Sodium 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:

Chlorine

(Cl)

21 atoms

The binding sites of Sodium 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 Sodium atom.
In total 6 binding sites of Sodium where determined in the Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2, PDB code: 6vr4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na2212 b:68.2 occ:1.00 NA A:NA2215 3.3 91.3 1.0 OE2 A:GLU717 3.5 97.3 1.0 OE1 A:GLU713 3.9 93.3 1.0 OE1 A:GLU717 4.1 93.4 1.0 CD A:GLU717 4.2 98.8 1.0 O A:ASN1020 4.2 0.7 1.0 CG2 A:THR1022 4.2 99.5 1.0 CE2 A:TYR730 4.3 91.4 1.0 ND2 A:ASN1020 4.4 0.9 1.0 OH A:TYR730 4.6 94.8 1.0 CD A:GLU713 4.6 93.2 1.0 CZ A:TYR730 5.0 97.9 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na2213 b:55.0 occ:1.00 OD2 A:ASP2065 3.2 0.4 1.0 O A:SER2064 4.1 94.3 1.0 CG2 A:THR2114 4.4 0.0 1.0 CE A:LYS2084 4.4 82.9 1.0 CG A:ASP2065 4.5 0.6 1.0 CA A:ASP2065 4.8 98.5 1.0 NH2 A:ARG2081 4.8 0.9 1.0 CD A:LYS2084 4.9 73.5 1.0 CG A:LYS2084 5.0 87.7 1.0

Sodium binding site 3 out of 6 in the Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na2214 b:49.7 occ:1.00 OE1 A:GLU1590 2.7 83.3 1.0 CD A:GLU1590 3.9 84.6 1.0 CD2 A:LEU1592 4.0 69.0 1.0 CD1 A:LEU1592 4.4 87.0 1.0 CD1 A:TRP1644 4.4 85.2 1.0 CG A:TRP1644 4.5 79.1 1.0 CB A:TRP1644 4.5 66.0 1.0 CB A:GLU1590 4.5 78.4 1.0 CG1 A:VAL1574 4.5 82.9 1.0 N A:HIS1641 4.6 65.3 1.0 OE2 A:GLU1590 4.6 0.2 1.0 CG1 A:VAL1640 4.7 66.3 1.0 CG A:LEU1592 4.7 71.9 1.0 CB A:VAL1574 4.8 77.6 1.0 CB A:HIS1641 4.8 78.8 1.0 CG A:GLU1590 4.8 68.5 1.0

Sodium binding site 4 out of 6 in the Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na2215 b:91.3 occ:1.00 ND2 A:ASN1020 3.2 0.9 1.0 NA A:NA2212 3.3 68.2 1.0 CG2 A:THR1022 3.5 99.5 1.0 OE2 A:GLU717 3.7 97.3 1.0 CG2 A:VAL727 4.1 85.0 1.0 CE1 A:HIS731 4.2 86.5 1.0 CD1 A:LEU721 4.4 83.2 1.0 CG A:ASN1020 4.4 0.6 1.0 CD A:GLU717 4.6 98.8 1.0 CB A:THR1022 4.8 86.6 1.0 O A:ASN1020 4.8 0.7 1.0 OD1 A:ASN1020 4.9 0.2 1.0 CE2 A:TYR730 4.9 91.4 1.0 OE1 A:GLU717 4.9 93.4 1.0 NE2 A:HIS731 4.9 88.3 1.0 CD2 A:TYR730 5.0 86.8 1.0

Sodium binding site 5 out of 6 in the Virion-Packaged Dna-Dependent Rna Polymerase of Crass-Like Phage PHI14:2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 B:Na2211 b:70.5 occ:1.00 CG2 B:THR1022 3.5 90.0 1.0 OE2 B:GLU717 3.5 79.3 1.0 ND2 B:ASN1020 3.7 0.2 1.0 O B:ASN1020 4.0 93.7 1.0 CD B:GLU717 4.5 74.6 1.0 OE1 B:GLU717 4.7 75.7 1.0 CB B:THR1022 5.0 85.5 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 B:Na2212 b:64.3 occ:1.00 OE1 B:GLU1590 2.8 90.0 1.0 CD B:GLU1590 4.0 89.0 1.0 CD1 B:TRP1644 4.4 79.1 1.0 CG B:TRP1644 4.5 65.0 1.0 CG1 B:VAL1574 4.5 81.1 1.0 CD1 B:LEU1592 4.6 0.7 1.0 CD2 B:LEU1592 4.6 64.7 1.0 OE2 B:GLU1590 4.6 81.6 1.0 CB B:TRP1644 4.6 60.1 1.0 CB B:VAL1574 4.7 71.0 1.0 CG1 B:VAL1640 4.8 65.0 1.0 CB B:GLU1590 4.8 82.3 1.0 NE1 B:TRP1644 4.9 74.4 1.0 CG B:GLU1590 4.9 78.5 1.0 CD2 B:TRP1644 5.0 63.8 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