Manganese in PDB 1w4a: P4 Protein From PHI12 in Complex with Ampcpp and Mn

The structure of P4 Protein From PHI12 in Complex with Ampcpp and Mn, PDB code: 1w4a 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)	30.00 / 2.40
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	105.600, 129.700, 159.300, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 18.9

The binding sites of Manganese atom in the P4 Protein From PHI12 in Complex with Ampcpp and Mn (pdb code 1w4a). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the P4 Protein From PHI12 in Complex with Ampcpp and Mn, PDB code: 1w4a:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the P4 Protein From PHI12 in Complex with Ampcpp and Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of P4 Protein From PHI12 in Complex with Ampcpp and Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:34.7 occ:1.00 C3A A:APC700 2.1 55.6 1.0 OG1 A:THR137 2.3 14.7 1.0 O A:HOH2200 2.6 31.6 1.0 O3G A:APC700 2.6 54.7 1.0 O3B A:APC700 2.9 60.2 1.0 PG A:APC700 3.1 50.0 1.0 PB A:APC700 3.2 42.7 1.0 CB A:THR137 3.4 10.5 1.0 PA A:APC700 3.5 38.9 1.0 O1A A:APC700 3.6 57.4 1.0 O1G A:APC700 3.7 71.8 1.0 O2B A:APC700 3.9 63.2 1.0 OD1 A:ASP189 4.0 33.1 1.0 N A:THR137 4.1 9.9 1.0 O A:HOH2199 4.1 16.4 1.0 O A:HOH2129 4.2 17.3 1.0 OE2 A:GLU160 4.2 48.9 1.0 CA A:THR137 4.2 11.8 1.0 O1B A:APC700 4.3 58.0 1.0 O2A A:APC700 4.3 53.2 1.0 NZ A:LYS192 4.4 83.6 1.0 CG2 A:THR137 4.6 17.2 1.0 O5' A:APC700 4.6 40.4 1.0 OD2 A:ASP189 4.6 30.5 1.0 O2G A:APC700 4.6 57.9 1.0 CG A:ASP189 4.8 31.6 1.0 CE A:LYS192 4.9 84.5 1.0 C5' A:APC700 5.0 52.4 1.0 OD1 A:ASN234 5.0 86.6 1.0

Manganese binding site 2 out of 3 in the P4 Protein From PHI12 in Complex with Ampcpp and Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of P4 Protein From PHI12 in Complex with Ampcpp and Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn701 b:37.4 occ:1.00 C3A B:APC700 2.1 56.8 1.0 OG1 B:THR137 2.5 11.3 1.0 O3B B:APC700 2.8 58.8 1.0 O3G B:APC700 2.9 54.3 1.0 PB B:APC700 3.0 45.5 1.0 PG B:APC700 3.3 58.3 1.0 CB B:THR137 3.5 8.8 1.0 O2B B:APC700 3.6 63.2 1.0 PA B:APC700 3.7 53.9 1.0 O1G B:APC700 3.9 78.4 1.0 O1A B:APC700 3.9 65.8 1.0 N B:THR137 3.9 14.6 1.0 OD1 B:ASP189 3.9 35.2 1.0 O B:HOH2193 4.1 20.8 1.0 OE2 B:GLU160 4.2 41.2 1.0 CA B:THR137 4.2 12.3 1.0 O B:HOH2118 4.2 21.8 1.0 O1B B:APC700 4.3 47.1 1.0 NZ B:LYS192 4.4 79.6 1.0 OD2 B:ASP189 4.5 30.9 1.0 O2A B:APC700 4.5 59.6 1.0 O5' B:APC700 4.6 47.3 1.0 CG B:ASP189 4.6 29.9 1.0 CG2 B:THR137 4.7 16.8 1.0 O2G B:APC700 4.8 64.7 1.0 CB B:LYS136 4.9 20.9 1.0 C B:LYS136 4.9 16.3 1.0 CE B:LYS192 4.9 79.0 1.0 C5' B:APC700 5.0 49.8 1.0

Manganese binding site 3 out of 3 in the P4 Protein From PHI12 in Complex with Ampcpp and Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of P4 Protein From PHI12 in Complex with Ampcpp and Mn within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn701 b:35.8 occ:1.00 C3A C:APC700 2.1 52.5 1.0 OG1 C:THR137 2.4 20.0 1.0 O C:HOH2202 2.4 23.4 1.0 O C:HOH2203 2.5 38.5 1.0 O3G C:APC700 2.7 50.0 1.0 O3B C:APC700 2.8 49.1 1.0 PB C:APC700 3.1 35.7 1.0 PG C:APC700 3.1 38.4 1.0 PA C:APC700 3.5 26.3 1.0 CB C:THR137 3.6 7.4 1.0 O1A C:APC700 3.7 56.2 1.0 O2B C:APC700 3.8 59.2 1.0 O1G C:APC700 3.8 65.5 1.0 OD1 C:ASP189 4.0 31.9 1.0 N C:THR137 4.0 7.1 1.0 O1B C:APC700 4.2 52.3 1.0 O C:HOH2199 4.2 22.6 1.0 CA C:THR137 4.3 11.9 1.0 O2A C:APC700 4.3 57.9 1.0 O C:HOH2119 4.3 15.7 1.0 NZ C:LYS192 4.4 79.4 1.0 OE2 C:GLU160 4.5 39.7 1.0 O2G C:APC700 4.6 56.2 1.0 OD2 C:ASP189 4.6 25.8 1.0 O5' C:APC700 4.6 36.5 1.0 CG2 C:THR137 4.7 17.2 1.0 CG C:ASP189 4.8 32.0 1.0 CE C:LYS192 4.8 79.5 1.0 OD1 C:ASN234 4.9 79.5 1.0 C5' C:APC700 5.0 47.8 1.0 NH2 B:ARG272 5.0 16.7 1.0 CB C:LYS136 5.0 15.5 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