Manganese in PDB 2w42: The Structure of A Piwi Protein From Archaeoglobus Fulgidus Complexed with A 16NT Dna Duplex.

The structure of The Structure of A Piwi Protein From Archaeoglobus Fulgidus Complexed with A 16NT Dna Duplex., PDB code: 2w42 was solved by J.S.Parker, S.M.Roe, D.Barford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	98.06 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.838, 61.384, 103.540, 75.80, 75.86, 79.47
R / Rfree (%)	20.5 / 24.3

The binding sites of Manganese atom in the The Structure of A Piwi Protein From Archaeoglobus Fulgidus Complexed with A 16NT Dna Duplex. (pdb code 2w42). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the The Structure of A Piwi Protein From Archaeoglobus Fulgidus Complexed with A 16NT Dna Duplex., PDB code: 2w42:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the The Structure of A Piwi Protein From Archaeoglobus Fulgidus Complexed with A 16NT Dna Duplex.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Structure of A Piwi Protein From Archaeoglobus Fulgidus Complexed with A 16NT Dna Duplex. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1428 b:14.6 occ:1.00 OP3 P:DT1 2.0 19.5 1.0 OE1 A:GLN159 2.0 14.5 1.0 OP1 P:DC3 2.1 19.4 1.0 O A:HOH2244 2.2 18.8 1.0 OXT A:LEU427 2.2 13.6 1.0 O A:LEU427 2.5 11.4 1.0 C A:LEU427 2.7 12.7 1.0 CD A:GLN159 3.0 18.4 1.0 P P:DT1 3.3 17.5 1.0 NE2 A:GLN159 3.4 24.3 1.0 P P:DC3 3.5 23.1 1.0 OP1 P:DT1 3.6 19.4 1.0 O3' P:DT2 3.9 20.2 1.0 NZ A:LYS163 3.9 14.7 1.0 NH2 A:ARG380 4.2 21.0 1.0 CA A:LEU427 4.2 12.4 1.0 NE A:ARG380 4.2 21.6 1.0 OP2 P:DC3 4.2 26.7 1.0 O5' P:DT1 4.2 18.7 1.0 O A:HOH2243 4.3 17.4 1.0 C5' P:DT1 4.3 20.1 1.0 OP2 P:DT1 4.3 12.4 1.0 CG A:GLN159 4.4 19.3 1.0 NE2 A:GLN137 4.5 15.3 1.0 O A:HOH2242 4.5 31.3 1.0 CE A:LYS163 4.5 14.1 1.0 O P:HOH2002 4.6 29.0 1.0 O5' P:DC3 4.6 21.3 1.0 OE1 A:GLN137 4.6 20.7 1.0 CZ A:ARG380 4.7 20.1 1.0 CB A:LEU427 4.8 11.9 1.0 CG A:ARG380 4.9 18.3 1.0 C5' P:DC3 4.9 29.0 1.0 CB A:GLN159 5.0 16.9 1.0

Manganese binding site 2 out of 2 in the The Structure of A Piwi Protein From Archaeoglobus Fulgidus Complexed with A 16NT Dna Duplex.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Structure of A Piwi Protein From Archaeoglobus Fulgidus Complexed with A 16NT Dna Duplex. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1428 b:23.3 occ:1.00 OXT B:LEU427 1.9 20.8 1.0 OP3 R:DT1 2.1 26.1 1.0 OP1 R:DC3 2.1 29.8 1.0 O B:HOH2143 2.2 24.9 1.0 OE1 B:GLN159 2.2 21.6 1.0 O B:LEU427 2.5 22.2 1.0 C B:LEU427 2.6 21.6 1.0 CD B:GLN159 3.2 24.9 1.0 P R:DT1 3.4 25.5 1.0 P R:DC3 3.4 28.9 1.0 OP1 R:DT1 3.6 22.8 1.0 NE2 B:GLN159 3.6 24.9 1.0 NZ B:LYS163 3.9 23.6 1.0 O3' R:DT2 4.0 28.4 1.0 CA B:LEU427 4.1 20.9 1.0 NE B:ARG380 4.1 24.3 1.0 OP2 R:DC3 4.2 31.0 1.0 NH2 B:ARG380 4.3 27.1 1.0 O5' R:DT1 4.3 26.6 1.0 OP2 R:DT1 4.3 24.2 1.0 O B:HOH2141 4.3 35.2 1.0 C5' R:DT1 4.4 32.4 1.0 CE B:LYS163 4.5 24.5 1.0 O B:HOH2142 4.5 37.1 1.0 NE2 B:GLN137 4.5 24.7 1.0 O5' R:DC3 4.5 28.8 1.0 CG B:GLN159 4.6 21.3 1.0 O R:HOH2005 4.6 36.7 1.0 CZ B:ARG380 4.7 27.3 1.0 OE1 B:GLN137 4.7 21.7 1.0 CB B:LEU427 4.7 20.4 1.0 CG B:ARG380 4.7 21.0 1.0 C5' R:DC3 4.8 32.4 1.0

J.S.Parker, E.A.Parizotto, M.Wang, S.M.Roe, D.Barford. Enhancement of the Seed-Target Recognition Step in Rna Silencing By A Piwi-Mid Domain Protein Mol.Cell V. 33 204 2009.
ISSN: ISSN 1097-2765
PubMed: 19187762
DOI: 10.1016/J.MOLCEL.2008.12.012