Manganese in PDB 2wc9: Crystal Structure of the G2P (Large Terminase) Nuclease Domain From the Bacteriophage SPP1 with Bound Mn

The structure of Crystal Structure of the G2P (Large Terminase) Nuclease Domain From the Bacteriophage SPP1 with Bound Mn, PDB code: 2wc9 was solved by C.Smits, M.Chechik, O.V.Kovalevskiy, M.B.Shevtsov, A.W.Foster, J.C.Alonso, A.A.Antson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.60 / 2.50
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.710, 69.710, 73.801, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 25.9

The binding sites of Manganese atom in the Crystal Structure of the G2P (Large Terminase) Nuclease Domain From the Bacteriophage SPP1 with Bound Mn (pdb code 2wc9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of the G2P (Large Terminase) Nuclease Domain From the Bacteriophage SPP1 with Bound Mn, PDB code: 2wc9:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of the G2P (Large Terminase) Nuclease Domain From the Bacteriophage SPP1 with Bound Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the G2P (Large Terminase) Nuclease Domain From the Bacteriophage SPP1 with Bound Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1413 b:44.9 occ:0.84 ND1 A:HIS400 2.5 35.8 1.0 OD1 A:ASP266 2.8 47.9 1.0 CG A:ASP266 3.3 43.0 1.0 CE1 A:HIS400 3.4 36.1 1.0 CG A:HIS400 3.5 36.4 1.0 OD2 A:ASP266 3.7 46.8 1.0 CB A:HIS400 3.8 35.4 1.0 CA A:HIS400 4.0 35.7 1.0 MN A:MN1414 4.0 43.4 0.2 CB A:ASP266 4.2 39.9 1.0 OD2 A:ASP403 4.4 36.5 1.0 O A:PRO273 4.4 36.4 1.0 CB A:ASP272 4.5 37.8 1.0 NE2 A:HIS400 4.6 36.5 1.0 OD1 A:ASN399 4.7 35.5 1.0 CD2 A:HIS400 4.7 35.1 1.0 N A:HIS400 4.8 36.0 1.0 N A:GLY268 4.8 38.9 1.0 CA A:GLY268 4.9 39.0 1.0 CG A:ASP272 5.0 38.9 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the G2P (Large Terminase) Nuclease Domain From the Bacteriophage SPP1 with Bound Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the G2P (Large Terminase) Nuclease Domain From the Bacteriophage SPP1 with Bound Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1414 b:43.4 occ:0.17 OD2 A:ASP266 1.9 46.8 1.0 OD1 A:ASP266 2.2 47.9 1.0 CG A:ASP266 2.3 43.0 1.0 OD2 A:ASP321 2.8 39.8 1.0 CG A:ASP321 3.2 37.1 1.0 CB A:ASP266 3.7 39.9 1.0 OH A:TYR407 3.8 33.0 1.0 OD1 A:ASP321 3.8 35.6 1.0 CB A:ASP321 3.9 36.0 1.0 N A:PHE267 4.0 39.0 1.0 MN A:MN1413 4.0 44.9 0.8 CA A:ASP266 4.2 39.4 1.0 C A:ASP266 4.5 39.0 1.0 CE2 A:TYR407 4.6 31.6 1.0 N A:GLY268 4.6 38.9 1.0 CZ A:TYR407 4.7 31.5 1.0 OD2 A:ASP403 4.8 36.5 1.0 OG A:SER323 5.0 31.9 1.0

C.Smits, M.Chechik, O.V.Kovalevskiy, M.B.Shevtsov, A.W.Foster, J.C.Alonso, A.A.Antson. Structural Basis For the Nuclease Activity of A Bacteriophage Large Terminase. Embo Rep. V. 10 592 2009.
ISSN: ISSN 1469-221X
PubMed: 19444313
DOI: 10.1038/EMBOR.2009.53