Manganese in PDB 5xsn: The Catalytic Domain of Gdpp with C-Di-Amp

The structure of The Catalytic Domain of Gdpp with C-Di-Amp, PDB code: 5xsn 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)	43.10 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.620, 117.465, 126.879, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 23.6

The binding sites of Manganese atom in the The Catalytic Domain of Gdpp with C-Di-Amp (pdb code 5xsn). 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 with C-Di-Amp, PDB code: 5xsn:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the The Catalytic Domain of Gdpp with C-Di-Amp


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 with C-Di-Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:46.0 occ:1.00 OD2 A:ASP349 2.1 40.7 1.0 O A:HOH815 2.3 44.4 1.0 NE2 A:HIS442 2.4 39.3 1.0 OD2 A:ASP497 2.4 35.4 1.0 OD1 A:ASP418 2.5 35.1 1.0 O A:HOH855 3.1 44.4 1.0 CG A:ASP349 3.2 37.5 1.0 CG A:ASP418 3.2 37.9 1.0 CD2 A:HIS442 3.3 36.2 1.0 OD2 A:ASP418 3.3 43.9 1.0 CE1 A:HIS442 3.4 36.8 1.0 CG A:ASP497 3.4 38.4 1.0 MN A:MN702 3.5 75.2 1.0 CB A:ASP349 3.5 36.3 1.0 OD1 A:ASP497 3.7 35.0 1.0 NE2 A:HIS443 4.0 54.3 1.0 CE1 A:HIS443 4.0 45.9 1.0 OD1 A:ASP349 4.3 37.0 1.0 OG1 A:THR465 4.3 36.2 1.0 N A:THR465 4.3 32.4 1.0 CG A:HIS442 4.5 38.4 1.0 ND1 A:HIS442 4.5 37.4 1.0 CA A:SER464 4.5 34.4 1.0 CB A:ASP418 4.6 37.9 1.0 CB A:SER464 4.7 33.6 1.0 CB A:ASP497 4.8 31.2 1.0 C A:SER464 5.0 31.8 1.0 CA A:ASP349 5.0 31.0 1.0

Manganese binding site 2 out of 4 in the The Catalytic Domain of Gdpp with C-Di-Amp


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 with C-Di-Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:75.2 occ:1.00 O A:HOH815 2.4 44.4 1.0 OD2 A:ASP418 2.4 43.9 1.0 OD2 A:ASP347 2.5 48.1 1.0 NE2 A:HIS343 2.7 41.8 1.0 OD1 A:ASP347 3.0 44.1 1.0 CG A:ASP347 3.1 43.3 1.0 CG A:ASP418 3.4 37.9 1.0 MN A:MN701 3.5 46.0 1.0 CE1 A:HIS343 3.5 38.2 1.0 CD2 A:HIS343 3.7 42.0 1.0 O A:HOH855 3.7 44.4 1.0 OD1 A:ASP418 3.8 35.1 1.0 CB A:ASP349 4.5 36.3 1.0 CB A:ASP347 4.6 35.1 1.0 O A:ASP418 4.6 33.5 1.0 ND1 A:HIS343 4.7 39.5 1.0 CB A:ASP418 4.7 37.9 1.0 N A:ALA350 4.8 32.2 1.0 CG A:HIS343 4.8 37.1 1.0 OD2 A:ASP349 4.8 40.7 1.0 OD1 A:ASP497 4.8 35.0 1.0 CB A:ALA350 5.0 39.0 1.0

Manganese binding site 3 out of 4 in the The Catalytic Domain of Gdpp with C-Di-Amp


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 with C-Di-Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn701 b:46.4 occ:1.00 OD2 B:ASP349 2.3 32.2 1.0 OD1 B:ASP418 2.3 34.0 1.0 OD2 B:ASP497 2.4 37.9 1.0 NE2 B:HIS442 2.5 38.8 1.0 OD2 B:ASP418 2.9 37.6 1.0 CG B:ASP418 2.9 36.4 1.0 CG B:ASP349 3.3 34.2 1.0 CD2 B:HIS442 3.4 33.1 1.0 CG B:ASP497 3.4 39.4 1.0 CE1 B:HIS442 3.5 39.2 1.0 MN B:MN702 3.6 80.1 1.0 CB B:ASP349 3.7 31.8 1.0 OD1 B:ASP497 3.8 35.9 1.0 NE2 B:HIS443 4.3 55.5 1.0 CE1 B:HIS443 4.3 48.3 1.0 N B:THR465 4.4 32.9 1.0 OG1 B:THR465 4.4 31.8 1.0 CB B:ASP418 4.4 31.0 1.0 CA B:SER464 4.4 31.1 1.0 OD1 B:ASP349 4.4 32.3 1.0 ND1 B:HIS442 4.6 33.1 1.0 CG B:HIS442 4.6 32.7 1.0 CB B:SER464 4.7 31.8 1.0 CB B:ASP497 4.8 34.4 1.0 C B:SER464 4.9 35.8 1.0

Manganese binding site 4 out of 4 in the The Catalytic Domain of Gdpp with C-Di-Amp


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 with C-Di-Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn702 b:80.1 occ:1.00 OD2 B:ASP347 2.5 47.8 1.0 OD2 B:ASP418 2.5 37.6 1.0 OD1 B:ASP347 2.5 40.4 1.0 NE2 B:HIS343 2.7 42.0 1.0 CG B:ASP347 2.8 40.7 1.0 CD2 B:HIS343 3.5 39.4 1.0 MN B:MN701 3.6 46.4 1.0 CG B:ASP418 3.6 36.4 1.0 CE1 B:HIS343 3.6 40.9 1.0 OD1 B:ASP418 4.2 34.0 1.0 CB B:ASP347 4.3 37.6 1.0 N B:ALA350 4.6 35.7 1.0 CB B:ASP349 4.6 31.8 1.0 CG B:HIS343 4.7 41.4 1.0 ND1 B:HIS343 4.7 46.3 1.0 CB B:ASP418 4.7 31.0 1.0 OD1 B:ASP497 4.7 35.9 1.0 CB B:ALA350 4.8 35.5 1.0 N B:ASP347 4.8 39.1 1.0 O B:HOH856 4.8 37.8 1.0 O B:ASP418 4.8 38.3 1.0 OD2 B:ASP349 4.9 32.2 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