Iodine in PDB 6z6e: Crystal Structure of the HK97 Bacteriophage Small Terminase

The structure of Crystal Structure of the HK97 Bacteriophage Small Terminase, PDB code: 6z6e was solved by H.K.H.Fung, M.Chechik, C.G.Baumann, A.A.Antson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.23 / 1.40
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	123.281, 123.281, 78.991, 90, 90, 120
R / Rfree (%)	15.9 / 17

The binding sites of Iodine atom in the Crystal Structure of the HK97 Bacteriophage Small Terminase (pdb code 6z6e). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Crystal Structure of the HK97 Bacteriophage Small Terminase, PDB code: 6z6e:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in the Crystal Structure of the HK97 Bacteriophage Small Terminase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of the HK97 Bacteriophage Small Terminase within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:34.5 occ:0.50 O A:HOH408 2.6 23.9 1.0 NE A:ARG107 3.4 21.4 1.0 O A:HOH396 3.5 39.5 1.0 CZ A:ARG107 3.9 23.3 1.0 CD A:ARG107 3.9 19.1 1.0 NH2 A:ARG107 4.2 22.0 1.0 CG A:ARG107 4.2 17.3 1.0 NH1 A:ARG107 4.6 26.1 1.0

Iodine binding site 2 out of 9 in the Crystal Structure of the HK97 Bacteriophage Small Terminase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of the HK97 Bacteriophage Small Terminase within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:23.6 occ:0.50 O A:HOH349 3.4 21.6 1.0 CA A:LYS100 3.8 17.1 1.0 N A:LYS100 4.0 16.2 1.0 CB A:LYS100 4.1 18.5 1.0 C A:ARG99 4.3 16.4 1.0 O A:ARG99 4.3 17.3 1.0 CG2 A:VAL103 4.4 20.2 1.0 CG A:LYS100 4.6 23.2 1.0 CB A:VAL103 4.6 18.8 1.0 CB A:ARG99 4.7 17.3 1.0 CG1 A:VAL103 5.0 19.2 1.0

Iodine binding site 3 out of 9 in the Crystal Structure of the HK97 Bacteriophage Small Terminase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of the HK97 Bacteriophage Small Terminase within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:28.3 occ:0.50 O A:HOH401 2.4 28.6 1.0 N A:PRO40 3.8 15.6 1.0 O A:HOH334 3.9 43.0 1.0 CA A:PRO40 3.9 15.6 1.0 CD A:PRO40 4.0 16.4 1.0 CD2 A:HIS43 4.1 16.7 1.0 C A:GLU39 4.1 14.9 1.0 CB A:GLU39 4.2 18.8 1.0 CB A:PRO40 4.2 17.1 1.0 CG A:PRO40 4.3 22.5 1.0 O A:GLU39 4.5 15.6 1.0 NE2 A:HIS43 4.7 17.4 1.0 CA A:GLU39 4.8 16.7 1.0 OE1 A:GLU39 4.8 29.7 1.0 O A:HOH365 4.9 32.9 1.0

Iodine binding site 4 out of 9 in the Crystal Structure of the HK97 Bacteriophage Small Terminase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of the HK97 Bacteriophage Small Terminase within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:38.0 occ:0.50 O B:HOH405 2.7 24.3 1.0 NE B:ARG107 3.4 22.8 1.0 O B:HOH396 3.5 39.9 1.0 O A:HOH335 3.8 25.6 1.0 CZ B:ARG107 3.8 25.0 1.0 CD B:ARG107 3.9 21.3 1.0 O A:ARG107 4.0 15.4 1.0 CB A:ALA111 4.1 14.2 1.0 NH2 B:ARG107 4.1 23.3 1.0 CG B:ARG107 4.2 17.1 1.0 CA A:THR108 4.3 13.8 1.0 C A:ARG107 4.3 13.9 1.0 N A:THR108 4.5 13.9 1.0 NH1 B:ARG107 4.6 27.5 1.0 OG1 A:THR108 4.7 15.8 1.0 CB A:ARG107 4.9 14.8 1.0

Iodine binding site 5 out of 9 in the Crystal Structure of the HK97 Bacteriophage Small Terminase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of the HK97 Bacteriophage Small Terminase within 5.0Å range: probe atom residue distance (Å) B Occ B:I202 b:25.8 occ:0.60 O A:HOH399 3.2 39.6 1.0 O A:HOH382 3.2 29.3 1.0 O B:HOH346 3.4 22.8 1.0 CA B:LYS100 3.8 17.3 1.0 CD B:LYS100 3.9 31.6 1.0 CB A:GLU104 4.0 17.1 1.0 NZ B:LYS100 4.1 42.1 1.0 N B:LYS100 4.1 16.0 1.0 CG A:GLN101 4.1 17.8 1.0 CB B:LYS100 4.1 21.1 1.0 CG A:GLU104 4.2 22.6 1.0 C B:ARG99 4.3 17.3 1.0 O B:ARG99 4.3 17.2 1.0 CG2 B:VAL103 4.4 20.1 1.0 CA A:GLN101 4.4 17.1 1.0 CE B:LYS100 4.6 44.1 1.0 CB B:VAL103 4.6 18.9 1.0 CB A:GLN101 4.6 17.4 1.0 CG B:LYS100 4.7 26.1 1.0 CB B:ARG99 4.8 16.0 1.0 O A:GLN101 4.9 16.4 1.0

Iodine binding site 6 out of 9 in the Crystal Structure of the HK97 Bacteriophage Small Terminase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of the HK97 Bacteriophage Small Terminase within 5.0Å range: probe atom residue distance (Å) B Occ B:I203 b:34.3 occ:0.50 N B:PRO40 3.9 17.1 1.0 CA B:PRO40 3.9 17.1 1.0 CD2 B:HIS43 4.0 20.7 1.0 CD B:PRO40 4.1 18.3 1.0 C B:GLU39 4.1 15.6 1.0 CB B:PRO40 4.2 18.9 1.0 CB B:GLU39 4.2 22.5 1.0 O B:GLU39 4.4 18.1 1.0 CG B:PRO40 4.5 23.8 1.0 O B:HOH302 4.5 36.3 1.0 NE2 B:HIS43 4.7 21.3 1.0 CA B:GLU39 4.8 17.8 1.0 OE1 B:GLU39 4.9 36.3 1.0 O B:HOH364 5.0 53.0 1.0

Iodine binding site 7 out of 9 in the Crystal Structure of the HK97 Bacteriophage Small Terminase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of the HK97 Bacteriophage Small Terminase within 5.0Å range: probe atom residue distance (Å) B Occ C:I201 b:32.2 occ:0.50 O C:HOH413 2.6 22.0 1.0 O C:HOH402 3.3 39.1 1.0 NE C:ARG107 3.5 19.4 1.0 O B:HOH318 3.9 25.4 1.0 CZ C:ARG107 3.9 21.8 1.0 CD C:ARG107 3.9 18.5 1.0 O B:ARG107 4.0 14.8 1.0 CB B:ALA111 4.1 13.2 1.0 NH2 C:ARG107 4.1 21.9 1.0 CG C:ARG107 4.2 16.3 1.0 CA B:THR108 4.3 13.9 1.0 C B:ARG107 4.3 14.0 1.0 N B:THR108 4.4 13.6 1.0 NH1 C:ARG107 4.6 25.4 1.0 OG1 B:THR108 4.7 15.1 1.0 CB B:ARG107 4.9 15.5 1.0

Iodine binding site 8 out of 9 in the Crystal Structure of the HK97 Bacteriophage Small Terminase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of the HK97 Bacteriophage Small Terminase within 5.0Å range: probe atom residue distance (Å) B Occ C:I202 b:24.9 occ:0.70 O C:HOH403 3.3 37.1 1.0 O B:HOH389 3.4 29.8 1.0 O C:HOH357 3.5 20.7 1.0 CA C:LYS100 3.8 17.0 1.0 CD C:LYS100 3.9 32.8 1.0 CB B:GLU104 4.0 17.9 1.0 NZ C:LYS100 4.1 48.3 1.0 CG B:GLN101 4.1 17.1 1.0 N C:LYS100 4.1 15.0 1.0 CB C:LYS100 4.1 18.7 1.0 CG B:GLU104 4.2 20.4 1.0 CG2 C:VAL103 4.3 18.2 1.0 O C:ARG99 4.3 15.5 1.0 C C:ARG99 4.3 14.4 1.0 CA B:GLN101 4.4 15.8 1.0 CB C:VAL103 4.6 16.0 1.0 CB B:GLN101 4.6 16.4 1.0 CE C:LYS100 4.6 45.6 1.0 CG C:LYS100 4.6 23.6 1.0 O C:HOH331 4.7 47.7 1.0 CB C:ARG99 4.8 15.6 1.0 O B:GLN101 4.9 15.7 1.0 CG1 C:VAL103 4.9 17.7 1.0 O C:HOH404 5.0 29.8 1.0

Iodine binding site 9 out of 9 in the Crystal Structure of the HK97 Bacteriophage Small Terminase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of the HK97 Bacteriophage Small Terminase within 5.0Å range: probe atom residue distance (Å) B Occ C:I203 b:36.2 occ:0.50 N C:PRO40 3.9 18.2 1.0 CA C:PRO40 3.9 18.5 1.0 CD2 C:HIS43 4.0 21.7 1.0 CD C:PRO40 4.1 19.8 1.0 C C:GLU39 4.1 17.2 1.0 CB C:PRO40 4.2 20.2 1.0 CB C:GLU39 4.2 21.7 1.0 O C:GLU39 4.4 18.4 1.0 CG C:PRO40 4.5 23.9 1.0 O C:HOH342 4.5 42.9 1.0 NE2 C:HIS43 4.7 23.3 1.0 OE1 C:GLU39 4.8 40.9 1.0 CA C:GLU39 4.8 18.9 1.0

H.K.H.Fung, S.Grimes, A.Huet, R.L.Duda, M.Chechik, J.Gault, C.V.Robinson, R.W.Hendrix, P.J.Jardine, J.F.Conway, C.G.Baumann, A.A.Antson. Structural Basis For Dna Packaging in the Cos Bacteriophage HK97 To Be Published.