Magnesium in PDB 1w46: P4 Protein From Bacteriophage PHI12 in Complex with Adp and Mg

The structure of P4 Protein From Bacteriophage PHI12 in Complex with Adp and Mg, PDB code: 1w46 was solved by E.J.Mancini, D.E.Kainov, J.M.Grimes, R.Tuma, D.H.Bamford, D.I.Stuart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.70
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	105.000, 128.400, 158.500, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 25.3

The binding sites of Magnesium atom in the P4 Protein From Bacteriophage PHI12 in Complex with Adp and Mg (pdb code 1w46). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the P4 Protein From Bacteriophage PHI12 in Complex with Adp and Mg, PDB code: 1w46:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the P4 Protein From Bacteriophage PHI12 in Complex with Adp and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of P4 Protein From Bacteriophage PHI12 in Complex with Adp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:79.6 occ:1.00 OG1 A:THR137 2.7 25.7 1.0 O1B A:ADP700 2.8 95.8 1.0 OG A:SER232 3.1 56.1 1.0 O2A A:ADP700 3.2 79.2 1.0 O A:HOH2069 3.2 39.4 1.0 OD1 A:ASP189 3.6 29.9 1.0 PB A:ADP700 3.9 93.7 1.0 O3B A:ADP700 3.9 91.1 1.0 CB A:THR137 4.0 31.6 1.0 CB A:SER232 4.1 36.9 1.0 O A:HOH2082 4.2 16.9 1.0 N A:THR137 4.2 23.2 1.0 PA A:ADP700 4.4 78.5 1.0 CA A:THR137 4.4 28.1 1.0 O3A A:ADP700 4.5 89.0 1.0 O A:HOH2111 4.6 26.2 1.0 OE2 A:GLU160 4.6 32.2 1.0 CB A:LYS136 4.7 20.6 1.0 CG A:ASP189 4.8 45.3 1.0 CB A:ASN234 4.9 82.6 1.0 CD A:GLU160 5.0 29.9 1.0 C A:LYS136 5.0 23.5 1.0 CB A:SER190 5.0 44.4 1.0

Magnesium binding site 2 out of 3 in the P4 Protein From Bacteriophage PHI12 in Complex with Adp and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of P4 Protein From Bacteriophage PHI12 in Complex with Adp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:74.7 occ:1.00 OG1 B:THR137 2.7 24.9 1.0 O1B B:ADP700 2.7 96.9 1.0 OG B:SER232 3.1 54.4 1.0 O2A B:ADP700 3.2 85.0 1.0 O B:HOH2075 3.5 39.6 1.0 OD1 B:ASP189 3.6 24.8 1.0 PB B:ADP700 3.8 94.6 1.0 O3B B:ADP700 3.9 90.3 1.0 CB B:THR137 4.0 33.8 1.0 CB B:SER232 4.1 36.7 1.0 N B:THR137 4.2 22.4 1.0 O B:HOH2077 4.3 17.2 1.0 PA B:ADP700 4.4 81.7 1.0 CA B:THR137 4.4 28.5 1.0 O3A B:ADP700 4.4 89.5 1.0 OE2 B:GLU160 4.6 23.6 1.0 CB B:LYS136 4.7 21.8 1.0 CG B:ASP189 4.8 44.4 1.0 CB B:ASN234 4.9 81.9 1.0 C B:LYS136 4.9 22.9 1.0 CD B:GLU160 5.0 28.4 1.0

Magnesium binding site 3 out of 3 in the P4 Protein From Bacteriophage PHI12 in Complex with Adp and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of P4 Protein From Bacteriophage PHI12 in Complex with Adp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg701 b:74.3 occ:1.00 OG1 C:THR137 2.7 31.0 1.0 O1B C:ADP700 2.8 93.9 1.0 OG C:SER232 3.1 52.4 1.0 O2A C:ADP700 3.2 80.0 1.0 OD1 C:ASP189 3.6 32.3 1.0 PB C:ADP700 3.9 90.3 1.0 O3B C:ADP700 3.9 90.3 1.0 CB C:THR137 4.0 32.5 1.0 CB C:SER232 4.1 35.3 1.0 N C:THR137 4.2 22.1 1.0 O C:HOH2069 4.3 16.1 1.0 O C:HOH2108 4.3 26.1 1.0 PA C:ADP700 4.4 78.2 1.0 CA C:THR137 4.4 27.2 1.0 O3A C:ADP700 4.5 88.2 1.0 OE2 C:GLU160 4.6 32.7 1.0 CB C:LYS136 4.7 26.0 1.0 CG C:ASP189 4.8 46.1 1.0 CB C:ASN234 4.9 82.8 1.0 CB C:SER190 5.0 41.5 1.0 CD C:GLU160 5.0 29.2 1.0 C C:LYS136 5.0 24.1 1.0

E.J.Mancini, D.E.Kainov, J.M.Grimes, R.Tuma, D.H.Bamford, D.I.Stuart. Atomic Snapshots of An Rna Packaging Motor Reveal Conformational Changes Linking Atp Hydrolysis to Rna Translocation Cell(Cambridge,Mass.) V. 118 743 2004.
ISSN: ISSN 0092-8674
PubMed: 15369673
DOI: 10.1016/J.CELL.2004.09.007