Magnesium in PDB 1w4b: P4 Protein From PHI12 in Complex with Product (Ampcpp Mg 22C)

The structure of P4 Protein From PHI12 in Complex with Product (Ampcpp Mg 22C), PDB code: 1w4b 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 / 2.30
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	105.300, 129.300, 158.900, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 19.6

The binding sites of Magnesium atom in the P4 Protein From PHI12 in Complex with Product (Ampcpp Mg 22C) (pdb code 1w4b). 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 PHI12 in Complex with Product (Ampcpp Mg 22C), PDB code: 1w4b:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the P4 Protein From PHI12 in Complex with Product (Ampcpp Mg 22C)


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 PHI12 in Complex with Product (Ampcpp Mg 22C) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:56.9 occ:1.00 OG1 A:THR137 2.7 20.0 1.0 OG A:SER232 3.0 53.0 1.0 O2A A:ADP700 3.2 0.6 1.0 O3B A:ADP700 3.2 0.9 1.0 OD1 A:ASP189 3.4 31.8 1.0 O2B A:ADP700 3.8 0.7 1.0 N A:THR137 3.9 21.8 1.0 CB A:SER232 4.0 24.7 1.0 CB A:THR137 4.0 18.4 1.0 O A:HOH2132 4.0 39.1 1.0 PB A:ADP700 4.1 0.2 1.0 CA A:THR137 4.2 20.3 1.0 CG A:ASP189 4.3 36.3 1.0 CB A:LYS136 4.3 17.1 1.0 OD2 A:ASP189 4.4 32.4 1.0 PA A:ADP700 4.4 0.7 1.0 O3A A:ADP700 4.5 0.3 1.0 O A:HOH2134 4.6 18.6 1.0 C A:LYS136 4.7 23.2 1.0 CB A:ASN234 4.7 69.5 1.0 OE2 A:GLU160 4.8 34.8 1.0

Magnesium binding site 2 out of 3 in the P4 Protein From PHI12 in Complex with Product (Ampcpp Mg 22C)


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 PHI12 in Complex with Product (Ampcpp Mg 22C) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:57.0 occ:1.00 OG1 B:THR137 2.8 16.5 1.0 OG B:SER232 3.0 47.2 1.0 O3B B:ADP700 3.2 0.6 1.0 O2A B:ADP700 3.2 0.4 1.0 OD1 B:ASP189 3.3 27.8 1.0 O B:HOH2124 3.4 38.7 1.0 O2B B:ADP700 3.8 0.8 1.0 CB B:SER232 4.0 23.4 1.0 N B:THR137 4.0 23.9 1.0 PB B:ADP700 4.0 0.1 1.0 CB B:THR137 4.0 20.4 1.0 CG B:ASP189 4.3 37.0 1.0 CB B:LYS136 4.3 20.4 1.0 CA B:THR137 4.3 21.4 1.0 OD2 B:ASP189 4.4 37.0 1.0 PA B:ADP700 4.4 0.2 1.0 O3A B:ADP700 4.5 0.0 1.0 CB B:ASN234 4.7 70.6 1.0 OE2 B:GLU160 4.7 27.3 1.0 C B:LYS136 4.7 24.3 1.0 O B:HOH2127 4.7 20.9 1.0

Magnesium binding site 3 out of 3 in the P4 Protein From PHI12 in Complex with Product (Ampcpp Mg 22C)


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 PHI12 in Complex with Product (Ampcpp Mg 22C) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg701 b:57.6 occ:1.00 OG1 C:THR137 2.8 20.5 1.0 OG C:SER232 3.0 50.2 1.0 O3B C:ADP700 3.1 0.2 1.0 O2A C:ADP700 3.1 0.5 1.0 OD1 C:ASP189 3.4 28.4 1.0 O C:HOH2112 3.5 34.2 1.0 O2B C:ADP700 3.8 0.8 1.0 N C:THR137 4.0 21.2 1.0 PB C:ADP700 4.0 0.4 1.0 CB C:SER232 4.0 26.4 1.0 CB C:THR137 4.0 19.2 1.0 CB C:LYS136 4.3 18.3 1.0 CA C:THR137 4.3 21.0 1.0 CG C:ASP189 4.3 37.0 1.0 PA C:ADP700 4.3 0.2 1.0 OD2 C:ASP189 4.4 36.8 1.0 O3A C:ADP700 4.5 0.2 1.0 CB C:ASN234 4.6 70.6 1.0 C C:LYS136 4.7 23.6 1.0 OE2 C:GLU160 4.8 32.7 1.0 O C:HOH2116 4.8 19.6 1.0 CG C:ASN234 5.0 77.6 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