Manganese in PDB 5o7f: Structure of the Inactive T.Maritima Pde (TM1595) D80N D154N Mutant with Gmp and MN2+

The structure of Structure of the Inactive T.Maritima Pde (TM1595) D80N D154N Mutant with Gmp and MN2+, PDB code: 5o7f was solved by G.Witte, D.Drexler, M.Mueller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.38 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.900, 105.620, 134.460, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 20.6

The binding sites of Manganese atom in the Structure of the Inactive T.Maritima Pde (TM1595) D80N D154N Mutant with Gmp and MN2+ (pdb code 5o7f). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of the Inactive T.Maritima Pde (TM1595) D80N D154N Mutant with Gmp and MN2+, PDB code: 5o7f:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Structure of the Inactive T.Maritima Pde (TM1595) D80N D154N Mutant with Gmp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of the Inactive T.Maritima Pde (TM1595) D80N D154N Mutant with Gmp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:23.8 occ:0.87 O A:HOH653 2.0 27.3 1.0 ND2 A:ASN80 2.1 26.3 1.0 NE2 A:HIS19 2.2 27.6 1.0 O A:HOH652 2.3 29.9 1.0 OD2 A:ASP23 2.4 31.8 1.0 OD1 A:ASP23 2.4 29.2 1.0 CG A:ASP23 2.7 33.4 1.0 CD2 A:HIS19 3.1 26.8 1.0 CG A:ASN80 3.1 31.1 1.0 CE1 A:HIS19 3.2 28.0 1.0 OD1 A:ASN80 3.5 27.1 1.0 O A:HOH537 3.7 39.1 1.0 O A:HOH648 3.7 30.5 1.0 N A:CYS26 3.9 21.3 1.0 CB A:CYS26 4.2 27.3 1.0 CB A:ASP23 4.2 29.1 1.0 O A:ASN80 4.3 31.5 1.0 CG A:HIS19 4.3 28.3 1.0 ND1 A:HIS19 4.3 28.4 1.0 CB A:ASP25 4.3 23.5 1.0 O A:HOH663 4.4 47.7 1.0 CB A:ASN80 4.4 26.4 1.0 CA A:CYS26 4.5 24.8 1.0 C A:ASP25 4.6 22.4 1.0 N A:ASP23 4.8 27.8 1.0 O3' A:5GP401 4.8 45.2 1.0 CA A:ASP25 4.9 20.7 1.0 MN A:MN403 4.9 29.1 1.0 NH2 A:ARG86 5.0 30.0 1.0 N A:ASP25 5.0 20.8 1.0 CA A:ASP23 5.0 28.9 1.0

Manganese binding site 2 out of 4 in the Structure of the Inactive T.Maritima Pde (TM1595) D80N D154N Mutant with Gmp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the Inactive T.Maritima Pde (TM1595) D80N D154N Mutant with Gmp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:29.1 occ:1.00 O A:HOH648 2.1 30.5 1.0 NE2 A:HIS105 2.1 29.9 1.0 O2' A:5GP401 2.1 45.1 1.0 O3' A:5GP401 2.2 45.2 1.0 NE2 A:HIS286 2.3 33.3 1.0 O A:HOH652 2.7 29.9 1.0 C2' A:5GP401 3.0 45.5 1.0 CD2 A:HIS105 3.0 23.9 1.0 C3' A:5GP401 3.1 45.6 1.0 CE1 A:HIS286 3.2 39.0 1.0 CE1 A:HIS105 3.2 27.2 1.0 CD2 A:HIS286 3.3 36.8 1.0 O A:HOH653 3.9 27.3 1.0 C4' A:5GP401 4.0 46.0 1.0 CG A:HIS105 4.2 27.1 1.0 O A:HOH537 4.2 39.1 1.0 O A:HOH527 4.2 35.2 1.0 ND1 A:HIS105 4.2 31.3 1.0 C1' A:5GP401 4.3 46.0 1.0 ND1 A:HIS286 4.3 37.1 1.0 CG A:HIS286 4.4 35.9 1.0 CE1 A:HIS104 4.5 24.9 1.0 O A:HOH704 4.5 61.6 1.0 NE2 A:HIS104 4.6 26.5 1.0 O4' A:5GP401 4.7 46.2 1.0 CA A:GLY285 4.7 29.2 1.0 MN A:MN402 4.9 23.8 0.9

Manganese binding site 3 out of 4 in the Structure of the Inactive T.Maritima Pde (TM1595) D80N D154N Mutant with Gmp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of the Inactive T.Maritima Pde (TM1595) D80N D154N Mutant with Gmp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:25.7 occ:0.91 ND2 B:ASN80 2.1 29.8 1.0 O B:HOH675 2.2 30.9 1.0 OD1 B:ASP23 2.2 29.4 1.0 O B:HOH687 2.2 29.8 1.0 NE2 B:HIS19 2.3 26.2 1.0 OD2 B:ASP23 2.3 31.2 1.0 CG B:ASP23 2.6 34.7 1.0 CG B:ASN80 3.2 30.2 1.0 CD2 B:HIS19 3.2 27.0 1.0 CE1 B:HIS19 3.3 27.8 1.0 OD1 B:ASN80 3.5 30.3 1.0 O B:HOH667 3.8 31.3 1.0 N B:CYS26 4.0 27.6 1.0 O B:HOH548 4.0 45.0 1.0 CB B:CYS26 4.1 28.2 1.0 CB B:ASP23 4.1 28.3 1.0 CB B:ASP25 4.2 24.3 1.0 O B:ASN80 4.3 31.2 1.0 CG B:HIS19 4.4 28.0 1.0 ND1 B:HIS19 4.4 29.8 1.0 CA B:CYS26 4.5 26.1 1.0 CB B:ASN80 4.5 26.8 1.0 O B:HOH521 4.5 43.3 1.0 N B:ASP23 4.6 28.0 1.0 O B:HOH698 4.6 48.5 1.0 C B:ASP25 4.6 25.7 1.0 MN B:MN403 4.7 26.4 0.8 O3' B:5GP401 4.8 51.3 1.0 CA B:ASP25 4.8 23.0 1.0 CA B:ASP23 4.8 26.4 1.0 N B:ASP25 4.9 25.1 1.0

Manganese binding site 4 out of 4 in the Structure of the Inactive T.Maritima Pde (TM1595) D80N D154N Mutant with Gmp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of the Inactive T.Maritima Pde (TM1595) D80N D154N Mutant with Gmp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:26.4 occ:0.84 O2' B:5GP401 2.1 52.0 1.0 O B:HOH667 2.1 31.3 1.0 NE2 B:HIS105 2.2 32.6 1.0 NE2 B:HIS286 2.2 37.5 1.0 O3' B:5GP401 2.2 51.3 1.0 O B:HOH687 2.5 29.8 1.0 C2' B:5GP401 3.0 52.3 1.0 C3' B:5GP401 3.1 51.9 1.0 CE1 B:HIS286 3.1 37.6 1.0 CD2 B:HIS105 3.1 31.3 1.0 CE1 B:HIS105 3.2 33.0 1.0 CD2 B:HIS286 3.2 35.9 1.0 O B:HOH675 3.7 30.9 1.0 O B:HOH548 3.9 45.0 1.0 C4' B:5GP401 4.0 52.0 1.0 O B:HOH521 4.2 43.3 1.0 ND1 B:HIS286 4.2 36.3 1.0 O B:HOH542 4.2 37.1 1.0 C1' B:5GP401 4.3 52.8 1.0 CG B:HIS105 4.3 29.4 1.0 ND1 B:HIS105 4.3 29.7 1.0 CG B:HIS286 4.3 35.5 1.0 CE1 B:HIS104 4.6 25.5 1.0 O4' B:5GP401 4.7 52.6 1.0 CA B:GLY285 4.7 29.0 1.0 MN B:MN402 4.7 25.7 0.9 NE2 B:HIS104 4.8 27.3 1.0

D.J.Drexler, M.Muller, C.A.Rojas-Cordova, A.M.Bandera, G.Witte. Structural and Biophysical Analysis of the Soluble Dhh/DHHA1-Type Phosphodiesterase TM1595 From Thermotoga Maritima. Structure V. 25 1887 2017.
ISSN: ISSN 1878-4186
PubMed: 29107484
DOI: 10.1016/J.STR.2017.10.001