Chlorine in PDB 5ngj: Crystal Structure of PB6, Major Tail Tube Protein of Bacteriophage T5

The structure of Crystal Structure of PB6, Major Tail Tube Protein of Bacteriophage T5, PDB code: 5ngj was solved by C.-A.Arnaud, G.Effantin, C.Vives, S.Engilberge, M.Bacia, P.Boulanger, E.Girard, G.Schoehn, C.Breyton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.00 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.790, 115.081, 83.366, 90.00, 111.88, 90.00
R / Rfree (%)	20.5 / 23.5

The binding sites of Chlorine atom in the Crystal Structure of PB6, Major Tail Tube Protein of Bacteriophage T5 (pdb code 5ngj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of PB6, Major Tail Tube Protein of Bacteriophage T5, PDB code: 5ngj:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Crystal Structure of PB6, Major Tail Tube Protein of Bacteriophage T5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of PB6, Major Tail Tube Protein of Bacteriophage T5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:56.8 occ:0.50 H A:ILE152 1.9 56.8 1.0 HB1 A:ALA97 2.6 57.2 1.0 HA A:GLN151 2.6 57.8 1.0 HB2 A:LEU131 2.8 53.8 1.0 O A:ALA97 2.8 52.3 1.0 N A:ILE152 2.9 58.7 1.0 HG13 A:ILE152 3.0 65.6 1.0 O A:ALA132 3.1 61.1 1.0 C A:ALA97 3.4 55.5 1.0 HB A:ILE152 3.5 64.9 1.0 CA A:GLN151 3.5 56.9 1.0 CB A:ALA97 3.6 55.9 1.0 HB3 A:LEU131 3.6 54.7 1.0 C A:GLN151 3.6 59.9 1.0 CB A:LEU131 3.6 54.0 1.0 HD12 A:LEU131 3.8 59.6 1.0 HB3 A:GLN151 3.9 56.9 1.0 CA A:ILE152 3.9 59.6 1.0 CG1 A:ILE152 3.9 66.1 1.0 CA A:ALA97 3.9 53.8 1.0 CB A:ILE152 3.9 64.1 1.0 NE2 A:GLN151 3.9 58.5 1.0 HE22 A:GLN151 3.9 58.3 1.0 HA A:ALA97 4.0 53.3 1.0 HB3 A:ALA97 4.0 57.1 1.0 CD A:GLN151 4.1 64.7 1.0 HD13 A:LEU131 4.2 60.8 1.0 HE21 A:GLN151 4.2 58.3 1.0 C A:ALA132 4.2 59.4 1.0 CB A:GLN151 4.2 58.7 1.0 O A:ILE152 4.3 59.4 1.0 HA A:LEU98 4.3 50.5 1.0 C A:LEU131 4.3 58.9 1.0 O A:CYS150 4.3 57.5 1.0 HB2 A:ALA97 4.3 55.3 1.0 OE1 A:GLN151 4.3 63.4 1.0 CD1 A:LEU131 4.4 60.1 1.0 N A:ALA132 4.4 54.5 1.0 N A:LEU98 4.4 52.5 1.0 C A:ILE152 4.5 60.6 1.0 H A:ALA132 4.5 52.6 1.0 HG12 A:ILE152 4.5 66.0 1.0 HA A:MET133 4.5 56.4 1.0 O A:LEU131 4.5 61.0 1.0 CA A:LEU131 4.5 54.3 1.0 N A:GLN151 4.6 56.8 1.0 H A:LEU131 4.6 55.1 1.0 CG A:LEU131 4.6 58.8 1.0 HD12 A:ILE152 4.7 80.0 1.0 HA A:ILE152 4.8 60.5 1.0 CG A:GLN151 4.8 52.8 1.0 CD1 A:ILE152 4.8 80.8 1.0 HB3 A:ALA132 4.8 54.3 1.0 O A:GLN151 4.8 61.0 1.0 CA A:LEU98 4.9 50.8 1.0 C A:CYS150 4.9 60.2 1.0 CA A:ALA132 4.9 54.4 1.0 HD11 A:ILE152 5.0 81.6 1.0

Chlorine binding site 2 out of 5 in the Crystal Structure of PB6, Major Tail Tube Protein of Bacteriophage T5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of PB6, Major Tail Tube Protein of Bacteriophage T5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:50.1 occ:0.50 H A:ASP125 1.9 61.2 1.0 H A:GLY111 2.6 55.2 1.0 HB2 A:SER100 2.7 51.3 1.0 O A:SER99 2.8 49.0 1.0 O A:ASN122 2.8 49.8 1.0 N A:ASP125 2.9 60.7 1.0 HA2 A:GLY111 2.9 56.1 1.0 HA A:PHE123 2.9 48.8 1.0 HB2 A:ASP125 3.1 67.4 1.0 HB A:THR110 3.1 65.4 1.0 N A:GLY111 3.2 56.0 1.0 H A:LYS124 3.2 55.0 1.0 N A:LYS124 3.4 54.1 1.0 CA A:GLY111 3.4 55.5 1.0 HB3 A:ASP125 3.4 66.3 1.0 HA A:SER100 3.5 49.8 1.0 CA A:ASP125 3.5 62.3 1.0 CB A:ASP125 3.5 67.0 1.0 C A:PHE123 3.6 54.3 1.0 CA A:PHE123 3.6 47.3 1.0 C A:ASP125 3.6 60.5 1.0 CB A:SER100 3.7 50.8 1.0 C A:ASN122 3.7 49.9 1.0 HB2 A:SER99 3.7 46.7 1.0 C A:SER99 3.7 53.0 1.0 HA3 A:GLY111 3.7 55.4 1.0 OD1 A:ASN122 3.9 55.9 1.0 C A:LYS124 4.0 60.9 1.0 CA A:SER100 4.0 50.7 1.0 HB3 A:ASN126 4.0 53.7 1.0 O A:ASP125 4.0 58.1 1.0 N A:PHE123 4.0 47.5 1.0 O A:HOH620 4.1 59.7 1.0 HG A:SER100 4.1 59.6 1.0 N A:ASN126 4.1 54.8 1.0 CB A:THR110 4.2 66.5 1.0 OG A:SER100 4.2 59.7 1.0 O A:PHE123 4.2 57.2 1.0 CA A:LYS124 4.2 54.8 1.0 C A:THR110 4.2 61.5 1.0 OG A:SER99 4.3 49.0 1.0 N A:SER100 4.3 50.9 1.0 CB A:SER99 4.3 46.8 1.0 H A:ASN126 4.4 54.6 1.0 HB2 A:LYS124 4.5 57.5 1.0 HB3 A:SER100 4.5 51.7 1.0 HA A:ASP125 4.5 63.8 1.0 HA A:THR110 4.5 58.2 1.0 H A:ASN122 4.6 48.9 1.0 CA A:THR110 4.6 58.7 1.0 CA A:SER99 4.7 48.6 1.0 HG1 A:THR110 4.7 73.7 1.0 OG1 A:THR110 4.8 73.5 1.0 C A:GLY111 4.8 56.8 1.0 CA A:ASN122 4.9 48.9 1.0 CB A:ASN126 4.9 54.3 1.0 H A:PHE123 5.0 48.2 1.0 HA A:ASN126 5.0 55.2 1.0 CB A:LYS124 5.0 57.1 1.0 CA A:ASN126 5.0 54.6 1.0 HA A:SER99 5.0 48.4 1.0 CG A:ASN122 5.0 54.6 1.0 CB A:PHE123 5.0 48.5 1.0

Chlorine binding site 3 out of 5 in the Crystal Structure of PB6, Major Tail Tube Protein of Bacteriophage T5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of PB6, Major Tail Tube Protein of Bacteriophage T5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:0.1 occ:1.00 H A:THR388 2.4 66.3 1.0 HG1 A:THR389 2.4 71.8 1.0 HG1 A:THR388 3.1 74.8 1.0 H A:THR389 3.1 66.1 1.0 HA A:VAL387 3.3 69.8 1.0 OG1 A:THR389 3.3 70.9 1.0 N A:THR388 3.4 65.5 1.0 HB A:VAL387 3.4 71.9 1.0 HG23 A:THR389 3.4 66.3 1.0 OG1 A:THR388 3.6 73.2 1.0 N A:THR389 3.8 66.1 1.0 CA A:VAL387 4.0 68.0 1.0 CB A:VAL387 4.1 72.5 1.0 C A:VAL387 4.2 68.2 1.0 CB A:THR389 4.2 69.7 1.0 CA A:THR388 4.2 64.6 1.0 CG2 A:THR389 4.2 66.2 1.0 HG12 A:VAL387 4.3 73.6 1.0 C A:THR388 4.4 67.5 1.0 HG23 A:THR388 4.4 71.9 1.0 CB A:THR388 4.4 72.2 1.0 HG21 A:THR389 4.5 67.0 1.0 CA A:THR389 4.6 67.5 1.0 CG1 A:VAL387 4.8 73.6 1.0 O A:THR389 4.9 75.5 1.0 CG2 A:THR388 5.0 71.4 1.0

Chlorine binding site 4 out of 5 in the Crystal Structure of PB6, Major Tail Tube Protein of Bacteriophage T5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of PB6, Major Tail Tube Protein of Bacteriophage T5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:92.3 occ:1.00 H A:GLY464 2.1 97.7 1.0 HD21 A:ASN391 2.9 76.8 1.0 N A:GLY464 3.0 98.5 1.0 HA3 A:GLY464 3.2 0.1 1.0 HA2 A:GLY463 3.3 89.0 1.0 CA A:GLY464 3.7 0.4 1.0 ND2 A:ASN391 3.8 74.9 1.0 C A:GLY463 4.0 99.1 1.0 CA A:GLY463 4.1 88.1 1.0 HD22 A:ASN391 4.3 75.0 1.0 O A:HOH691 4.3 87.9 1.0 HA2 A:GLY464 4.4 0.0 1.0 HA3 A:GLY463 4.5 88.0 1.0 CG A:ASN391 4.6 79.7 1.0 OD1 A:ASN391 4.6 69.8 1.0 C A:GLY464 4.8 0.6 1.0 H A:GLU465 4.8 0.5 1.0

Chlorine binding site 5 out of 5 in the Crystal Structure of PB6, Major Tail Tube Protein of Bacteriophage T5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of PB6, Major Tail Tube Protein of Bacteriophage T5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl505 b:91.7 occ:0.80 H A:ALA103 2.6 63.5 1.0 HH21 A:ARG102 3.2 0.3 1.0 NH2 A:ARG102 3.3 0.2 1.0 HB3 A:ARG102 3.3 63.0 1.0 HA A:ARG102 3.5 62.4 1.0 HB3 A:ALA103 3.6 61.8 1.0 HH22 A:ARG102 3.6 0.3 1.0 N A:ALA103 3.6 63.4 1.0 CZ A:ARG102 3.7 0.9 1.0 HB2 A:ALA103 3.8 62.2 1.0 HE A:ARG102 3.8 0.5 1.0 NE A:ARG102 3.9 0.2 1.0 CB A:ALA103 4.1 63.3 1.0 CB A:ARG102 4.1 62.1 1.0 CA A:ARG102 4.2 62.1 1.0 HG2 A:ARG102 4.3 70.6 1.0 NH1 A:ARG102 4.4 0.7 1.0 C A:ARG102 4.4 65.9 1.0 CA A:ALA103 4.5 62.2 1.0 HH12 A:ARG102 4.6 0.8 1.0 CG A:ARG102 4.7 70.0 1.0 CD A:ARG102 4.9 90.0 1.0 HH11 A:ARG102 5.0 0.2 1.0

C.A.Arnaud, G.Effantin, C.Vives, S.Engilberge, M.Bacia, P.Boulanger, E.Girard, G.Schoehn, C.Breyton. Bacteriophage T5 Tail Tube Structure Suggests A Trigger Mechanism For Siphoviridae Dna Ejection. Nat Commun V. 8 1953 2017.
ISSN: ESSN 2041-1723
PubMed: 29209037
DOI: 10.1038/S41467-017-02049-3