Magnesium in PDB 1ytu: Structural Basis For 5'-End-Specific Recognition of the Guide Rna Strand By the A. Fulgidus Piwi Protein

The structure of Structural Basis For 5'-End-Specific Recognition of the Guide Rna Strand By the A. Fulgidus Piwi Protein, PDB code: 1ytu was solved by J.B.Ma, Y.R.Yuan, G.Meister, Y.Pei, T.Tuschl, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	238.747, 238.747, 52.042, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 26.6

The binding sites of Magnesium atom in the Structural Basis For 5'-End-Specific Recognition of the Guide Rna Strand By the A. Fulgidus Piwi Protein (pdb code 1ytu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structural Basis For 5'-End-Specific Recognition of the Guide Rna Strand By the A. Fulgidus Piwi Protein, PDB code: 1ytu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structural Basis For 5'-End-Specific Recognition of the Guide Rna Strand By the A. Fulgidus Piwi Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis For 5'-End-Specific Recognition of the Guide Rna Strand By the A. Fulgidus Piwi Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg428 b:48.7 occ:1.00 OP1 C:A3 1.9 58.5 1.0 OP3 C:A1 2.0 49.6 1.0 O A:LEU427 2.1 51.6 1.0 OE1 A:GLN159 2.2 48.6 1.0 O C:HOH57 2.2 52.1 1.0 OXT A:LEU427 2.3 50.9 1.0 C A:LEU427 2.6 51.4 1.0 CD A:GLN159 3.2 49.5 1.0 P C:A1 3.4 56.3 1.0 P C:A3 3.4 59.7 1.0 OP1 C:A1 3.7 49.3 1.0 NE2 A:GLN159 3.7 50.5 1.0 C5' C:A1 4.0 58.8 1.0 NZ A:LYS163 4.0 47.5 1.0 O3' C:G2 4.0 57.3 1.0 O5' C:A1 4.1 55.5 1.0 CA A:LEU427 4.2 51.1 1.0 NH2 A:ARG380 4.2 64.8 1.0 O5' C:A3 4.2 61.7 1.0 NE2 A:GLN137 4.3 55.3 1.0 OP2 C:A3 4.3 59.9 1.0 OP2 C:A1 4.5 56.3 1.0 CG A:GLN159 4.5 44.8 1.0 NE A:ARG380 4.6 60.5 1.0 OE1 A:GLN137 4.8 53.9 1.0 CB A:LEU427 4.8 50.3 1.0 CE A:LYS163 4.9 49.1 1.0 CZ A:ARG380 4.9 63.7 1.0

Magnesium binding site 2 out of 2 in the Structural Basis For 5'-End-Specific Recognition of the Guide Rna Strand By the A. Fulgidus Piwi Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis For 5'-End-Specific Recognition of the Guide Rna Strand By the A. Fulgidus Piwi Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg428 b:31.4 occ:1.00 OP3 E:A1 1.9 50.4 1.0 OE1 B:GLN159 2.0 47.4 1.0 O E:HOH17 2.1 28.7 1.0 OXT B:LEU427 2.1 49.1 1.0 OP1 E:A3 2.1 44.0 1.0 O B:LEU427 2.2 47.5 1.0 C B:LEU427 2.5 47.9 1.0 CD B:GLN159 3.1 49.3 1.0 P E:A1 3.2 50.8 1.0 OP1 E:A1 3.4 48.1 1.0 NE2 B:GLN159 3.5 50.0 1.0 P E:A3 3.6 49.2 1.0 NZ B:LYS163 3.8 46.1 1.0 C5' E:A1 3.9 47.4 1.0 O5' E:A1 4.0 46.6 1.0 NH2 B:ARG380 4.0 48.9 1.0 CA B:LEU427 4.0 47.2 1.0 O3' E:G2 4.1 49.0 1.0 NE B:ARG380 4.2 52.5 1.0 OP2 E:A1 4.3 51.7 1.0 NE2 B:GLN137 4.4 43.3 1.0 CE B:LYS163 4.4 50.0 1.0 CG B:GLN159 4.4 48.4 1.0 O5' E:A3 4.5 53.4 1.0 OP2 E:A3 4.5 52.3 1.0 CZ B:ARG380 4.6 52.0 1.0 OE1 B:GLN137 4.7 47.4 1.0 CB B:LEU427 4.7 45.8 1.0 N B:LEU427 4.9 48.7 1.0 CD B:GLN137 5.0 46.8 1.0

J.B.Ma, Y.R.Yuan, G.Meister, Y.Pei, T.Tuschl, D.J.Patel. Structural Basis For 5'-End-Specific Recognition of Guide Rna By the A. Fulgidus Piwi Protein. Nature V. 434 666 2005.
ISSN: ISSN 0028-0836
PubMed: 15800629
DOI: 10.1038/NATURE03514