Lead in PDB 2ex3: Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein

All present enzymatic activity of Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein:
2.7.7.7;

The structure of Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein, PDB code: 2ex3 was solved by S.Kamtekar, A.J.Berman, J.Wang, M.De Vega, L.Blanco, M.Salas, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.85 / 3.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	304.933, 220.281, 217.165, 90.00, 45.40, 90.00
R / Rfree (%)	20 / 22.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Lead atom in the Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein (pdb code 2ex3). This binding sites where shown within 5.0 Angstroms radius around Lead atom.
In total 16 binding sites of Lead where determined in the Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein, PDB code: 2ex3:
Jump to Lead binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Lead binding site 1 out of 16 in the Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 1 of Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb701 b:0.1 occ:0.60 OD1 A:ASP169 2.6 0.4 1.0 CG A:ASP169 3.3 0.7 1.0 OD2 A:ASP169 3.4 0.4 1.0 PB A:PB702 3.8 1.0 0.4 CE A:LYS131 4.6 0.8 1.0 NZ A:LYS131 4.7 0.0 1.0 CB A:ASP169 4.7 99.4 1.0 OD1 A:ASP145 4.7 0.6 1.0 CG1 A:VAL130 4.8 90.8 1.0

Lead binding site 2 out of 16 in the Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 2 of Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb702 b:1.0 occ:0.40 OD2 A:ASP169 3.0 0.4 1.0 OE2 A:GLU14 3.2 0.8 1.0 OH A:TYR148 3.4 0.9 1.0 OD1 A:ASP145 3.5 0.6 1.0 PB A:PB701 3.8 0.1 0.6 CD1 A:ILE146 3.9 0.6 1.0 CG A:ASP169 4.0 0.7 1.0 CD A:GLU14 4.1 0.3 1.0 OD1 A:ASP169 4.3 0.4 1.0 OE1 A:GLU14 4.5 1.0 1.0 CG1 A:ILE146 4.5 0.5 1.0 CG A:ASP145 4.6 0.9 1.0 CZ A:TYR148 4.7 0.5 1.0 CB A:ILE146 4.8 0.6 1.0 CB A:TYR165 4.9 89.2 1.0 N A:ILE146 4.9 0.5 1.0

Lead binding site 3 out of 16 in the Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 3 of Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb703 b:0.4 occ:0.40 OE2 A:GLU221 2.9 0.1 1.0 OE1 A:GLU221 3.2 0.4 1.0 CD A:GLU221 3.4 0.2 1.0 CG2 I:VAL276 4.3 96.0 1.0 CG1 A:VAL270 4.7 85.0 1.0 CG A:GLU221 4.9 0.9 1.0

Lead binding site 4 out of 16 in the Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 4 of Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Pb704 b:0.4 occ:0.40 OD1 C:ASP169 2.5 0.6 1.0 OD2 C:ASP169 3.0 0.9 1.0 CG C:ASP169 3.1 0.2 1.0 PB C:PB705 3.8 0.4 0.4 CB C:ASP169 4.6 0.9 1.0 OD1 C:ASP145 4.7 0.1 1.0 CE C:LYS131 4.8 0.6 1.0 CD2 C:TYR165 4.9 92.5 1.0 O C:TYR165 4.9 94.6 1.0

Lead binding site 5 out of 16 in the Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 5 of Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Pb705 b:0.4 occ:0.40 OD2 C:ASP169 3.1 0.9 1.0 OE2 C:GLU14 3.1 0.3 1.0 CG C:ASP169 3.5 0.2 1.0 OD1 C:ASP169 3.7 0.6 1.0 PB C:PB704 3.8 0.4 0.4 CD1 C:ILE146 3.9 0.7 1.0 OH C:TYR148 4.0 0.0 1.0 CD C:GLU14 4.1 0.3 1.0 CB C:ASP169 4.4 0.9 1.0 OD1 C:ASP145 4.5 0.1 1.0 OE1 C:GLU14 4.5 0.9 1.0 CG1 C:ILE146 4.7 0.7 1.0 O C:TYR165 4.9 94.6 1.0

Lead binding site 6 out of 16 in the Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 6 of Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Pb706 b:0.2 occ:0.40 OE2 C:GLU221 3.8 0.1 1.0 CG1 C:VAL270 3.9 87.0 1.0 OE1 C:GLU221 4.1 0.1 1.0 OE2 C:GLU272 4.3 0.1 1.0 CD C:GLU221 4.4 0.0 1.0 CD1 G:ILE269 4.5 99.6 1.0 OG C:SER349 4.5 95.6 1.0

Lead binding site 7 out of 16 in the Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 7 of Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein within 5.0Å range: probe atom residue distance (Å) B Occ E:Pb707 b:0.1 occ:0.40 OE2 E:GLU14 2.9 0.5 1.0 OD2 E:ASP169 3.2 0.7 1.0 CG E:ASP169 3.4 0.5 1.0 OD1 E:ASP169 3.4 0.8 1.0 CD E:GLU14 4.0 0.8 1.0 CD1 E:ILE146 4.0 0.9 1.0 OH E:TYR148 4.0 0.8 1.0 PB E:PB708 4.1 0.9 0.6 CB E:ASP169 4.4 0.2 1.0 OE1 E:GLU14 4.6 1.0 1.0 CG1 E:ILE146 4.8 0.7 1.0 O E:TYR165 4.8 97.7 1.0 CG E:GLU14 4.9 97.5 1.0

Lead binding site 8 out of 16 in the Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 8 of Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein within 5.0Å range: probe atom residue distance (Å) B Occ E:Pb708 b:0.9 occ:0.60 OD1 E:ASP169 2.6 0.8 1.0 OD2 E:ASP169 3.1 0.7 1.0 CG E:ASP169 3.2 0.5 1.0 PB E:PB707 4.1 0.1 0.4 CE E:LYS131 4.3 0.1 1.0 NZ E:LYS131 4.6 0.9 1.0 OD1 E:ASP145 4.7 0.2 1.0 CB E:ASP169 4.7 0.2 1.0 CG1 E:VAL130 4.7 95.2 1.0

Lead binding site 9 out of 16 in the Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 9 of Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein within 5.0Å range: probe atom residue distance (Å) B Occ E:Pb709 b:0.2 occ:0.40 OE2 E:GLU221 4.0 0.9 1.0 OE2 E:GLU272 4.0 0.2 1.0 CD1 A:ILE269 4.3 0.2 1.0 OG E:SER349 4.4 94.0 1.0 OE1 E:GLU221 4.5 0.4 1.0 CG1 E:VAL270 4.5 81.5 1.0 CD E:GLU221 4.6 0.1 1.0 CB E:SER349 4.9 88.4 1.0 CE1 A:TYR281 4.9 89.4 1.0

Lead binding site 10 out of 16 in the Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 10 of Bacteriophage PHI29 Dna Polymerase Bound to Terminal Protein within 5.0Å range: probe atom residue distance (Å) B Occ G:Pb710 b:0.5 occ:0.60 OD1 G:ASP169 2.6 0.8 1.0 CG G:ASP169 3.4 0.8 1.0 OD2 G:ASP169 3.5 0.6 1.0 PB G:PB711 3.8 0.2 0.4 CE G:LYS131 4.5 0.3 1.0 OD1 G:ASP145 4.5 0.4 1.0 CD2 G:TYR165 4.7 88.9 1.0 CB G:ASP169 4.7 99.5 1.0 O G:TYR165 4.9 94.6 1.0 O G:GLY144 5.0 0.5 1.0 CG G:ASP145 5.0 0.1 1.0 CG G:LYS131 5.0 0.4 1.0

S.Kamtekar, A.J.Berman, J.Wang, J.M.Lazaro, M.De Vega, L.Blanco, M.Salas, T.A.Steitz. The PHI29 Dna Polymerase:Protein-Primer Structure Suggests A Model For the Initiation to Elongation Transition Embo J. V. 25 1335 2006.
ISSN: ISSN 0261-4189
PubMed: 16511564
DOI: 10.1038/SJ.EMBOJ.7601027