Chlorine in PDB 6vr4: Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2

The structure of Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2, PDB code: 6vr4 was solved by P.G.Leiman, M.L.Sokolova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.93 / 3.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	266.441, 297.181, 92.015, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 23.9

The structure of Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2 also contains other interesting chemical elements:

Sodium

(Na)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Chlorine atom in the Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2 (pdb code 6vr4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 21 binding sites of Chlorine where determined in the Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2, PDB code: 6vr4:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 21 in the Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2201 b:67.5 occ:1.00 CG2 A:ILE1754 3.2 80.9 1.0 OD1 A:ASP1214 3.3 86.8 1.0 OD1 A:ASN1753 3.3 0.4 1.0 ND2 A:ASN1753 3.7 0.8 1.0 CG A:ASN1753 3.9 0.4 1.0 CG A:ASP1214 4.4 82.2 1.0 CB A:ILE1754 4.6 62.8 1.0 CB A:TYR1856 4.9 60.6 1.0 CG A:TYR1856 4.9 53.9 1.0 CD1 A:TYR1856 4.9 54.2 1.0 N A:ILE1754 5.0 78.5 1.0

Chlorine binding site 2 out of 21 in the Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2202 b:96.6 occ:1.00 CG2 A:THR662 3.3 81.0 1.0 CE A:LYS642 3.7 0.2 1.0 OG A:SER659 3.8 1.0 1.0 CD1 A:LEU1534 4.0 81.7 1.0 O A:THR660 4.5 67.8 1.0 CD A:LYS642 4.5 86.3 1.0 CD1 A:LEU669 4.5 1.0 1.0 CB A:SER659 4.6 75.0 1.0 N A:LEU1534 4.7 62.6 1.0 CA A:LEU1534 4.7 62.0 1.0 CB A:THR662 4.7 74.3 1.0 NZ A:LYS642 4.8 0.8 1.0 CD A:LYS1537 4.8 75.7 1.0 CB A:GLN1533 4.8 65.0 1.0 C A:GLN1533 4.8 71.2 1.0 O A:GLN1533 4.9 86.4 1.0 CA A:THR662 5.0 75.1 1.0 OE1 A:GLN1533 5.0 93.5 1.0

Chlorine binding site 3 out of 21 in the Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2203 b:72.9 occ:1.00 OG A:SER547 3.3 72.0 1.0 CB A:SER547 4.1 76.0 1.0 CE1 A:HIS670 4.2 65.0 1.0 CD1 A:ILE339 4.4 86.4 1.0 OG A:SER550 4.5 72.3 1.0 CB A:SER550 4.5 68.2 1.0 NE2 A:HIS670 4.5 73.4 1.0 N A:SER547 4.5 64.9 1.0 CB A:ILE339 4.6 79.1 1.0 CG1 A:ILE339 4.6 64.4 1.0 O A:ARG545 4.8 67.8 1.0 CB A:ALA544 4.8 80.4 1.0 OG A:SER337 4.8 73.9 1.0 CA A:SER547 5.0 69.8 1.0

Chlorine binding site 4 out of 21 in the Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2204 b:83.7 occ:1.00 N A:LYS1232 3.5 58.2 1.0 O A:LYS1232 3.7 66.4 1.0 CD2 A:LEU1231 4.0 76.1 1.0 NE2 A:GLN1477 4.1 97.6 1.0 CA A:LEU1231 4.1 58.5 1.0 C A:LEU1231 4.3 63.3 1.0 CA A:LYS1232 4.3 57.8 1.0 CB A:LEU1231 4.4 58.8 1.0 C A:LYS1232 4.5 58.0 1.0 CB A:LYS1232 4.5 57.9 1.0 CG A:LEU1231 4.8 64.1 1.0

Chlorine binding site 5 out of 21 in the Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2205 b:96.0 occ:1.00 CA A:ASP733 3.8 85.0 1.0 ND2 A:ASN747 3.8 87.9 1.0 CD2 A:HIS729 3.8 79.5 1.0 N A:ALA734 3.9 93.6 1.0 O A:LYS886 3.9 0.8 1.0 CB A:ASP733 4.2 96.5 1.0 C A:ASP733 4.3 89.6 1.0 O A:THR732 4.3 0.6 1.0 CG A:ASN747 4.3 94.6 1.0 OD1 A:ASN747 4.5 0.4 1.0 CG A:HIS729 4.6 81.8 1.0 O A:ALA745 4.6 96.8 1.0 CB A:HIS729 4.6 85.5 1.0 O A:HIS729 4.6 95.9 1.0 CA A:HIS729 4.7 74.0 1.0 N A:ASP733 4.8 96.5 1.0 NE2 A:HIS729 4.9 92.5 1.0 CA A:ALA734 4.9 87.4 1.0 C A:LYS886 4.9 94.6 1.0 C A:THR732 5.0 0.8 1.0

Chlorine binding site 6 out of 21 in the Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2206 b:79.2 occ:1.00 OE1 A:GLN987 3.8 81.5 1.0 CE2 A:TYR990 3.9 88.0 1.0 CD2 A:TYR990 4.1 82.4 1.0 CZ2 A:TRP982 4.4 58.5 1.0 NE2 A:GLN987 4.4 79.8 1.0 CB A:ALA973 4.5 81.4 1.0 CD A:GLN987 4.5 82.5 1.0 CH2 A:TRP982 4.8 57.6 1.0 CZ A:TYR990 4.8 78.0 1.0 CE2 A:TRP982 5.0 60.2 1.0

Chlorine binding site 7 out of 21 in the Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2207 b:80.0 occ:1.00 OD1 A:ASN1917 3.0 0.4 1.0 ND2 A:ASN370 3.4 99.3 1.0 CG A:ASN1917 4.2 0.1 1.0 CZ A:PHE2093 4.2 98.5 1.0 CE2 A:PHE2093 4.4 86.4 1.0 CG2 A:THR1916 4.6 1.0 1.0 CG A:ASN370 4.7 0.7 1.0 ND2 A:ASN1917 4.8 96.3 1.0 OH A:TYR1909 4.8 79.6 1.0 CE1 A:PHE2093 4.9 0.9 1.0 CB A:LEU1960 4.9 89.5 1.0

Chlorine binding site 8 out of 21 in the Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2208 b:80.7 occ:1.00 CG2 A:THR357 3.5 0.4 1.0 CE1 A:HIS833 3.9 0.8 1.0 ND1 A:HIS833 4.0 0.7 1.0 NE2 A:HIS833 4.2 0.3 1.0 CG A:HIS833 4.3 1.0 1.0 N A:THR357 4.3 0.4 1.0 CD2 A:HIS833 4.4 0.4 1.0 CB A:ASN356 4.6 0.0 1.0 CB A:THR357 4.8 0.5 1.0 O A:THR357 5.0 0.1 1.0

Chlorine binding site 9 out of 21 in the Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2209 b:78.7 occ:1.00 NZ A:LYS673 3.6 70.7 1.0 CD A:LYS673 4.1 56.2 1.0 O A:VAL363 4.1 89.9 1.0 OH A:TYR342 4.2 78.5 1.0 CE A:LYS673 4.2 66.0 1.0 CZ A:TYR342 4.3 78.2 1.0 CD1 A:ILE657 4.7 80.2 1.0 CE1 A:TYR342 4.7 79.0 1.0 CE2 A:TYR342 4.7 82.4 1.0

Chlorine binding site 10 out of 21 in the Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2210 b:94.5 occ:1.00 N A:ASN504 3.4 0.3 1.0 CB A:ASN504 3.7 0.5 1.0 CG1 A:ILE503 3.8 0.1 1.0 CD A:LYS507 3.8 0.7 1.0 CA A:ASN504 4.1 92.7 1.0 CB A:LYS507 4.2 0.4 1.0 O A:ASN504 4.3 0.7 1.0 C A:ILE503 4.3 0.9 1.0 CA A:ILE503 4.3 0.6 1.0 CG A:LYS507 4.6 0.3 1.0 CB A:ILE503 4.6 0.3 1.0 CD1 A:ILE503 4.7 0.4 1.0 C A:ASN504 4.7 0.1 1.0 OD1 A:ASN508 4.8 0.5 1.0 NZ A:LYS507 4.9 0.4 1.0 CE A:LYS507 4.9 0.6 1.0 CG A:ASN504 4.9 0.1 1.0

A.V.Drobysheva, S.A.Panafidina, M.V.Kolesnik, E.I.Klimuk, L.Minakhin, M.V.Yakunina, S.Borukhov, E.Nilsson, K.Holmfeldt, N.Yutin, K.S.Makarova, E.V.Koonin, K.V.Severinov, P.G.Leiman, M.L.Sokolova. Structure and Function of Virion Rna Polymerase of A Crass-Like Phage. Nature 2020.
ISSN: ESSN 1476-4687
PubMed: 33208949
DOI: 10.1038/S41586-020-2921-5