Manganese in PDB 5nna: Isatin Hydrolase A (Iha) From Labrenzia Aggregata Bound to Benzyl Benzoate

The structure of Isatin Hydrolase A (Iha) From Labrenzia Aggregata Bound to Benzyl Benzoate, PDB code: 5nna was solved by T.Sommer, K.Bjerregaard-Andersen, J.P.Morth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.54 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	37.690, 70.670, 92.920, 108.23, 95.94, 101.48
R / Rfree (%)	14.8 / 17.7

The binding sites of Manganese atom in the Isatin Hydrolase A (Iha) From Labrenzia Aggregata Bound to Benzyl Benzoate (pdb code 5nna). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Isatin Hydrolase A (Iha) From Labrenzia Aggregata Bound to Benzyl Benzoate, PDB code: 5nna:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Isatin Hydrolase A (Iha) From Labrenzia Aggregata Bound to Benzyl Benzoate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Isatin Hydrolase A (Iha) From Labrenzia Aggregata Bound to Benzyl Benzoate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:10.2 occ:0.60 O A:HOH413 2.2 12.7 1.0 NE2 A:HIS73 2.2 13.4 1.0 ND1 A:HIS69 2.2 11.6 1.0 OD1 A:ASP75 2.2 12.8 1.0 O A:HOH559 2.2 11.4 0.5 OE1 A:GLN219 2.3 15.2 0.5 O A:HOH559 2.6 11.4 0.5 CD2 A:HIS73 2.8 15.2 1.0 CG A:ASP75 3.0 9.9 1.0 OD2 A:ASP75 3.0 11.0 1.0 CD A:GLN219 3.1 10.7 0.5 CE1 A:HIS69 3.1 9.8 1.0 CG A:HIS69 3.2 7.0 1.0 NE2 A:GLN219 3.3 8.0 0.5 CE1 A:HIS73 3.4 10.6 1.0 NE2 A:GLN219 3.4 10.9 0.5 CB A:HIS69 3.6 8.0 1.0 OE1 A:GLN219 3.7 12.7 0.5 CD A:GLN219 3.8 10.3 0.5 NE2 A:HIS79 4.1 9.0 1.0 CG A:HIS73 4.1 9.4 1.0 NE2 A:HIS69 4.3 10.0 1.0 ND1 A:HIS73 4.3 10.1 1.0 CD2 A:HIS69 4.3 7.6 1.0 O A:HOH406 4.3 20.0 1.0 CD2 A:HIS79 4.4 10.3 1.0 CA A:HIS69 4.4 6.9 1.0 CB A:ASP75 4.4 7.5 1.0 CG A:GLN219 4.5 9.9 0.5 CE1 A:HIS79 4.8 9.8 1.0 NE2 A:HIS207 4.9 11.5 1.0 O A:HIS69 5.0 10.1 1.0 CG A:GLN219 5.0 10.6 0.5

Manganese binding site 2 out of 4 in the Isatin Hydrolase A (Iha) From Labrenzia Aggregata Bound to Benzyl Benzoate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Isatin Hydrolase A (Iha) From Labrenzia Aggregata Bound to Benzyl Benzoate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:6.1 occ:0.67 NE2 B:HIS73 2.1 12.0 1.0 O B:HOH584 2.1 8.4 0.6 OE1 B:GLN219 2.1 11.3 0.6 ND1 B:HIS69 2.1 10.2 1.0 O B:HOH424 2.2 8.8 1.0 OD1 B:ASP75 2.2 10.7 1.0 O B:HOH584 2.4 10.0 0.4 CD2 B:HIS73 3.0 12.6 1.0 CE1 B:HIS69 3.0 4.9 1.0 CG B:ASP75 3.0 8.8 1.0 CD B:GLN219 3.0 10.5 0.6 OD2 B:ASP75 3.1 12.0 1.0 CE1 B:HIS73 3.2 10.8 1.0 CG B:HIS69 3.2 5.6 1.0 NE2 B:GLN219 3.3 8.7 0.6 NE2 B:GLN219 3.4 9.8 0.4 CB B:HIS69 3.6 6.4 1.0 OE1 B:GLN219 3.7 8.7 0.4 CD B:GLN219 3.8 10.6 0.4 O B:HOH401 3.9 26.8 1.0 NE2 B:HIS79 4.1 9.2 1.0 CG B:HIS73 4.2 8.2 1.0 NE2 B:HIS69 4.2 8.4 1.0 O B:HOH413 4.2 14.5 1.0 ND1 B:HIS73 4.2 6.8 1.0 CD2 B:HIS69 4.3 4.8 1.0 CG B:GLN219 4.4 8.1 0.6 CB B:ASP75 4.5 6.4 1.0 CA B:HIS69 4.5 5.2 1.0 CD2 B:HIS79 4.5 8.6 1.0 CE1 B:HIS79 4.8 6.0 1.0 CG B:GLN219 4.9 8.3 0.4 NE2 B:HIS207 4.9 8.9 1.0 O B:HIS69 5.0 8.6 1.0

Manganese binding site 3 out of 4 in the Isatin Hydrolase A (Iha) From Labrenzia Aggregata Bound to Benzyl Benzoate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Isatin Hydrolase A (Iha) From Labrenzia Aggregata Bound to Benzyl Benzoate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn302 b:6.7 occ:0.68 NE2 C:HIS73 2.1 12.6 1.0 O C:HOH583 2.1 7.8 0.6 OE1 C:GLN219 2.1 12.4 0.6 ND1 C:HIS69 2.1 10.9 1.0 O C:HOH414 2.2 10.5 1.0 OD1 C:ASP75 2.2 9.6 1.0 O C:HOH583 2.4 8.4 0.4 CD2 C:HIS73 2.9 13.6 1.0 CG C:ASP75 3.0 11.0 1.0 CD C:GLN219 3.0 9.4 0.6 CE1 C:HIS69 3.0 7.1 1.0 OD2 C:ASP75 3.1 13.8 1.0 CE1 C:HIS73 3.1 10.8 1.0 CG C:HIS69 3.2 7.2 1.0 NE2 C:GLN219 3.3 8.4 0.6 NE2 C:GLN219 3.4 11.1 0.4 CB C:HIS69 3.6 6.4 1.0 OE1 C:GLN219 3.7 9.2 0.4 CD C:GLN219 3.8 9.8 0.4 O C:HOH401 3.8 24.9 1.0 NE2 C:HIS79 4.1 8.5 1.0 CG C:HIS73 4.1 10.7 1.0 ND1 C:HIS73 4.2 9.4 1.0 O C:HOH417 4.2 15.8 1.0 NE2 C:HIS69 4.2 9.2 1.0 CD2 C:HIS69 4.3 6.4 1.0 CG C:GLN219 4.4 8.9 0.6 CA C:HIS69 4.4 6.0 1.0 CB C:ASP75 4.4 6.7 1.0 CD2 C:HIS79 4.5 9.5 1.0 CE1 C:HIS79 4.8 8.1 1.0 CG C:GLN219 4.9 10.5 0.4 NE2 C:HIS207 4.9 10.3 1.0 O C:HIS69 5.0 8.0 1.0

Manganese binding site 4 out of 4 in the Isatin Hydrolase A (Iha) From Labrenzia Aggregata Bound to Benzyl Benzoate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Isatin Hydrolase A (Iha) From Labrenzia Aggregata Bound to Benzyl Benzoate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn302 b:12.3 occ:0.60 O D:HOH426 2.1 15.9 1.0 NE2 D:HIS73 2.1 16.6 1.0 O D:HOH552 2.2 11.6 0.4 ND1 D:HIS69 2.2 16.6 1.0 OE1 D:GLN219 2.2 18.1 0.5 OD1 D:ASP75 2.2 13.2 1.0 O D:HOH552 2.6 17.3 0.6 CD2 D:HIS73 2.9 15.0 1.0 CG D:ASP75 3.0 14.3 1.0 OD2 D:ASP75 3.0 15.2 1.0 CE1 D:HIS69 3.1 12.1 1.0 CD D:GLN219 3.1 13.3 0.5 CG D:HIS69 3.2 10.3 1.0 CE1 D:HIS73 3.3 17.1 1.0 NE2 D:GLN219 3.4 7.7 0.5 NE2 D:GLN219 3.5 13.0 0.5 CB D:HIS69 3.6 9.6 1.0 OE1 D:GLN219 3.9 13.5 0.5 CD D:GLN219 3.9 13.0 0.5 NE2 D:HIS79 4.1 11.7 1.0 CG D:HIS73 4.1 10.8 1.0 O D:HOH411 4.3 23.4 1.0 NE2 D:HIS69 4.3 12.6 1.0 ND1 D:HIS73 4.3 10.7 1.0 CD2 D:HIS69 4.3 10.2 1.0 CD2 D:HIS79 4.4 14.1 1.0 CB D:ASP75 4.4 9.5 1.0 CA D:HIS69 4.4 9.2 1.0 CG D:GLN219 4.5 10.3 0.5 CE1 D:HIS79 4.8 12.8 1.0 NE2 D:HIS207 4.9 15.6 1.0 O D:HIS69 5.0 12.4 1.0

T.Sommer, K.Bjerregaard-Andersen, L.Uribe, M.Etzerodt, G.Diezemann, J.Gauss, M.Cascella, J.P.Morth. A Fundamental Catalytic Difference Between Zinc and Manganese Dependent Enzymes Revealed in A Bacterial Isatin Hydrolase. Sci Rep V. 8 13104 2018.
ISSN: ESSN 2045-2322
PubMed: 30166577
DOI: 10.1038/S41598-018-31259-Y