Zinc in PDB 4l8h: Bacteriophage Qbeta Coat Protein in Complex with Rna Operator Hairpin

The structure of Bacteriophage Qbeta Coat Protein in Complex with Rna Operator Hairpin, PDB code: 4l8h was solved by J.Rumnieks, K.Tars, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.63 / 2.40
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	75.840, 75.840, 303.490, 90.00, 90.00, 120.00
R / Rfree (%)	25.3 / 28.8

The binding sites of Zinc atom in the Bacteriophage Qbeta Coat Protein in Complex with Rna Operator Hairpin (pdb code 4l8h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Bacteriophage Qbeta Coat Protein in Complex with Rna Operator Hairpin, PDB code: 4l8h:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Bacteriophage Qbeta Coat Protein in Complex with Rna Operator Hairpin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bacteriophage Qbeta Coat Protein in Complex with Rna Operator Hairpin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:19.4 occ:1.00 OD1 B:ASP102 2.0 17.7 1.0 OE2 B:GLU103 2.1 19.9 1.0 OE1 B:GLU103 2.5 17.9 1.0 CD B:GLU103 2.6 19.6 1.0 CG B:ASP102 2.8 18.0 1.0 OD2 B:ASP102 2.9 17.4 1.0 NZ A:LYS13 3.6 40.5 1.0 CG B:GLU103 4.1 19.7 1.0 CB B:ASP102 4.3 20.1 1.0 O B:HOH343 4.3 45.1 1.0 N B:GLU103 4.5 21.7 1.0 N B:ASP102 4.6 22.1 1.0 CA B:ASP102 4.9 21.6 1.0 CE A:LYS13 5.0 38.2 1.0

Zinc binding site 2 out of 6 in the Bacteriophage Qbeta Coat Protein in Complex with Rna Operator Hairpin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bacteriophage Qbeta Coat Protein in Complex with Rna Operator Hairpin within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn101 b:62.5 occ:1.00 N7 R:G7 2.4 47.8 1.0 C8 R:G7 3.3 46.6 1.0 C5 R:G7 3.5 46.7 1.0 O6 R:G7 3.8 51.2 1.0 OP2 R:G7 4.0 41.9 1.0 C6 R:G7 4.0 48.0 1.0 O4 R:U8 4.4 23.2 0.6 N9 R:G7 4.5 44.5 1.0 C4 R:G7 4.6 46.3 1.0 C4 R:U6 4.6 42.1 1.0 O4 R:U6 4.8 43.6 1.0 N3 R:U6 4.8 39.6 1.0 C5 R:U6 4.9 40.4 1.0 C5 R:U8 5.0 21.5 0.6 O5' R:G7 5.0 41.0 1.0

Zinc binding site 3 out of 6 in the Bacteriophage Qbeta Coat Protein in Complex with Rna Operator Hairpin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Bacteriophage Qbeta Coat Protein in Complex with Rna Operator Hairpin within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn102 b:78.5 occ:1.00 N7 R:G13 2.4 41.9 0.6 O A:HOH229 2.5 42.7 1.0 O R:HOH202 2.6 54.2 1.0 NZ A:LYS67 3.0 44.9 1.0 C8 R:G13 3.2 43.0 0.6 C5 R:G13 3.5 40.8 0.6 O6 R:G13 3.9 38.8 0.6 CE A:LYS67 4.0 43.1 1.0 C6 R:G13 4.1 40.2 0.6 O4' R:A12 4.3 30.0 0.6 N9 R:G13 4.5 43.8 0.6 C4 R:G13 4.6 42.0 0.6

Zinc binding site 4 out of 6 in the Bacteriophage Qbeta Coat Protein in Complex with Rna Operator Hairpin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Bacteriophage Qbeta Coat Protein in Complex with Rna Operator Hairpin within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn103 b:97.3 occ:1.00 N7 R:G17 2.7 52.0 1.0 O6 R:G17 3.4 52.9 1.0 C5 R:G17 3.6 51.2 1.0 N7 R:A16 3.7 52.5 1.0 C8 R:G17 3.8 51.4 1.0 C6 R:G17 3.8 51.7 1.0 C8 R:A16 4.1 54.7 1.0 OP2 R:A16 4.2 48.1 0.6 C5 R:A16 4.4 51.7 1.0 OP2 R:G17 4.8 45.8 0.6 C4 R:G17 4.9 50.6 1.0 N6 R:A16 4.9 49.0 1.0 N9 R:G17 5.0 50.5 1.0 C6 R:A16 5.0 50.6 1.0

Zinc binding site 5 out of 6 in the Bacteriophage Qbeta Coat Protein in Complex with Rna Operator Hairpin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Bacteriophage Qbeta Coat Protein in Complex with Rna Operator Hairpin within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn104 b:82.6 occ:1.00 OP1 R:U6 2.2 51.1 1.0 OP2 R:A5 3.0 51.4 1.0 O5' R:A5 3.1 54.3 1.0 P R:A5 3.5 52.5 1.0 P R:U6 3.5 50.3 1.0 O3' R:C4 3.9 49.0 0.6 C3' R:C4 4.0 43.1 0.6 O3' R:A5 4.1 49.5 1.0 C5' R:A5 4.2 51.0 1.0 C2' R:C4 4.3 40.8 0.6 OP2 R:U6 4.4 51.8 1.0 O5' R:U6 4.6 48.5 1.0 C3' R:A5 4.7 50.2 1.0 C5 R:U6 4.8 40.4 1.0 CE A:LYS63 4.9 45.1 1.0 NZ A:LYS63 4.9 44.5 1.0 OP1 R:A5 4.9 55.0 1.0 O2' R:C4 5.0 39.4 0.6

Zinc binding site 6 out of 6 in the Bacteriophage Qbeta Coat Protein in Complex with Rna Operator Hairpin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Bacteriophage Qbeta Coat Protein in Complex with Rna Operator Hairpin within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn105 b:59.1 occ:1.00 OD2 A:ASP91 1.8 35.8 1.0 N1 R:A11 2.2 27.4 0.6 O A:HOH201 2.2 17.6 1.0 O R:HOH201 2.6 15.1 1.0 N6 R:A11 2.9 20.9 0.6 C6 R:A11 2.9 26.7 0.6 CG A:ASP91 3.0 34.6 1.0 C2 R:A11 3.2 26.0 0.6 OD1 A:ASP91 3.8 40.8 1.0 CB A:ASP91 3.9 31.4 1.0 N4 R:C9 4.1 26.5 0.6 C5 R:A11 4.2 28.5 0.6 N3 R:A11 4.4 27.2 0.6 CG2 B:THR93 4.5 22.6 1.0 CB B:THR93 4.5 22.4 1.0 CB A:TYR89 4.7 33.2 1.0 C4 R:A11 4.8 29.2 0.6 O B:THR93 4.8 22.3 1.0 CE B:LYS63 4.9 30.7 1.0 CB B:SER95 4.9 23.4 1.0 C4 R:C9 5.0 27.1 0.6

J.Rumnieks, K.Tars. Crystal Structure of the Bacteriophage Q Beta Coat Protein in Complex with the Rna Operator of the Replicase Gene. J.Mol.Biol. V. 426 1039 2014.
ISSN: ISSN 0022-2836
PubMed: 24035813
DOI: 10.1016/J.JMB.2013.08.025