.0 OE2 B:GLU299 3.4 66.5 1.0 CB B:HIS242 3.5 46.0 1.0 CB B:ASP216 3.6 49.8 1.0 CE1 B:HIS219 3.8 54.7 1.0 OD1 B:ASP216 4.2 50.7 1.0 CG B:GLU185 4.2 52.2 1.0 NE2 B:HIS242 4.2 72.7 1.0 CG B:GLU299 4.3 54.9 1.0 CD2 B:HIS242 4.3 58.8 1.0 CB B:GLU299 4.4 57.1 1.0 CD B:LYS244 4.5 54.5 1.0 CD2 B:LEU214 4.6 56.3 1.0 ND1 B:HIS219 4.7 50.8 1.0 NE2 B:HIS219 4.7 54.1 1.0 NZ B:LYS244 4.9 67.7 1.0

Manganese binding site 5 out of 6 in the The Crystal Structure of 2-Hydroxy-3-Keto-Glucal Hydratase Athyd From A. Tumefaciens


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Crystal Structure of 2-Hydroxy-3-Keto-Glucal Hydratase Athyd From A. Tumefaciens within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn401 b:54.6 occ:1.00 OE2 E:GLU185 2.0 57.6 1.0 OD2 E:ASP216 2.0 74.5 1.0 ND1 E:HIS242 2.1 61.6 1.0 OE1 E:GLU299 2.2 74.2 1.0 CD E:GLU185 2.8 64.2 1.0 CD E:GLU299 3.1 75.3 1.0 OE1 E:GLU185 3.1 66.7 1.0 CE1 E:HIS242 3.1 63.9 1.0 CG E:ASP216 3.1 57.9 1.0 CG E:HIS242 3.1 57.1 1.0 CB E:HIS242 3.4 56.5 1.0 OE2 E:GLU299 3.5 80.8 1.0 CB E:ASP216 3.6 56.4 1.0 CE1 E:HIS219 3.8 69.4 1.0 CG E:GLU185 4.2 66.0 1.0 OD1 E:ASP216 4.2 61.2 1.0 NE2 E:HIS242 4.2 59.5 1.0 CD2 E:HIS242 4.3 53.1 1.0 CG E:GLU299 4.3 62.3 1.0 CB E:GLU299 4.4 58.0 1.0 CD2 E:LEU214 4.5 58.1 1.0 ND1 E:HIS219 4.6 57.1 1.0 CD E:LYS244 4.7 59.1 1.0 NE2 E:HIS219 4.8 67.9 1.0 CA E:HIS242 4.9 59.9 1.0 CA E:ASP216 5.0 52.7 1.0

Manganese binding site 6 out of 6 in the The Crystal Structure of 2-Hydroxy-3-Keto-Glucal Hydratase Athyd From A. Tumefaciens


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Crystal Structure of 2-Hydroxy-3-Keto-Glucal Hydratase Athyd From A. Tumefaciens within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn401 b:53.3 occ:1.00 OE2 F:GLU185 1.9 54.4 1.0 OD2 F:ASP216 2.0 76.6 1.0 ND1 F:HIS242 2.1 63.8 1.0 OE1 F:GLU299 2.2 73.3 1.0 CD F:GLU185 2.9 60.8 1.0 CE1 F:HIS242 3.0 63.1 1.0 CG F:HIS242 3.1 60.6 1.0 CD F:GLU299 3.1 68.9 1.0 CG F:ASP216 3.1 64.7 1.0 OE1 F:GLU185 3.2 65.2 1.0 CB F:HIS242 3.4 53.5 1.0 OE2 F:GLU299 3.5 71.0 1.0 CB F:ASP216 3.7 54.2 1.0 CE1 F:HIS219 3.9 62.0 1.0 NE2 F:HIS242 4.1 64.5 1.0 CG F:GLU185 4.2 61.5 1.0 CD2 F:HIS242 4.2 65.7 1.0 OD1 F:ASP216 4.2 69.1 1.0 CG F:GLU299 4.3 57.9 1.0 CB F:GLU299 4.5 50.4 1.0 CD F:LYS244 4.5 58.3 1.0 CD2 F:LEU214 4.6 65.9 1.0 ND1 F:HIS219 4.6 59.4 1.0 NE2 F:HIS219 4.8 66.7 1.0 CA F:HIS242 4.9 54.5 1.0 NZ F:LYS244 5.0 72.7 1.0

K.Kastner, J.Bitter, M.Pfeiffer, C.Grininger, G.Oberdorfer, T.Pavkov-Keller, H.Weber, B.Nidetzky. Enzyme Machinery For Bacterial Glucoside Metabolism Through A Conserved Non-Hydrolytic Pathway. Angew.Chem.Int.Ed.Engl. 10681 2024.
ISSN: ESSN 1521-3773
PubMed: 39041709
DOI: 10.1002/ANIE.202410681