Manganese in PDB 3dw9: Sgrai with Cognate Dna and Manganese Bound

All present enzymatic activity of Sgrai with Cognate Dna and Manganese Bound:
3.1.21.4;

The structure of Sgrai with Cognate Dna and Manganese Bound, PDB code: 3dw9 was solved by P.W.Dunten, N.C.Horton, E.J.Little, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.62 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.261, 117.101, 63.702, 90.00, 112.96, 90.00
R / Rfree (%)	17.4 / 24

The binding sites of Manganese atom in the Sgrai with Cognate Dna and Manganese Bound (pdb code 3dw9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Sgrai with Cognate Dna and Manganese Bound, PDB code: 3dw9:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Sgrai with Cognate Dna and Manganese Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Sgrai with Cognate Dna and Manganese Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn340 b:34.4 occ:1.00 O A:PHE241 2.1 35.2 1.0 O A:HOH365 2.2 34.9 1.0 O A:HOH347 2.2 26.0 1.0 O A:HOH348 2.2 22.2 1.0 OD2 A:ASP188 2.2 34.9 1.0 OP1 F:DC8 2.3 34.8 1.0 CG A:ASP188 3.1 36.3 1.0 OD1 A:ASP188 3.3 38.3 1.0 C A:PHE241 3.3 33.8 1.0 P F:DC8 3.3 34.0 1.0 N A:PHE241 3.8 34.5 1.0 O5' F:DC8 3.9 33.8 1.0 OP2 F:DC8 3.9 33.6 1.0 CA A:PHE241 4.0 34.4 1.0 O A:HOH359 4.0 29.3 1.0 C5' F:DC8 4.1 31.4 1.0 OE2 A:GLU103 4.2 42.8 1.0 O A:HOH342 4.2 27.0 1.0 CB A:PHE241 4.3 33.7 1.0 O A:HOH346 4.3 36.5 1.0 N A:LYS242 4.4 32.4 1.0 OP2 F:DC9 4.4 32.1 1.0 CB A:ASP188 4.4 36.5 1.0 O3' F:DA7 4.5 34.1 1.0 CG A:LYS242 4.6 32.5 1.0 C A:ALA240 4.7 34.3 1.0 CA A:LYS242 4.7 31.9 1.0 CA A:ALA240 5.0 34.0 1.0

Manganese binding site 2 out of 4 in the Sgrai with Cognate Dna and Manganese Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Sgrai with Cognate Dna and Manganese Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn341 b:34.2 occ:0.30 OE1 A:GLU103 2.0 44.9 1.0 O A:LEU150 2.1 34.5 1.0 OD1 A:ASN149 2.3 45.8 1.0 O A:HOH345 2.5 48.0 1.0 O A:ASP188 2.5 36.7 1.0 C A:LEU150 3.2 35.8 1.0 CD A:GLU103 3.2 40.0 1.0 N A:LEU150 3.4 37.1 1.0 CG A:ASN149 3.5 41.2 1.0 C A:ASP188 3.5 36.2 1.0 CA A:ASP188 3.7 36.0 1.0 O A:HOH346 3.7 36.5 1.0 CA A:LEU150 3.8 36.5 1.0 OE2 A:GLU103 4.0 42.8 1.0 CB A:ASP188 4.0 36.5 1.0 C A:ASN149 4.0 38.4 1.0 ND2 A:ASN149 4.2 39.4 1.0 CG A:GLU103 4.2 40.0 1.0 N A:PRO151 4.3 35.9 1.0 CA A:ASN149 4.4 39.5 1.0 CB A:LEU150 4.5 35.9 1.0 CB A:ASN149 4.6 40.5 1.0 CA A:PRO151 4.6 35.4 1.0 O A:ASN149 4.7 37.9 1.0 N A:LEU189 4.7 36.0 1.0 CG A:ASP188 4.9 36.3 1.0 C A:PRO151 4.9 34.6 1.0

Manganese binding site 3 out of 4 in the Sgrai with Cognate Dna and Manganese Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Sgrai with Cognate Dna and Manganese Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn340 b:32.1 occ:1.00 OD1 B:ASP188 2.1 36.8 1.0 O B:PHE241 2.1 31.2 1.0 OP1 E:DC8 2.1 26.3 1.0 O E:HOH38 2.2 23.9 1.0 O B:HOH347 2.3 23.1 1.0 O B:HOH357 2.5 26.0 1.0 CG B:ASP188 3.0 34.5 1.0 OD2 B:ASP188 3.3 37.2 1.0 P E:DC8 3.3 31.0 1.0 C B:PHE241 3.3 29.7 1.0 N B:PHE241 3.7 30.3 1.0 O5' E:DC8 3.8 30.3 1.0 C5' E:DC8 3.8 27.5 1.0 OP2 E:DC8 3.9 31.1 1.0 O E:HOH21 3.9 42.2 1.0 CA B:PHE241 4.0 29.6 1.0 OE1 B:GLU103 4.0 29.6 1.0 O B:HOH344 4.1 31.3 1.0 O E:HOH20 4.2 30.3 1.0 CB B:PHE241 4.3 28.6 1.0 CB B:ASP188 4.4 34.1 1.0 N B:LYS242 4.4 30.4 1.0 OP2 E:DC9 4.5 26.0 1.0 O3' E:DA7 4.5 31.7 1.0 CG B:LYS242 4.5 28.5 1.0 C B:ALA240 4.6 29.7 1.0 CA B:LYS242 4.8 29.5 1.0 CD B:GLU103 4.9 28.6 1.0 CA B:ALA240 5.0 29.5 1.0

Manganese binding site 4 out of 4 in the Sgrai with Cognate Dna and Manganese Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Sgrai with Cognate Dna and Manganese Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn341 b:36.1 occ:0.40 OE2 B:GLU103 2.1 31.7 1.0 O B:LEU150 2.1 36.8 1.0 OD1 B:ASN149 2.4 45.5 1.0 O B:ASP188 2.4 35.0 1.0 O B:HOH345 2.5 50.0 1.0 O B:HOH375 2.6 23.2 0.4 C B:LEU150 3.2 35.3 1.0 C B:ASP188 3.3 34.8 1.0 N B:LEU150 3.3 35.3 1.0 CD B:GLU103 3.3 28.6 1.0 CA B:ASP188 3.5 34.2 1.0 CG B:ASN149 3.6 38.1 1.0 O E:HOH22 3.7 57.4 1.0 O E:HOH21 3.8 42.2 1.0 CA B:LEU150 3.8 35.3 1.0 CB B:ASP188 3.8 34.1 1.0 OE1 B:GLU103 4.1 29.6 1.0 C B:ASN149 4.1 34.5 1.0 O B:HOH455 4.1 34.3 0.6 CG B:GLU103 4.3 32.6 1.0 ND2 B:ASN149 4.4 36.8 1.0 N B:PRO151 4.4 34.8 1.0 CB B:LEU150 4.4 34.7 1.0 CA B:ASN149 4.5 34.5 1.0 N B:LEU189 4.5 36.2 1.0 CG B:ASP188 4.6 34.5 1.0 CB B:ASN149 4.7 35.9 1.0 O B:PRO187 4.7 32.9 1.0 CA B:PRO151 4.7 35.1 1.0 N B:ASP188 4.8 33.0 1.0 OD2 B:ASP188 4.8 37.2 1.0 O B:ASN149 5.0 34.5 1.0 C B:PRO151 5.0 35.4 1.0

P.W.Dunten, E.J.Little, M.T.Gregory, V.M.Manohar, M.Dalton, D.Hough, J.Bitinaite, N.C.Horton. The Structure of Sgrai Bound to Dna; Recognition of An 8 Base Pair Target. Nucleic Acids Res. V. 36 5405 2008.
ISSN: ISSN 0305-1048
PubMed: 18701646
DOI: 10.1093/NAR/GKN510