Manganese in PDB 5xt3: The Catalytic Domain of Gdpp with C-Di-Gmp

The structure of The Catalytic Domain of Gdpp with C-Di-Gmp, PDB code: 5xt3 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)	43.51 / 2.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.374, 117.042, 130.152, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 26.2

The binding sites of Manganese atom in the The Catalytic Domain of Gdpp with C-Di-Gmp (pdb code 5xt3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the The Catalytic Domain of Gdpp with C-Di-Gmp, PDB code: 5xt3:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the The Catalytic Domain of Gdpp with C-Di-Gmp


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-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:71.2 occ:1.00 OD2 A:ASP349 2.2 50.5 1.0 O A:HOH833 2.4 60.0 1.0 OD2 A:ASP497 2.4 64.8 1.0 OD1 A:ASP418 2.5 53.3 1.0 NE2 A:HIS442 2.8 60.3 1.0 O A:HOH866 2.9 64.3 1.0 OD2 A:ASP418 3.0 58.8 1.0 CG A:ASP418 3.1 56.6 1.0 CG A:ASP349 3.2 54.1 1.0 CD2 A:HIS442 3.5 60.1 1.0 CG A:ASP497 3.5 57.0 1.0 CB A:ASP349 3.5 51.7 1.0 MN A:MN702 3.6 95.1 1.0 CE1 A:HIS442 3.9 62.8 1.0 OD1 A:ASP497 3.9 58.3 1.0 CE1 A:HIS443 3.9 73.6 1.0 NE2 A:HIS443 4.3 71.3 1.0 OD1 A:ASP349 4.3 55.9 1.0 N A:THR465 4.5 52.8 1.0 OG1 A:THR465 4.6 57.2 1.0 CA A:SER464 4.6 53.2 1.0 CB A:ASP418 4.6 60.4 1.0 CB A:SER464 4.7 52.8 1.0 CG A:HIS442 4.8 64.9 1.0 CB A:ASP497 4.8 48.9 1.0 ND1 A:HIS442 4.9 59.7 1.0 CA A:ASP349 5.0 47.9 1.0

Manganese binding site 2 out of 3 in the The Catalytic Domain of Gdpp with C-Di-Gmp


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-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:95.1 occ:1.00 NE2 A:HIS343 2.6 56.7 1.0 O A:HOH833 2.7 60.0 1.0 OD1 A:ASP347 2.8 65.0 1.0 OD2 A:ASP418 2.8 58.8 1.0 CE1 A:HIS343 3.3 59.3 1.0 OD2 A:ASP347 3.4 57.7 1.0 CG A:ASP347 3.5 58.2 1.0 CD2 A:HIS343 3.5 63.4 1.0 MN A:MN701 3.6 71.2 1.0 CG A:ASP418 3.7 56.6 1.0 O A:HOH866 4.0 64.3 1.0 OD1 A:ASP418 4.1 53.3 1.0 ND1 A:HIS343 4.3 61.2 1.0 O A:ASP418 4.4 62.7 1.0 CG A:HIS343 4.4 61.2 1.0 CB A:ASP418 4.8 60.4 1.0 CB A:ASP347 4.9 53.1 1.0 CB A:ASP349 4.9 51.7 1.0

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


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-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn701 b:59.2 occ:1.00 OD2 B:ASP386 2.3 45.3 1.0 OD1 B:ASP455 2.4 46.1 1.0 O B:HOH809 2.4 50.9 1.0 NE2 B:HIS479 2.5 47.4 1.0 OD2 B:ASP534 2.5 54.4 1.0 O B:HOH849 2.7 60.9 1.0 OD2 B:ASP455 2.8 48.8 1.0 CG B:ASP455 2.9 46.6 1.0 CG B:ASP386 3.3 46.1 1.0 CG B:ASP534 3.4 54.1 1.0 CD2 B:HIS479 3.4 45.0 1.0 CE1 B:HIS479 3.4 47.9 1.0 OD1 B:ASP534 3.6 52.0 1.0 CB B:ASP386 3.8 43.6 1.0 NE2 B:HIS480 4.1 60.5 1.0 CB B:ASP455 4.4 48.9 1.0 OD1 B:ASP386 4.4 46.0 1.0 N B:THR502 4.5 39.5 1.0 CA B:SER501 4.5 44.3 1.0 ND1 B:HIS479 4.5 49.2 1.0 CG B:HIS479 4.6 48.2 1.0 OG1 B:THR502 4.7 42.3 1.0 CB B:ASP534 4.8 50.8 1.0 OD2 B:ASP384 4.8 55.2 1.0 CE1 B:HIS480 4.8 61.2 1.0 CB B:SER501 4.9 45.8 1.0 OD1 B:ASP384 5.0 55.2 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