Iodine in PDB 7jq7: The Phi-28 GP11 Dna Packaging Motor

The structure of The Phi-28 GP11 Dna Packaging Motor, PDB code: 7jq7 was solved by M.C.Morais, M.A.White, E.Dill, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.69 / 2.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	112.2, 112.2, 354.2, 90, 90, 90
R / Rfree (%)	23.5 / 28.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 130; Page 14, Binding sites: 131 - 131;

Binding sites:

The binding sites of Iodine atom in the The Phi-28 GP11 Dna Packaging Motor (pdb code 7jq7). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 131 binding sites of Iodine where determined in the The Phi-28 GP11 Dna Packaging Motor, PDB code: 7jq7:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 131 in the The Phi-28 GP11 Dna Packaging Motor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of The Phi-28 GP11 Dna Packaging Motor within 5.0Å range: probe atom residue distance (Å) B Occ A:I401 b:35.2 occ:0.48 HA A:ARG179 2.9 83.8 1.0 H A:GLU180 2.9 87.0 1.0 H A:ASP181 3.2 81.0 1.0 HG2 A:ARG179 3.3 76.3 1.0 N A:GLU180 3.7 72.5 1.0 CA A:ARG179 3.8 69.8 1.0 HB3 A:ARG179 3.9 79.4 1.0 N A:ASP181 4.1 67.5 1.0 HB3 A:ASP181 4.1 78.6 1.0 CB A:ARG179 4.1 66.2 1.0 CG A:ARG179 4.1 63.6 1.0 HB2 A:ASP181 4.2 78.6 1.0 O A:LYS178 4.2 82.6 1.0 C A:ARG179 4.3 70.8 1.0 CZ A:ARG179 4.3 55.3 1.0 HB2 A:GLU180 4.4 101.4 1.0 NH1 A:ARG179 4.4 55.2 1.0 HH11 A:ARG179 4.5 66.3 1.0 HH12 A:ARG179 4.5 66.3 1.0 CB A:ASP181 4.5 65.5 1.0 NE A:ARG179 4.6 57.4 1.0 NH2 A:ARG179 4.6 53.3 1.0 CA A:GLU180 4.7 74.3 1.0 HH22 A:ARG179 4.8 63.9 1.0 HG3 A:ARG179 4.8 76.3 1.0 CA A:ASP181 4.9 64.6 1.0 HE A:ARG179 4.9 68.9 1.0 N A:ARG179 4.9 72.0 1.0 C A:GLU180 4.9 69.4 1.0 HG2 A:GLU180 4.9 109.6 1.0 CD A:ARG179 4.9 59.4 1.0 HH21 A:ARG179 4.9 63.9 1.0 CB A:GLU180 5.0 84.5 1.0

Iodine binding site 2 out of 131 in the The Phi-28 GP11 Dna Packaging Motor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of The Phi-28 GP11 Dna Packaging Motor within 5.0Å range: probe atom residue distance (Å) B Occ A:I402 b:53.0 occ:0.66 HA A:GLU340 3.2 43.0 1.0 HG2 A:GLU340 3.4 57.2 1.0 HB2 A:GLN343 3.4 60.5 1.0 HB3 A:GLN343 3.7 60.5 1.0 HG3 A:GLN344 3.8 77.0 1.0 HE21 A:GLN344 3.8 101.7 1.0 HZ1 A:LYS366 3.9 85.6 1.0 HB3 A:GLU340 3.9 49.1 1.0 CB A:GLN343 4.0 50.4 1.0 CA A:GLU340 4.0 35.8 1.0 CG A:GLU340 4.2 47.6 1.0 HG3 A:GLN343 4.2 64.1 1.0 CB A:GLU340 4.3 40.9 1.0 O A:GLU340 4.3 34.5 1.0 HZ3 A:LYS366 4.4 85.6 1.0 NZ A:LYS366 4.5 71.3 1.0 HG2 A:GLN344 4.5 77.0 1.0 NE2 A:GLN344 4.5 84.8 1.0 CG A:GLN344 4.6 64.2 1.0 H A:GLN344 4.6 60.0 1.0 C A:GLU340 4.6 34.5 1.0 HZ2 A:LYS366 4.7 85.6 1.0 CG A:GLN343 4.7 53.4 1.0 HG3 A:GLU340 4.7 57.2 1.0

Iodine binding site 3 out of 131 in the The Phi-28 GP11 Dna Packaging Motor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of The Phi-28 GP11 Dna Packaging Motor within 5.0Å range: probe atom residue distance (Å) B Occ A:I403 b:75.1 occ:0.74 HG1 A:THR206 2.8 86.4 1.0 H A:HIS207 3.0 60.8 1.0 HD2 A:HIS207 3.0 63.6 1.0 HA A:THR206 3.2 78.4 1.0 OG1 A:THR206 3.6 72.0 1.0 HD11 A:ILE259 3.6 40.7 1.0 N A:HIS207 3.8 50.6 1.0 HG21 A:THR261 3.8 48.4 1.0 CD2 A:HIS207 3.8 53.0 1.0 HB2 A:HIS207 4.0 58.9 1.0 CA A:THR206 4.0 65.3 1.0 HG1 A:THR261 4.0 45.0 1.0 HB A:THR206 4.1 83.4 1.0 CB A:THR206 4.1 69.5 1.0 HG23 A:THR261 4.3 48.4 1.0 HH A:TYR204 4.4 33.8 1.0 C A:THR206 4.4 54.0 1.0 CD1 A:ILE259 4.4 33.9 1.0 CG2 A:THR261 4.5 40.4 1.0 CG A:HIS207 4.5 51.0 1.0 CB A:HIS207 4.6 49.1 1.0 HD13 A:ILE259 4.6 40.7 1.0 OG1 A:THR261 4.6 37.5 1.0 HD12 A:ILE259 4.8 40.7 1.0 H A:GLU208 4.8 59.0 1.0 CA A:HIS207 4.8 49.1 1.0 O A:LEU205 4.8 64.4 1.0 NE2 A:HIS207 4.9 51.4 1.0 OH A:TYR204 5.0 28.1 1.0

Iodine binding site 4 out of 131 in the The Phi-28 GP11 Dna Packaging Motor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of The Phi-28 GP11 Dna Packaging Motor within 5.0Å range: probe atom residue distance (Å) B Occ A:I404 b:53.6 occ:0.82 HD2 A:PHE339 3.0 40.6 1.0 HB2 A:LEU367 3.0 79.9 1.0 H A:LEU367 3.2 74.3 1.0 HG3 A:LYS336 3.3 81.0 1.0 HA A:LYS336 3.4 73.0 1.0 HD13 A:LEU331 3.5 88.4 1.0 HD11 A:LEU331 3.5 88.4 1.0 HD12 A:LEU331 3.6 88.4 1.0 CD1 A:LEU331 3.7 73.6 1.0 HZ2 A:LYS336 3.8 78.9 1.0 CD2 A:PHE339 3.8 33.8 1.0 HA A:LYS366 3.9 62.7 1.0 N A:LEU367 3.9 61.9 1.0 HD12 A:LEU367 3.9 84.3 1.0 CB A:LEU367 4.0 66.6 1.0 HE2 A:PHE339 4.0 41.5 1.0 CG A:LYS336 4.2 67.5 1.0 CA A:LYS336 4.3 60.8 1.0 HA A:LYS332 4.3 75.6 1.0 CE2 A:PHE339 4.4 34.6 1.0 HB2 A:LYS336 4.4 78.9 1.0 CA A:LEU367 4.4 66.2 1.0 HB2 A:PHE339 4.5 38.7 1.0 HG A:LEU367 4.5 83.7 1.0 HG2 A:LYS336 4.5 81.0 1.0 CB A:LYS336 4.5 65.8 1.0 HB3 A:LEU367 4.6 79.9 1.0 CG A:LEU367 4.6 69.8 1.0 NZ A:LYS336 4.7 65.7 1.0 CD1 A:LEU367 4.7 70.3 1.0 CA A:LYS366 4.7 52.3 1.0 C A:LYS366 4.7 56.0 1.0 HG3 A:LYS366 4.7 67.7 1.0 O A:LEU367 4.8 72.7 1.0 N A:LYS336 4.8 68.7 1.0 O A:LEU365 4.9 55.4 1.0 CG A:PHE339 4.9 33.7 1.0 HZ3 A:LYS336 5.0 78.9 1.0

Iodine binding site 5 out of 131 in the The Phi-28 GP11 Dna Packaging Motor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of The Phi-28 GP11 Dna Packaging Motor within 5.0Å range: probe atom residue distance (Å) B Occ A:I405 b:51.0 occ:0.72 OE2 A:GLU357 2.8 67.4 1.0 HG2 A:GLU353 3.0 79.7 1.0 HZ1 A:LYS301 3.0 95.8 1.0 CD A:GLU357 3.1 69.5 1.0 OE1 A:GLU357 3.1 71.6 1.0 HG22 A:THR354 3.1 24.2 1.0 HG11 A:VAL299 3.5 30.2 1.0 HA A:THR354 3.6 44.5 1.0 HG23 A:THR354 3.7 24.2 1.0 HE22 A:GLN280 3.8 119.0 1.0 NZ A:LYS301 3.8 79.8 1.0 CG A:GLU353 3.9 66.4 1.0 CG2 A:THR354 3.9 20.2 1.0 OE2 A:GLU353 3.9 71.7 1.0 HG21 A:VAL299 4.0 29.9 1.0 HG3 A:GLU357 4.0 83.5 1.0 HZ2 A:LYS301 4.1 95.8 1.0 HB3 A:GLU353 4.1 71.6 1.0 HZ3 A:LYS301 4.1 95.8 1.0 CG A:GLU357 4.2 69.6 1.0 OE1 A:GLN280 4.2 95.6 1.0 CD A:GLU353 4.3 71.4 1.0 N A:THR354 4.3 42.3 1.0 CA A:THR354 4.3 37.1 1.0 O A:GLU353 4.3 45.5 1.0 C A:GLU353 4.3 46.3 1.0 CG1 A:VAL299 4.3 25.1 1.0 HG12 A:VAL299 4.4 30.2 1.0 HB A:VAL299 4.5 30.0 1.0 HG3 A:GLU353 4.5 79.7 1.0 NE2 A:GLN280 4.5 99.2 1.0 CB A:GLU353 4.5 59.7 1.0 HG21 A:THR354 4.6 24.2 1.0 H A:THR354 4.6 50.8 1.0 HB2 A:GLU357 4.6 78.0 1.0 HE3 A:LYS301 4.7 84.8 1.0 CB A:THR354 4.7 26.0 1.0 CB A:VAL299 4.8 25.0 1.0 CD A:GLN280 4.8 94.3 1.0 CG2 A:VAL299 4.8 24.9 1.0 CE A:LYS301 4.8 70.6 1.0 HG2 A:GLU357 4.9 83.5 1.0 CB A:GLU357 5.0 65.0 1.0

Iodine binding site 6 out of 131 in the The Phi-28 GP11 Dna Packaging Motor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of The Phi-28 GP11 Dna Packaging Motor within 5.0Å range: probe atom residue distance (Å) B Occ A:I406 b:52.3 occ:0.47 HZ3 A:LYS244 2.8 68.5 1.0 H B:ASP219 3.0 61.7 1.0 HB3 B:GLU218 3.0 66.9 1.0 HZ2 A:LYS244 3.2 68.5 1.0 H B:GLU218 3.2 54.8 1.0 HZ1 A:LYS244 3.2 68.5 1.0 NZ A:LYS244 3.3 57.1 1.0 HB3 B:ARG217 3.3 56.6 1.0 HE2 B:TYR220 3.4 53.7 1.0 HB2 B:ASP219 3.7 74.3 1.0 N B:ASP219 3.8 51.4 1.0 N B:GLU218 3.8 45.6 1.0 CB B:GLU218 3.9 55.8 1.0 OD2 B:ASP219 3.9 71.3 1.0 CE2 B:TYR220 4.0 44.7 1.0 HB2 B:GLU218 4.1 66.9 1.0 CG B:ASP219 4.1 68.7 1.0 CB B:ARG217 4.2 47.1 1.0 CA B:GLU218 4.3 51.5 1.0 CB B:ASP219 4.3 61.9 1.0 HH B:TYR220 4.3 57.1 1.0 HD2 B:TYR220 4.4 53.2 1.0 HB2 B:ARG217 4.4 56.6 1.0 OE1 B:GLU218 4.5 62.4 1.0 C B:GLU218 4.5 51.1 1.0 CD2 B:TYR220 4.5 44.4 1.0 HD2 B:ARG217 4.6 53.0 1.0 CA B:ASP219 4.7 53.5 1.0 OD1 B:ASP219 4.7 70.4 1.0 C B:ARG217 4.7 44.5 1.0 CE A:LYS244 4.7 52.4 1.0 CZ B:TYR220 4.7 44.4 1.0 OH B:TYR220 4.8 47.6 1.0 H B:TYR220 4.9 48.2 1.0 CA B:ARG217 5.0 45.1 1.0

Iodine binding site 7 out of 131 in the The Phi-28 GP11 Dna Packaging Motor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of The Phi-28 GP11 Dna Packaging Motor within 5.0Å range: probe atom residue distance (Å) B Occ A:I407 b:68.1 occ:0.82 H A:ASN111 3.0 70.1 1.0 HA A:ILE109 3.1 56.8 1.0 HG3 A:LYS66 3.3 66.5 1.0 H A:ARG110 3.5 62.3 1.0 O A:ALA108 3.7 42.9 1.0 HB2 A:LYS66 3.7 62.5 1.0 N A:ASN111 3.8 58.4 1.0 HG2 A:LYS66 3.8 66.5 1.0 N A:ARG110 3.8 51.9 1.0 CA A:ILE109 3.8 47.4 1.0 HA A:ASN111 3.9 67.7 1.0 CG A:LYS66 3.9 55.5 1.0 HB1 A:ALA108 4.0 46.6 1.0 C A:ILE109 4.0 48.9 1.0 C A:ALA108 4.0 41.4 1.0 N A:ILE109 4.1 45.1 1.0 H A:LYS112 4.3 56.0 1.0 CB A:LYS66 4.3 52.0 1.0 HZ3 A:LYS66 4.4 52.5 1.0 HB3 A:ALA108 4.4 46.6 1.0 CA A:ASN111 4.4 56.4 1.0 CB A:ALA108 4.6 38.8 1.0 H A:ILE109 4.6 54.2 1.0 HA A:ARG110 4.6 67.2 1.0 CA A:ARG110 4.6 56.0 1.0 C A:ARG110 4.7 60.9 1.0 HD22 A:ASN111 4.7 73.3 1.0 O A:ILE109 4.7 46.7 1.0 HB3 A:LYS66 4.8 62.5 1.0 CA A:ALA108 4.9 39.9 1.0 ND2 A:ASN111 5.0 61.1 1.0 N A:LYS112 5.0 46.6 1.0 O A:LYS112 5.0 43.1 1.0

Iodine binding site 8 out of 131 in the The Phi-28 GP11 Dna Packaging Motor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of The Phi-28 GP11 Dna Packaging Motor within 5.0Å range: probe atom residue distance (Å) B Occ A:I408 b:76.5 occ:0.72 HB3 E:PHE238 3.3 48.6 1.0 HG3 A:GLU173 3.3 70.5 1.0 HD3 A:LYS176 3.4 80.8 1.0 HA A:GLU173 3.5 48.3 1.0 HZ2 A:LYS176 3.7 75.2 1.0 HB2 E:PHE238 3.8 48.6 1.0 HG23 E:VAL239 3.9 41.0 1.0 HG22 A:ILE172 3.9 36.5 1.0 CB E:PHE238 4.0 40.5 1.0 HG22 E:VAL239 4.1 41.0 1.0 CG A:GLU173 4.2 58.7 1.0 HA E:VAL239 4.3 44.8 1.0 CA A:GLU173 4.3 40.3 1.0 CD A:LYS176 4.4 67.3 1.0 HB2 A:GLU173 4.4 57.5 1.0 C E:PHE238 4.5 46.4 1.0 CG2 E:VAL239 4.5 34.2 1.0 NZ A:LYS176 4.5 62.7 1.0 O E:PHE238 4.5 45.7 1.0 CB A:GLU173 4.6 47.9 1.0 N E:VAL239 4.6 42.2 1.0 HE3 A:LYS176 4.6 77.5 1.0 HB3 A:LYS176 4.7 80.6 1.0 HG2 A:GLU173 4.7 70.5 1.0 N A:GLU173 4.7 36.0 1.0 CE A:LYS176 4.7 64.6 1.0 H E:VAL239 4.8 50.6 1.0 CG2 A:ILE172 4.8 30.4 1.0 HD2 A:LYS176 4.9 80.8 1.0 CA E:PHE238 4.9 46.1 1.0 CA E:VAL239 4.9 37.3 1.0 HG2 A:LYS176 4.9 82.1 1.0 HZ1 A:LYS176 5.0 75.2 1.0 O A:LYS176 5.0 77.3 1.0 HD2 E:PHE238 5.0 39.7 1.0 H A:GLU173 5.0 43.2 1.0

Iodine binding site 9 out of 131 in the The Phi-28 GP11 Dna Packaging Motor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of The Phi-28 GP11 Dna Packaging Motor within 5.0Å range: probe atom residue distance (Å) B Occ A:I409 b:70.3 occ:0.73 HA A:ILE289 3.5 34.1 1.0 HA A:PRO290 3.7 30.4 1.0 HD3 A:PRO290 3.8 30.1 1.0 C A:ILE289 3.8 28.5 1.0 N A:PRO290 3.8 25.2 1.0 HG3 A:PRO290 3.9 30.2 1.0 CA A:ILE289 4.0 28.4 1.0 O A:LYS288 4.0 31.3 1.0 C A:LYS288 4.2 33.5 1.0 O A:ILE289 4.2 31.6 1.0 CD A:PRO290 4.2 25.1 1.0 N A:ILE289 4.2 30.1 1.0 CA A:PRO290 4.3 25.3 1.0 CG A:PRO290 4.5 25.2 1.0 CB A:LYS288 4.5 25.4 1.0 H A:ILE289 4.7 36.1 1.0 CB A:PRO290 4.9 25.2 1.0

Iodine binding site 10 out of 131 in the The Phi-28 GP11 Dna Packaging Motor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of The Phi-28 GP11 Dna Packaging Motor within 5.0Å range: probe atom residue distance (Å) B Occ A:I410 b:70.7 occ:0.79 HE A:ARG260 2.5 67.1 1.0 HH21 A:ARG260 3.1 73.7 1.0 NE A:ARG260 3.3 55.9 1.0 HG2 A:ARG260 3.6 55.7 1.0 HB2 A:ASN345 3.6 33.2 1.0 HB3 A:ARG260 3.6 52.1 1.0 HD22 A:ASN345 3.6 48.0 1.0 HB3 A:ASN345 3.6 33.2 1.0 HA A:ARG260 3.7 47.2 1.0 NH2 A:ARG260 3.8 61.4 1.0 HD21 A:ASN258 3.9 64.8 1.0 CZ A:ARG260 4.0 58.9 1.0 CB A:ASN345 4.0 27.6 1.0 CG A:ARG260 4.1 46.4 1.0 CB A:ARG260 4.2 43.4 1.0 CD A:ARG260 4.3 52.2 1.0 ND2 A:ASN345 4.3 40.0 1.0 CA A:ARG260 4.4 39.3 1.0 HH22 A:ARG260 4.5 73.7 1.0 H A:ASN345 4.6 44.8 1.0 HD2 A:ARG260 4.7 62.6 1.0 CG A:ASN345 4.7 33.0 1.0 H A:THR261 4.7 47.1 1.0 ND2 A:ASN258 4.8 54.0 1.0 HD21 A:ASN345 5.0 48.0 1.0

J.Pajak, E.Dill, E.Reyes-Aldrete, M.A.White, B.A.Kelch, P.J.Jardine, G.Arya, M.C.Morais. Atomistic Basis of Force Generation, Translocation, and Coordination in A Viral Genome Packaging Motor. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 34050764
DOI: 10.1093/NAR/GKAB372