Manganese in PDB 5nnb: Isatin Hydrolase A (Iha) From Labrenzia Aggregata with Isatinate Bound

The structure of Isatin Hydrolase A (Iha) From Labrenzia Aggregata with Isatinate Bound, PDB code: 5nnb 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)	19.51 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	38.346, 69.923, 93.536, 108.23, 95.26, 103.76
R / Rfree (%)	18.8 / 22.8

The binding sites of Manganese atom in the Isatin Hydrolase A (Iha) From Labrenzia Aggregata with Isatinate Bound (pdb code 5nnb). 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 with Isatinate Bound, PDB code: 5nnb:
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 with Isatinate Bound


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 with Isatinate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:24.7 occ:1.00 OD1 A:ASP75 2.1 36.6 1.0 NE2 A:HIS73 2.1 21.7 1.0 ND1 A:HIS69 2.1 21.5 1.0 OE1 A:GLN219 2.2 30.2 1.0 OD2 A:ASP75 2.2 40.5 1.0 CG A:ASP75 2.5 31.8 1.0 O10 A:92K302 2.7 51.4 1.0 CD2 A:HIS73 2.8 21.4 1.0 O11 A:92K302 3.0 55.5 1.0 CE1 A:HIS69 3.1 23.7 1.0 CD A:GLN219 3.1 32.0 1.0 CG A:HIS69 3.1 22.6 1.0 C09 A:92K302 3.2 50.7 1.0 CE1 A:HIS73 3.2 22.1 1.0 NE2 A:GLN219 3.4 23.3 1.0 CB A:HIS69 3.5 22.2 1.0 CB A:ASP75 4.0 26.3 1.0 CG A:HIS73 4.1 21.5 1.0 O A:HOH423 4.1 31.6 1.0 O A:HOH410 4.1 43.7 1.0 ND1 A:HIS73 4.2 22.0 1.0 NE2 A:HIS69 4.2 22.6 1.0 CA A:HIS69 4.3 22.1 1.0 CD2 A:HIS69 4.3 21.8 1.0 NE2 A:HIS79 4.3 23.8 1.0 CD2 A:HIS79 4.4 21.4 1.0 CG A:GLN219 4.5 31.1 1.0 C07 A:92K302 4.6 41.6 1.0 CA A:ASP75 4.7 24.4 1.0 NE2 A:HIS207 4.9 35.6 1.0 O A:HOH473 4.9 30.7 1.0 N A:ASP75 4.9 24.8 1.0 O A:HIS69 4.9 22.9 1.0 O A:PHE74 5.0 20.6 1.0 O08 A:92K302 5.0 41.0 1.0

Manganese binding site 2 out of 4 in the Isatin Hydrolase A (Iha) From Labrenzia Aggregata with Isatinate Bound


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 with Isatinate Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:27.5 occ:1.00 NE2 B:HIS73 2.1 29.0 1.0 OD2 B:ASP75 2.1 38.1 1.0 ND1 B:HIS69 2.1 30.7 1.0 OD1 B:ASP75 2.3 32.7 1.0 OE1 B:GLN219 2.4 34.0 1.0 CG B:ASP75 2.5 31.8 1.0 O10 B:92K302 2.8 50.6 1.0 CD2 B:HIS73 2.9 24.0 1.0 O11 B:92K302 3.0 51.5 1.0 CE1 B:HIS69 3.1 30.5 1.0 CG B:HIS69 3.1 25.9 1.0 CE1 B:HIS73 3.2 23.4 1.0 C09 B:92K302 3.3 49.2 1.0 CD B:GLN219 3.3 31.8 1.0 CB B:HIS69 3.5 24.8 1.0 NE2 B:GLN219 3.5 29.0 1.0 O B:HOH401 3.9 34.6 1.0 CB B:ASP75 4.0 25.9 1.0 CG B:HIS73 4.1 26.4 1.0 O B:HOH456 4.1 40.3 1.0 NE2 B:HIS79 4.2 29.4 1.0 ND1 B:HIS73 4.2 27.0 1.0 CD2 B:HIS79 4.2 27.8 1.0 NE2 B:HIS69 4.2 28.6 1.0 CD2 B:HIS69 4.3 26.8 1.0 CA B:HIS69 4.3 23.4 1.0 CG B:GLN219 4.7 31.1 1.0 C07 B:92K302 4.7 45.4 1.0 CA B:ASP75 4.7 25.9 1.0 O B:PHE74 5.0 27.3 1.0 NE2 B:HIS207 5.0 39.0 1.0 O B:HIS69 5.0 22.1 1.0

Manganese binding site 3 out of 4 in the Isatin Hydrolase A (Iha) From Labrenzia Aggregata with Isatinate Bound


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 with Isatinate Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:32.4 occ:1.00 OD1 C:ASP75 2.1 38.3 1.0 ND1 C:HIS69 2.2 43.0 1.0 O C:HOH430 2.2 43.2 1.0 NE2 C:HIS73 2.2 41.8 1.0 OE1 C:GLN219 2.2 56.8 1.0 OD2 C:ASP75 2.3 43.6 1.0 CG C:ASP75 2.5 36.8 1.0 CD2 C:HIS73 2.9 31.1 1.0 CG C:HIS69 3.1 39.6 1.0 CE1 C:HIS69 3.1 42.8 1.0 CD C:GLN219 3.2 54.3 1.0 CE1 C:HIS73 3.4 41.3 1.0 CB C:HIS69 3.4 35.4 1.0 NE2 C:GLN219 3.4 48.1 1.0 CB C:ASP75 4.0 35.0 1.0 CG C:HIS73 4.1 30.5 1.0 NE2 C:HIS79 4.1 47.4 1.0 NE2 C:HIS69 4.2 42.2 1.0 CD2 C:HIS79 4.2 46.0 1.0 CD2 C:HIS69 4.2 41.7 1.0 CA C:HIS69 4.3 32.5 1.0 ND1 C:HIS73 4.3 32.0 1.0 CG C:GLN219 4.6 56.5 1.0 CA C:ASP75 4.7 33.4 1.0 O C:HIS69 5.0 34.7 1.0 NE2 C:HIS207 5.0 57.7 1.0

Manganese binding site 4 out of 4 in the Isatin Hydrolase A (Iha) From Labrenzia Aggregata with Isatinate Bound


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 with Isatinate Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn301 b:25.4 occ:1.00 OD1 D:ASP75 2.0 32.1 1.0 NE2 D:HIS73 2.1 21.4 1.0 ND1 D:HIS69 2.1 21.6 1.0 OE1 D:GLN219 2.2 26.0 1.0 OD2 D:ASP75 2.3 38.6 1.0 CG D:ASP75 2.5 33.4 1.0 O11 D:92K302 2.7 46.9 1.0 CD2 D:HIS73 2.9 21.5 1.0 CD D:GLN219 3.1 30.9 1.0 CE1 D:HIS69 3.1 21.8 1.0 CG D:HIS69 3.1 21.8 1.0 CE1 D:HIS73 3.2 21.5 1.0 O10 D:92K302 3.2 49.8 1.0 C09 D:92K302 3.3 45.2 1.0 NE2 D:GLN219 3.4 23.6 1.0 CB D:HIS69 3.5 21.8 1.0 CB D:ASP75 4.0 30.3 1.0 O D:HOH417 4.0 38.3 1.0 O D:HOH403 4.0 25.4 1.0 CG D:HIS73 4.1 21.6 1.0 NE2 D:HIS69 4.2 22.1 1.0 ND1 D:HIS73 4.2 21.6 1.0 CD2 D:HIS69 4.3 22.1 1.0 CA D:HIS69 4.3 22.0 1.0 NE2 D:HIS79 4.4 21.8 1.0 CG D:GLN219 4.4 22.3 1.0 CD2 D:HIS79 4.5 21.9 1.0 CA D:ASP75 4.7 21.9 1.0 C07 D:92K302 4.8 37.2 1.0 N D:ASP75 5.0 21.8 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