Bromine in PDB 6z6d: Crystal Structure of the HK97 Bacteriophage Large Terminase

The structure of Crystal Structure of the HK97 Bacteriophage Large Terminase, PDB code: 6z6d 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)	103.23 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	211.787, 39.146, 65.45, 90, 103.39, 90
R / Rfree (%)	20.5 / 25.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Bromine atom in the Crystal Structure of the HK97 Bacteriophage Large Terminase (pdb code 6z6d). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 18 binding sites of Bromine where determined in the Crystal Structure of the HK97 Bacteriophage Large Terminase, PDB code: 6z6d:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 18 in the Crystal Structure of the HK97 Bacteriophage Large Terminase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of the HK97 Bacteriophage Large Terminase within 5.0Å range: probe atom residue distance (Å) B Occ A:Br601 b:44.5 occ:1.00 ND2 A:ASN190 3.4 27.6 1.0 N A:ALA455 3.5 37.3 1.0 CG2 A:VAL271 3.7 38.8 1.0 CB A:ASP454 3.8 34.9 1.0 CB A:ALA455 4.0 40.6 1.0 CA A:ASP454 4.0 34.9 1.0 CB A:ASN190 4.1 28.2 1.0 O A:ALA189 4.2 30.5 1.0 CG A:ASN190 4.2 28.2 1.0 C A:ASP454 4.3 36.4 1.0 CA A:ALA455 4.4 39.4 1.0 C A:ALA189 4.4 29.4 1.0 CB A:SER272 4.4 28.8 1.0 CA A:ASN190 4.5 27.6 1.0 O A:HOH733 4.5 37.1 1.0 N A:SER272 4.5 30.7 1.0 CB A:ALA189 4.5 29.4 1.0 N A:ASN190 4.6 28.4 1.0 CA A:SER272 4.8 30.1 1.0 CG A:ASP454 4.9 39.0 1.0 C A:VAL271 5.0 31.8 1.0

Bromine binding site 2 out of 18 in the Crystal Structure of the HK97 Bacteriophage Large Terminase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of the HK97 Bacteriophage Large Terminase within 5.0Å range: probe atom residue distance (Å) B Occ A:Br602 b:40.0 occ:0.53 N A:GLY414 3.3 43.4 1.0 CA A:GLY414 3.5 41.8 1.0 N A:ASP417 3.6 36.6 1.0 CA A:GLY412 3.6 44.4 1.0 O A:HOH776 3.7 45.4 1.0 CB A:ASP417 3.7 44.0 1.0 C A:GLY414 3.7 40.4 1.0 C A:GLY412 3.8 45.2 1.0 CG A:ASP417 3.9 48.0 1.0 O A:GLY414 4.0 36.3 1.0 N A:GLN413 4.0 43.6 1.0 N A:LYS416 4.1 37.8 1.0 OD1 A:ASP417 4.3 51.6 1.0 CA A:ASP417 4.3 39.7 1.0 O A:GLY412 4.3 45.1 1.0 CB A:LYS416 4.3 36.9 1.0 N A:PHE415 4.4 38.5 1.0 OD2 A:ASP417 4.4 51.3 1.0 C A:GLN413 4.5 44.3 1.0 C A:LYS416 4.5 38.3 1.0 CA A:LYS416 4.5 38.0 1.0 N A:GLY412 4.8 41.7 1.0 CA A:GLN413 4.9 44.9 1.0 C A:PHE415 5.0 35.0 1.0

Bromine binding site 3 out of 18 in the Crystal Structure of the HK97 Bacteriophage Large Terminase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of the HK97 Bacteriophage Large Terminase within 5.0Å range: probe atom residue distance (Å) B Occ A:Br603 b:30.8 occ:0.42 ND2 A:ASN98 3.2 25.3 1.0 CB A:ASN98 3.8 28.3 1.0 CG A:ASN98 4.0 28.4 1.0 CA A:ILE95 4.2 28.4 1.0 CG1 A:ILE95 4.3 30.0 1.0 O A:ALA94 4.7 28.3 1.0 O A:ILE95 4.8 31.7 1.0 CB A:ILE95 4.8 28.1 1.0 N A:ILE95 4.8 28.0 1.0 C A:ALA94 5.0 26.8 1.0

Bromine binding site 4 out of 18 in the Crystal Structure of the HK97 Bacteriophage Large Terminase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of the HK97 Bacteriophage Large Terminase within 5.0Å range: probe atom residue distance (Å) B Occ A:Br604 b:37.6 occ:0.40 CA A:SER205 3.8 28.6 1.0 CB A:SER205 3.9 25.6 1.0 N A:SER205 3.9 29.1 1.0 C A:LYS204 4.1 33.2 1.0 O A:LYS204 4.3 33.7 1.0 CB A:LYS204 4.4 32.2 1.0 CA A:LYS204 4.9 33.7 1.0

Bromine binding site 5 out of 18 in the Crystal Structure of the HK97 Bacteriophage Large Terminase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of the HK97 Bacteriophage Large Terminase within 5.0Å range: probe atom residue distance (Å) B Occ A:Br605 b:41.2 occ:0.50 BR A:BR605 0.0 41.2 0.5 BR A:BR605 3.1 41.5 0.5 NH1 A:ARG56 3.5 37.4 1.0 CG A:ARG56 3.7 33.1 1.0 CB A:ARG56 3.7 31.8 1.0 CD A:ARG56 3.8 37.0 1.0 CE A:LYS57 4.2 43.6 1.0 NZ A:LYS57 4.4 48.0 1.0 CZ A:ARG56 4.5 38.1 1.0 CD1 A:LEU265 4.6 28.6 1.0 NE A:ARG56 4.6 37.9 1.0 CG A:LYS57 4.8 35.1 1.0

Bromine binding site 6 out of 18 in the Crystal Structure of the HK97 Bacteriophage Large Terminase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of the HK97 Bacteriophage Large Terminase within 5.0Å range: probe atom residue distance (Å) B Occ A:Br605 b:41.5 occ:0.50 BR A:BR605 0.0 41.5 0.5 BR A:BR605 3.1 41.2 0.5 OD1 A:ASN266 3.4 29.2 1.0 O A:HOH701 3.5 41.0 1.0 CE A:LYS57 3.8 43.6 1.0 CB A:ARG56 4.2 31.8 1.0 CG A:ASN266 4.3 26.8 1.0 ND2 A:ASN266 4.4 26.6 1.0 NE2 A:GLN248 4.4 50.9 1.0 CD A:LYS57 4.5 39.1 1.0 NH2 A:ARG240 4.6 40.6 1.0 CG A:ARG56 4.7 33.1 1.0 CB A:LEU265 4.8 27.2 1.0 CD1 A:LEU265 4.8 28.6 1.0 CG A:LYS57 4.8 35.1 1.0 NZ A:LYS57 4.9 48.0 1.0

Bromine binding site 7 out of 18 in the Crystal Structure of the HK97 Bacteriophage Large Terminase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of the HK97 Bacteriophage Large Terminase within 5.0Å range: probe atom residue distance (Å) B Occ A:Br606 b:32.9 occ:0.42 O A:HOH728 3.4 60.6 1.0 N A:LYS57 3.4 29.9 1.0 O A:HOH783 3.5 31.6 1.0 CE A:LYS60 3.8 28.4 1.0 CA A:LYS57 4.0 31.0 1.0 CD A:ARG56 4.0 37.0 1.0 O A:HOH719 4.1 33.7 1.0 O A:HOH782 4.3 43.9 1.0 CA A:ARG56 4.4 31.5 1.0 C A:ARG56 4.4 30.3 1.0 NZ A:LYS60 4.4 29.6 1.0 CG A:LYS57 4.6 35.1 1.0 CB A:ARG56 4.6 31.8 1.0 CB A:LYS60 4.7 27.7 1.0 CB A:LYS57 4.9 33.1 1.0 O A:HOH764 4.9 20.9 1.0 BR A:BR611 5.0 30.5 0.3 CG A:ARG56 5.0 33.1 1.0

Bromine binding site 8 out of 18 in the Crystal Structure of the HK97 Bacteriophage Large Terminase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of the HK97 Bacteriophage Large Terminase within 5.0Å range: probe atom residue distance (Å) B Occ A:Br607 b:19.2 occ:0.28 O A:HIS71 2.8 25.3 1.0 OG1 A:THR81 2.9 26.3 1.0 O A:HOH724 3.0 27.2 1.0 N A:VAL78 3.3 27.1 1.0 CG2 A:VAL130 3.5 26.4 1.0 CG2 A:VAL78 3.6 27.9 1.0 CG1 A:VAL130 3.7 25.2 1.0 O A:VAL78 3.8 24.9 1.0 CA A:ALA77 3.8 27.5 1.0 O A:GLU76 3.9 29.6 1.0 C A:HIS71 3.9 25.4 1.0 C A:ALA77 4.1 27.2 1.0 CB A:THR81 4.1 29.2 1.0 CG2 A:ILE83 4.2 27.1 1.0 CB A:VAL130 4.2 25.7 1.0 CA A:VAL78 4.3 27.7 1.0 CB A:HIS71 4.4 24.8 1.0 C A:VAL78 4.5 27.0 1.0 CA A:HIS71 4.5 24.5 1.0 CG2 A:ILE148 4.5 32.8 1.0 CB A:VAL78 4.5 27.3 1.0 C A:GLU76 4.6 28.0 1.0 N A:ALA77 4.6 27.8 1.0 CB A:ALA77 4.7 27.8 1.0 CG2 A:THR81 4.8 30.7 1.0 ND1 A:HIS71 4.8 23.9 1.0

Bromine binding site 9 out of 18 in the Crystal Structure of the HK97 Bacteriophage Large Terminase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Crystal Structure of the HK97 Bacteriophage Large Terminase within 5.0Å range: probe atom residue distance (Å) B Occ A:Br608 b:29.1 occ:0.34 OG A:SER427 3.0 51.6 1.0 O A:HOH744 3.8 44.1 1.0 CG2 A:THR424 4.0 31.6 1.0 CB A:SER427 4.1 41.5 1.0 CA A:THR424 4.3 31.3 1.0 OG1 A:THR424 4.4 30.5 1.0 CB A:THR424 4.5 31.3 1.0 O A:THR424 4.6 30.8 1.0 C A:THR424 5.0 30.5 1.0

Bromine binding site 10 out of 18 in the Crystal Structure of the HK97 Bacteriophage Large Terminase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Crystal Structure of the HK97 Bacteriophage Large Terminase within 5.0Å range: probe atom residue distance (Å) B Occ A:Br609 b:31.7 occ:0.37 OG A:SER405 3.1 37.6 1.0 C A:LEU406 3.5 40.8 1.0 N A:PRO407 3.5 39.6 1.0 C A:SER405 3.6 40.8 1.0 O A:SER405 3.6 41.3 1.0 N A:LEU406 3.6 41.4 1.0 CB A:SER405 3.7 39.5 1.0 CA A:LEU406 3.9 41.2 1.0 O A:LEU406 3.9 38.7 1.0 CD A:PRO407 3.9 39.1 1.0 CA A:PRO407 4.0 39.4 1.0 CB A:PRO407 4.2 38.1 1.0 CA A:SER405 4.3 39.5 1.0 CG A:PRO407 4.5 39.1 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.