Manganese in PDB 4m8d: Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate

The structure of Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate, PDB code: 4m8d was solved by K.Bjerregaard-Andersen, T.Sommer, J.K.Jensen, B.Jochimsen, M.Etzerodt, J.P.Morth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.98 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.980, 51.820, 357.090, 90.00, 91.92, 90.00
R / Rfree (%)	15.2 / 19.2

The structure of Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate also contains other interesting chemical elements:

Calcium

(Ca)

16 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate (pdb code 4m8d). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate, PDB code: 4m8d:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:14.4 occ:1.00 O10 A:23J302 1.9 45.0 1.0 OD1 A:ASP79 2.1 12.8 1.0 NE2 A:HIS77 2.2 11.1 1.0 C09 A:23J302 2.2 41.2 1.0 O11 A:23J302 2.2 38.2 1.0 O A:HOH717 2.2 25.6 1.0 ND1 A:HIS73 2.3 14.8 1.0 CD2 A:HIS77 3.0 10.2 1.0 CG A:ASP79 3.1 14.6 1.0 CE1 A:HIS73 3.2 14.6 1.0 CE1 A:HIS77 3.3 12.5 1.0 CG A:HIS73 3.3 11.3 1.0 OD2 A:ASP79 3.4 15.8 1.0 CB A:HIS73 3.6 11.5 1.0 C07 A:23J302 3.6 38.0 1.0 NE2 A:HIS83 3.8 20.0 1.0 O08 A:23J302 4.1 37.2 1.0 CD2 A:HIS83 4.2 18.1 1.0 CG A:HIS77 4.2 12.8 1.0 O A:HOH438 4.3 20.5 1.0 ND1 A:HIS77 4.3 12.7 1.0 NE2 A:HIS73 4.3 13.0 1.0 CD2 A:HIS73 4.4 13.2 1.0 CB A:ASP79 4.4 12.5 1.0 CA A:HIS73 4.5 11.3 1.0 CE1 A:HIS83 4.6 18.7 1.0 NE2 A:HIS212 4.7 20.8 1.0 C05 A:23J302 4.7 34.8 1.0 C06 A:23J302 4.8 33.9 1.0 CA A:ASP79 4.9 12.6 1.0

Manganese binding site 2 out of 12 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:17.5 occ:1.00 OD1 B:ASP79 2.1 15.1 1.0 O10 B:23J302 2.1 31.7 0.7 NE2 B:HIS77 2.2 13.2 1.0 O B:HOH460 2.2 25.6 1.0 O11 B:23J302 2.2 24.5 0.7 ND1 B:HIS73 2.2 17.3 1.0 C09 B:23J302 2.3 28.3 0.7 CD2 B:HIS77 3.1 11.8 1.0 CG B:ASP79 3.1 16.3 1.0 CE1 B:HIS73 3.1 16.8 1.0 CE1 B:HIS77 3.2 15.3 1.0 CG B:HIS73 3.2 15.8 1.0 OD2 B:ASP79 3.4 15.7 1.0 CB B:HIS73 3.6 14.6 1.0 C07 B:23J302 3.6 28.9 0.7 NE2 B:HIS83 3.8 22.9 1.0 O08 B:23J302 4.0 26.8 0.7 CD2 B:HIS83 4.2 22.8 1.0 O B:HOH436 4.2 18.9 1.0 NE2 B:HIS73 4.2 15.9 1.0 CG B:HIS77 4.2 11.3 1.0 ND1 B:HIS77 4.3 11.7 1.0 CD2 B:HIS73 4.3 15.0 1.0 CB B:ASP79 4.4 12.5 1.0 CA B:HIS73 4.5 14.0 1.0 CE1 B:HIS83 4.5 24.0 1.0 C05 B:23J302 4.8 32.9 0.7 CA B:ASP79 4.9 12.0 1.0 NE2 B:HIS212 4.9 26.2 1.0 C06 B:23J302 4.9 33.1 0.7

Manganese binding site 3 out of 12 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:22.2 occ:1.00 O11 C:23J302 2.0 52.1 0.8 O C:HOH637 2.1 27.7 1.0 OD1 C:ASP79 2.2 21.3 1.0 ND1 C:HIS73 2.2 23.6 1.0 NE2 C:HIS77 2.2 24.6 1.0 C09 C:23J302 2.3 47.9 0.8 O10 C:23J302 2.5 47.2 0.8 CE1 C:HIS73 3.1 24.0 1.0 CG C:ASP79 3.1 27.5 1.0 CD2 C:HIS77 3.1 22.2 1.0 CG C:HIS73 3.2 24.5 1.0 CE1 C:HIS77 3.3 24.6 1.0 OD2 C:ASP79 3.3 21.7 1.0 C07 C:23J302 3.5 44.5 0.8 CB C:HIS73 3.6 22.0 1.0 O08 C:23J302 3.8 43.7 0.8 NE2 C:HIS83 3.9 30.5 1.0 O C:HOH469 4.2 31.6 1.0 NE2 C:HIS73 4.2 22.2 1.0 CD2 C:HIS83 4.2 29.9 1.0 CG C:HIS77 4.3 19.8 1.0 CD2 C:HIS73 4.3 22.1 1.0 ND1 C:HIS77 4.3 20.4 1.0 CB C:ASP79 4.5 21.0 1.0 CA C:HIS73 4.5 21.2 1.0 NE2 C:HIS212 4.7 36.3 1.0 CE1 C:HIS83 4.7 31.0 1.0 C05 C:23J302 4.8 40.9 0.8 CA C:ASP79 4.9 20.2 1.0 C06 C:23J302 4.9 39.6 0.8

Manganese binding site 4 out of 12 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn301 b:18.5 occ:1.00 O10 D:23J302 1.9 42.0 0.8 OD1 D:ASP79 2.1 18.4 1.0 O11 D:23J302 2.2 34.5 0.8 C09 D:23J302 2.2 37.3 0.8 ND1 D:HIS73 2.2 18.4 1.0 NE2 D:HIS77 2.2 16.0 1.0 O D:HOH530 2.3 25.4 1.0 CG D:ASP79 3.0 19.5 1.0 CD2 D:HIS77 3.1 16.6 1.0 CE1 D:HIS73 3.1 16.9 1.0 CG D:HIS73 3.2 17.8 1.0 OD2 D:ASP79 3.3 19.5 1.0 CE1 D:HIS77 3.3 18.2 1.0 CB D:HIS73 3.6 18.6 1.0 C07 D:23J302 3.6 35.5 0.8 NE2 D:HIS83 3.8 24.9 1.0 O08 D:23J302 4.1 35.9 0.8 CD2 D:HIS83 4.2 24.2 1.0 NE2 D:HIS73 4.2 18.3 1.0 CG D:HIS77 4.3 16.2 1.0 CD2 D:HIS73 4.3 19.8 1.0 ND1 D:HIS77 4.3 16.0 1.0 CB D:ASP79 4.4 15.4 1.0 O D:HOH447 4.4 22.4 1.0 CE1 D:HIS83 4.5 23.3 1.0 CA D:HIS73 4.5 15.8 1.0 NE2 D:HIS212 4.7 22.7 1.0 C05 D:23J302 4.8 32.0 0.8 C06 D:23J302 4.8 29.6 0.8 CA D:ASP79 4.9 15.0 1.0

Manganese binding site 5 out of 12 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn301 b:15.8 occ:1.00 O10 E:23J302 2.0 40.5 0.8 OD1 E:ASP79 2.1 15.8 1.0 ND1 E:HIS73 2.2 15.3 1.0 NE2 E:HIS77 2.2 16.1 1.0 O E:HOH472 2.3 24.4 1.0 C09 E:23J302 2.3 37.4 0.8 O11 E:23J302 2.4 32.7 0.8 CG E:ASP79 3.1 14.8 1.0 CD2 E:HIS77 3.1 15.4 1.0 CE1 E:HIS73 3.1 22.8 1.0 CG E:HIS73 3.3 17.4 1.0 CE1 E:HIS77 3.3 15.1 1.0 OD2 E:ASP79 3.3 17.4 1.0 CB E:HIS73 3.6 15.3 1.0 C07 E:23J302 3.7 38.5 0.8 NE2 E:HIS83 3.7 22.1 1.0 CD2 E:HIS83 4.1 17.7 1.0 O08 E:23J302 4.2 39.2 0.8 O E:HOH665 4.2 23.1 1.0 NE2 E:HIS73 4.3 15.4 1.0 CG E:HIS77 4.3 14.6 1.0 ND1 E:HIS77 4.4 13.0 1.0 CD2 E:HIS73 4.4 15.4 1.0 CB E:ASP79 4.5 11.8 1.0 CA E:HIS73 4.5 14.6 1.0 CE1 E:HIS83 4.5 21.4 1.0 NE2 E:HIS212 4.8 23.0 1.0 C05 E:23J302 4.9 36.7 0.8 C06 E:23J302 4.9 35.3 0.8 CA E:ASP79 4.9 13.6 1.0

Manganese binding site 6 out of 12 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn301 b:16.8 occ:1.00 OD1 F:ASP79 2.1 16.2 1.0 O11 F:23J302 2.2 27.6 0.6 O10 F:23J302 2.2 24.5 0.6 NE2 F:HIS77 2.2 11.7 1.0 O F:HOH498 2.2 30.6 1.0 ND1 F:HIS73 2.2 14.8 1.0 C09 F:23J302 2.3 25.1 0.6 CD2 F:HIS77 3.1 11.2 1.0 CG F:ASP79 3.1 16.7 1.0 CE1 F:HIS73 3.1 16.8 1.0 CG F:HIS73 3.2 14.6 1.0 CE1 F:HIS77 3.2 13.5 1.0 OD2 F:ASP79 3.4 16.4 1.0 CB F:HIS73 3.6 13.4 1.0 C07 F:23J302 3.7 25.6 0.6 NE2 F:HIS83 3.9 22.4 1.0 O F:HOH719 4.1 19.5 1.0 O08 F:23J302 4.1 21.1 0.6 CD2 F:HIS83 4.2 21.2 1.0 CG F:HIS77 4.3 12.5 1.0 NE2 F:HIS73 4.3 15.0 1.0 ND1 F:HIS77 4.3 10.8 1.0 CD2 F:HIS73 4.3 14.4 1.0 CB F:ASP79 4.4 13.5 1.0 CA F:HIS73 4.5 15.1 1.0 CE1 F:HIS83 4.6 23.5 1.0 NE2 F:HIS212 4.9 23.3 1.0 CA F:ASP79 4.9 11.6 1.0 C05 F:23J302 4.9 29.8 0.6 C06 F:23J302 4.9 30.6 0.6

Manganese binding site 7 out of 12 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn301 b:22.8 occ:1.00 OD1 G:ASP79 2.1 23.0 1.0 O11 G:23J302 2.2 38.3 0.7 ND1 G:HIS73 2.2 24.9 1.0 O G:HOH465 2.2 28.7 1.0 O10 G:23J302 2.3 37.1 0.7 NE2 G:HIS77 2.3 20.9 1.0 C09 G:23J302 2.4 38.8 0.7 CG G:ASP79 3.0 19.1 1.0 CD2 G:HIS77 3.0 21.0 1.0 CE1 G:HIS73 3.1 24.7 1.0 CG G:HIS73 3.3 24.3 1.0 OD2 G:ASP79 3.3 21.3 1.0 CE1 G:HIS77 3.5 20.7 1.0 CB G:HIS73 3.6 22.9 1.0 NE2 G:HIS83 3.8 31.4 1.0 C07 G:23J302 3.9 40.5 0.7 CD2 G:HIS83 4.0 30.3 1.0 O G:HOH454 4.2 28.9 1.0 NE2 G:HIS73 4.3 21.5 1.0 CG G:HIS77 4.3 20.9 1.0 O08 G:23J302 4.3 37.6 0.7 CD2 G:HIS73 4.4 23.6 1.0 CB G:ASP79 4.4 17.2 1.0 ND1 G:HIS77 4.5 19.9 1.0 CA G:HIS73 4.6 22.2 1.0 CE1 G:HIS83 4.6 31.3 1.0 C03 G:23J302 4.7 45.6 0.3 NE2 G:HIS212 4.7 28.1 1.0 CA G:ASP79 4.8 19.2 1.0 O G:PHE78 5.0 18.6 1.0

Manganese binding site 8 out of 12 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range: probe atom residue distance (Å) B Occ H:Mn301 b:24.1 occ:1.00 O10 H:23J302 2.0 43.6 0.8 OD1 H:ASP79 2.1 25.9 1.0 ND1 H:HIS73 2.2 24.7 1.0 NE2 H:HIS77 2.2 25.4 1.0 O H:HOH635 2.2 31.1 1.0 O11 H:23J302 2.3 36.3 0.8 C09 H:23J302 2.3 39.3 0.8 CD2 H:HIS77 3.0 22.3 1.0 CE1 H:HIS73 3.1 25.2 1.0 CG H:ASP79 3.1 26.1 1.0 CG H:HIS73 3.2 24.9 1.0 CE1 H:HIS77 3.3 24.3 1.0 OD2 H:ASP79 3.4 27.1 1.0 CB H:HIS73 3.6 25.2 1.0 C07 H:23J302 3.7 41.7 0.8 NE2 H:HIS83 3.9 29.8 1.0 O08 H:23J302 4.1 43.0 0.8 O H:HOH451 4.2 25.5 1.0 NE2 H:HIS73 4.2 24.9 1.0 CD2 H:HIS83 4.2 27.4 1.0 CG H:HIS77 4.3 22.1 1.0 ND1 H:HIS77 4.3 24.8 1.0 CD2 H:HIS73 4.3 25.3 1.0 CB H:ASP79 4.4 21.9 1.0 CA H:HIS73 4.5 24.7 1.0 NE2 H:HIS212 4.6 29.5 1.0 CE1 H:HIS83 4.6 31.8 1.0 C05 H:23J302 4.8 39.9 0.8 C06 H:23J302 4.9 40.2 0.8 CA H:ASP79 4.9 21.9 1.0

Manganese binding site 9 out of 12 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn301 b:16.5 occ:1.00 OD1 I:ASP79 2.1 14.1 1.0 O11 I:23J302 2.1 42.1 0.9 NE2 I:HIS77 2.2 14.0 1.0 ND1 I:HIS73 2.2 15.9 1.0 O10 I:23J302 2.3 38.4 0.9 O I:HOH482 2.3 24.6 1.0 C09 I:23J302 2.4 39.7 0.9 CG I:ASP79 3.0 16.4 1.0 CD2 I:HIS77 3.1 12.9 1.0 CE1 I:HIS73 3.1 15.6 1.0 CE1 I:HIS77 3.2 14.9 1.0 CG I:HIS73 3.3 15.5 1.0 OD2 I:ASP79 3.3 17.8 1.0 CB I:HIS73 3.7 14.3 1.0 C07 I:23J302 3.9 37.4 0.9 NE2 I:HIS83 3.9 19.9 1.0 O I:HOH681 4.2 20.0 1.0 CD2 I:HIS83 4.2 19.5 1.0 CG I:HIS77 4.3 14.3 1.0 NE2 I:HIS73 4.3 15.3 1.0 ND1 I:HIS77 4.3 14.9 1.0 O08 I:23J302 4.3 37.4 0.9 CD2 I:HIS73 4.4 12.4 1.0 CB I:ASP79 4.4 15.1 1.0 CA I:HIS73 4.6 11.8 1.0 CE1 I:HIS83 4.6 21.3 1.0 NE2 I:HIS212 4.7 22.0 1.0 CA I:ASP79 4.9 14.8 1.0 C05 I:23J302 5.0 36.9 0.9

Manganese binding site 10 out of 12 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn301 b:18.6 occ:1.00 O10 J:23J302 2.0 37.1 0.8 O11 J:23J302 2.1 37.3 0.8 OD1 J:ASP79 2.1 17.4 1.0 C09 J:23J302 2.2 38.1 0.8 ND1 J:HIS73 2.2 16.0 1.0 NE2 J:HIS77 2.2 17.6 1.0 O J:HOH433 2.2 26.7 1.0 CD2 J:HIS77 3.0 13.9 1.0 CE1 J:HIS73 3.1 18.6 1.0 CG J:ASP79 3.1 17.1 1.0 CG J:HIS73 3.3 16.1 1.0 CE1 J:HIS77 3.3 18.4 1.0 OD2 J:ASP79 3.4 19.1 1.0 C07 J:23J302 3.6 38.7 0.8 CB J:HIS73 3.7 15.6 1.0 NE2 J:HIS83 3.9 22.3 1.0 O08 J:23J302 4.0 40.1 0.8 CD2 J:HIS83 4.2 20.8 1.0 NE2 J:HIS73 4.2 17.2 1.0 CG J:HIS77 4.3 16.3 1.0 O J:HOH658 4.3 28.0 1.0 CD2 J:HIS73 4.4 15.4 1.0 ND1 J:HIS77 4.4 16.5 1.0 CB J:ASP79 4.4 15.3 1.0 CA J:HIS73 4.5 14.4 1.0 CE1 J:HIS83 4.6 23.1 1.0 NE2 J:HIS212 4.6 26.9 1.0 C05 J:23J302 4.7 35.9 0.8 C06 J:23J302 4.7 34.8 0.8 CA J:ASP79 4.9 16.9 1.0

K.Bjerregaard-Andersen, T.Sommer, J.K.Jensen, B.Jochimsen, M.Etzerodt, J.P.Morth. A Proton Wire and Water Channel Revealed in the Crystal Structure of Isatin Hydrolase. J.Biol.Chem. V. 289 21351 2014.
ISSN: ISSN 0021-9258
PubMed: 24917679
DOI: 10.1074/JBC.M114.568824