Manganese in PDB 4yvz: Structure of Thermotoga Maritima Disa in Complex with 3'-Datp/MN2+

All present enzymatic activity of Structure of Thermotoga Maritima Disa in Complex with 3'-Datp/MN2+:
2.7.7.85;

The structure of Structure of Thermotoga Maritima Disa in Complex with 3'-Datp/MN2+, PDB code: 4yvz was solved by M.Mueller, T.Deimling, K.-P.Hopfner, G.Witte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	168.79 / 2.50
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	107.490, 107.490, 168.790, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 21.9

The binding sites of Manganese atom in the Structure of Thermotoga Maritima Disa in Complex with 3'-Datp/MN2+ (pdb code 4yvz). 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 Thermotoga Maritima Disa in Complex with 3'-Datp/MN2+, PDB code: 4yvz:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Structure of Thermotoga Maritima Disa in Complex with 3'-Datp/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 Thermotoga Maritima Disa in Complex with 3'-Datp/MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:45.1 occ:1.00 O3G A:3AT403 2.1 44.0 1.0 O A:HOH519 2.2 40.1 1.0 OD2 A:ASP75 2.2 42.4 1.0 O B:HOH557 2.3 48.2 1.0 O1A A:3AT403 2.3 32.6 1.0 O2B A:3AT403 2.3 32.7 1.0 CG A:ASP75 3.1 32.6 1.0 PG A:3AT403 3.2 32.1 1.0 OD1 A:ASP75 3.3 33.2 1.0 PB A:3AT403 3.3 32.8 1.0 O3B A:3AT403 3.5 32.5 1.0 PA A:3AT403 3.6 32.8 1.0 O1G A:3AT403 3.7 32.1 1.0 O3A A:3AT403 3.8 44.3 1.0 O B:HOH511 4.2 31.9 1.0 NH1 B:ARG130 4.3 41.7 1.0 O2A A:3AT403 4.3 33.1 1.0 CB A:ASP75 4.4 41.4 1.0 O2G A:3AT403 4.4 32.0 1.0 O A:HOH547 4.5 62.8 1.0 NH1 B:ARG128 4.5 88.6 1.0 O1B A:3AT403 4.7 37.5 1.0 O5' A:3AT403 4.8 32.8 1.0 C5' A:3AT403 5.0 32.5 1.0

Manganese binding site 2 out of 4 in the Structure of Thermotoga Maritima Disa in Complex with 3'-Datp/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 Thermotoga Maritima Disa in Complex with 3'-Datp/MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:0.2 occ:1.00 O A:GLU229 2.3 74.7 1.0 OD1 A:ASP232 2.5 64.2 1.0 OD2 A:ASP233 2.8 76.7 1.0 OD2 A:ASP232 3.1 61.5 1.0 CG A:ASP232 3.1 60.3 1.0 C A:GLU229 3.5 71.2 1.0 CG A:ASP233 4.0 73.0 1.0 CA A:GLU229 4.3 67.2 1.0 N A:ASP230 4.4 66.7 1.0 CA A:ASP230 4.4 68.0 1.0 N A:ASP233 4.6 40.8 1.0 CB A:ASP232 4.6 47.9 1.0 CB A:ASP233 4.8 54.5 1.0 C A:ASP230 4.9 57.1 1.0 CB A:GLU229 4.9 68.7 1.0 OD1 A:ASP233 4.9 84.6 1.0 N A:ASP232 4.9 43.5 1.0 OD1 A:ASP230 5.0 86.2 1.0

Manganese binding site 3 out of 4 in the Structure of Thermotoga Maritima Disa in Complex with 3'-Datp/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 Thermotoga Maritima Disa in Complex with 3'-Datp/MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:43.1 occ:1.00 O1G B:3AT401 2.1 50.9 1.0 O1B B:3AT401 2.2 33.6 1.0 O2A B:3AT401 2.2 32.8 1.0 O B:HOH513 2.2 32.5 1.0 OD2 B:ASP75 2.3 43.8 1.0 O B:HOH549 2.5 36.8 1.0 CG B:ASP75 3.0 41.0 1.0 OD1 B:ASP75 3.1 32.9 1.0 PB B:3AT401 3.2 33.3 1.0 PG B:3AT401 3.2 32.6 1.0 PA B:3AT401 3.4 33.1 1.0 O3B B:3AT401 3.4 32.9 1.0 O3A B:3AT401 3.6 33.4 1.0 O2G B:3AT401 3.8 40.7 1.0 O1A B:3AT401 4.0 33.4 1.0 CB B:ASP75 4.2 38.3 1.0 O3G B:3AT401 4.4 32.4 1.0 O2B B:3AT401 4.5 33.7 1.0 O A:HOH520 4.5 48.1 1.0 O5' B:3AT401 4.6 34.2 1.0 NH1 A:ARG130 4.7 38.0 1.0 C5' B:3AT401 4.9 32.7 1.0

Manganese binding site 4 out of 4 in the Structure of Thermotoga Maritima Disa in Complex with 3'-Datp/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 Thermotoga Maritima Disa in Complex with 3'-Datp/MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:90.0 occ:1.00 O B:GLU229 2.4 68.5 1.0 OD1 B:ASP233 2.5 91.1 1.0 OD2 B:ASP232 2.7 61.4 1.0 OD1 B:ASP232 2.7 81.3 1.0 CG B:ASP232 3.0 62.6 1.0 CG B:ASP233 3.5 83.4 1.0 C B:GLU229 3.6 66.2 1.0 OD2 B:ASP233 4.1 95.3 1.0 CA B:ASP230 4.2 57.8 1.0 N B:ASP233 4.3 45.0 1.0 N B:ASP230 4.4 59.6 1.0 CB B:ASP232 4.5 43.2 1.0 CA B:GLU229 4.5 63.8 1.0 CB B:ASP233 4.6 60.7 1.0 C B:ASP230 4.7 45.8 1.0 N B:ASP232 4.7 38.9 1.0 OD1 B:ASP230 4.8 73.8 1.0 CG B:GLU229 4.9 83.1 1.0 CA B:ASP232 5.0 45.7 1.0 CA B:ASP233 5.0 47.5 1.0

M.Muller, T.Deimling, K.P.Hopfner, G.Witte. Structural Analysis of the Diadenylate Cyclase Reaction of Dna-Integrity Scanning Protein A (Disa) and Its Inhibition By 3'-Datp. Biochem.J. V. 469 367 2015.
ISSN: ESSN 1470-8728
PubMed: 26014055
DOI: 10.1042/BJ20150373