Manganese in PDB 5xsi: The Catalytic Domain of Gdpp

The structure of The Catalytic Domain of Gdpp, PDB code: 5xsi was solved by F.Wang, L.Gu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.42 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.085, 117.091, 127.445, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 22.6

The binding sites of Manganese atom in the The Catalytic Domain of Gdpp (pdb code 5xsi). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The Catalytic Domain of Gdpp, PDB code: 5xsi:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the The Catalytic Domain of Gdpp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Catalytic Domain of Gdpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn700 b:31.0 occ:1.00 O A:HOH861 2.2 25.3 1.0 OD2 A:ASP349 2.2 28.8 1.0 OD2 A:ASP497 2.3 28.4 1.0 NE2 A:HIS442 2.3 29.5 1.0 OD1 A:ASP418 2.4 23.4 1.0 O A:HOH832 2.7 38.7 1.0 CG A:ASP418 3.1 26.6 1.0 OD2 A:ASP418 3.1 26.6 1.0 CG A:ASP349 3.2 26.9 1.0 CE1 A:HIS442 3.3 29.8 1.0 CG A:ASP497 3.3 29.4 1.0 CD2 A:HIS442 3.3 28.3 1.0 CB A:ASP349 3.5 26.4 1.0 MN A:MN701 3.6 50.9 1.0 OD1 A:ASP497 3.7 29.0 1.0 CE1 A:HIS443 4.0 41.0 1.0 N A:THR465 4.2 20.5 1.0 OG1 A:THR465 4.2 25.6 1.0 NE2 A:HIS443 4.2 47.4 1.0 OD1 A:ASP349 4.3 24.6 1.0 ND1 A:HIS442 4.4 30.6 1.0 CG A:HIS442 4.5 32.5 1.0 CA A:SER464 4.5 27.3 1.0 CB A:ASP418 4.5 24.8 1.0 CB A:ASP497 4.7 28.2 1.0 CB A:SER464 4.8 23.6 1.0 O A:HOH975 4.8 48.0 1.0 C A:SER464 4.9 25.9 1.0 CA A:ASP349 4.9 26.9 1.0 CB A:THR465 5.0 25.6 1.0

Manganese binding site 2 out of 4 in the The Catalytic Domain of Gdpp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Catalytic Domain of Gdpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:50.9 occ:1.00 O A:HOH861 2.3 25.3 1.0 OD2 A:ASP418 2.3 26.6 1.0 OD2 A:ASP347 2.4 34.0 1.0 NE2 A:HIS343 2.7 32.6 1.0 O A:HOH975 2.8 48.0 1.0 OD1 A:ASP347 2.9 30.3 1.0 CG A:ASP347 3.0 31.4 1.0 CG A:ASP418 3.4 26.6 1.0 CD2 A:HIS343 3.5 35.6 1.0 MN A:MN700 3.6 31.0 1.0 O A:HOH832 3.6 38.7 1.0 CE1 A:HIS343 3.7 32.2 1.0 OD1 A:ASP418 3.9 23.4 1.0 O A:ASP418 4.4 28.5 1.0 CB A:ASP347 4.5 22.7 1.0 CB A:ASP418 4.6 24.8 1.0 N A:ALA350 4.6 23.5 1.0 CG A:HIS343 4.7 35.6 1.0 CB A:ALA350 4.7 27.0 1.0 CB A:ASP349 4.7 26.4 1.0 ND1 A:HIS343 4.7 32.1 1.0 CE1 A:HIS443 4.8 41.0 1.0 O A:HOH940 4.9 43.7 1.0 OD1 A:ASP497 4.9 29.0 1.0 OD2 A:ASP349 4.9 28.8 1.0 NE2 A:HIS443 5.0 47.4 1.0

Manganese binding site 3 out of 4 in the The Catalytic Domain of Gdpp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Catalytic Domain of Gdpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn700 b:31.4 occ:1.00 O B:HOH824 2.1 28.7 1.0 OD2 B:ASP349 2.2 25.9 1.0 OD1 B:ASP418 2.3 29.3 1.0 OD2 B:ASP497 2.4 28.9 1.0 NE2 B:HIS442 2.4 29.9 1.0 OD2 B:ASP418 2.9 28.8 1.0 O B:HOH890 3.0 38.7 1.0 CG B:ASP418 3.0 29.1 1.0 CG B:ASP349 3.2 26.0 1.0 CG B:ASP497 3.3 30.8 1.0 CD2 B:HIS442 3.3 28.8 1.0 CE1 B:HIS442 3.4 32.1 1.0 CB B:ASP349 3.5 22.4 1.0 MN B:MN701 3.6 50.7 1.0 OD1 B:ASP497 3.6 24.5 1.0 CE1 B:HIS443 4.1 42.8 1.0 N B:THR465 4.3 26.3 1.0 OD1 B:ASP349 4.3 23.9 1.0 OG1 B:THR465 4.4 25.1 1.0 CA B:SER464 4.4 26.2 1.0 NE2 B:HIS443 4.4 42.1 1.0 CB B:ASP418 4.5 25.3 1.0 CG B:HIS442 4.5 32.2 1.0 ND1 B:HIS442 4.5 31.4 1.0 CB B:ASP497 4.7 26.9 1.0 CB B:SER464 4.7 26.8 1.0 C B:SER464 4.9 29.7 1.0 CA B:ASP349 4.9 25.0 1.0 OD1 B:ASP347 5.0 33.4 1.0

Manganese binding site 4 out of 4 in the The Catalytic Domain of Gdpp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Catalytic Domain of Gdpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn701 b:50.7 occ:1.00 OD2 B:ASP347 2.3 39.0 1.0 O B:HOH824 2.4 28.7 1.0 OD2 B:ASP418 2.4 28.8 1.0 NE2 B:HIS343 2.6 32.4 1.0 OD1 B:ASP347 2.7 33.4 1.0 O B:HOH925 2.7 41.2 1.0 CG B:ASP347 2.8 31.6 1.0 CD2 B:HIS343 3.4 33.0 1.0 CG B:ASP418 3.5 29.1 1.0 CE1 B:HIS343 3.5 37.0 1.0 MN B:MN700 3.6 31.4 1.0 O B:HOH890 3.7 38.7 1.0 OD1 B:ASP418 4.0 29.3 1.0 CB B:ASP347 4.3 29.2 1.0 O B:HOH820 4.5 43.5 1.0 N B:ALA350 4.6 23.5 1.0 CG B:HIS343 4.6 32.3 1.0 ND1 B:HIS343 4.6 33.8 1.0 O B:ASP418 4.6 28.6 1.0 CB B:ASP349 4.7 22.4 1.0 CB B:ASP418 4.7 25.3 1.0 CB B:ALA350 4.7 25.8 1.0 O B:HOH901 4.7 35.7 1.0 OD1 B:ASP497 4.7 24.5 1.0 N B:ASP347 4.8 30.2 1.0 OD2 B:ASP349 5.0 25.9 1.0

F.Wang, Q.He, K.Su, T.Wei, S.Xu, L.Gu. Structural and Biochemical Characterization of the Catalytic Domains of Gdpp Reveals A Unified Hydrolysis Mechanism For the Dhh/DHHA1 Phosphodiesterase Biochem. J. V. 475 191 2018.
ISSN: ESSN 1470-8728
PubMed: 29203646
DOI: 10.1042/BCJ20170739