Magnesium in PDB 1pjo: Crystal Structure of An Rna/Dna Hybrid of Hiv-1 Ppt

The structure of Crystal Structure of An Rna/Dna Hybrid of Hiv-1 Ppt, PDB code: 1pjo was solved by M.L.Kopka, L.Lavelle, G.W.Han, H.-L.Ng, R.E.Dickerson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.595, 40.755, 45.740, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / 15.6

The binding sites of Magnesium atom in the Crystal Structure of An Rna/Dna Hybrid of Hiv-1 Ppt (pdb code 1pjo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of An Rna/Dna Hybrid of Hiv-1 Ppt, PDB code: 1pjo:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of An Rna/Dna Hybrid of Hiv-1 Ppt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of An Rna/Dna Hybrid of Hiv-1 Ppt within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg31 b:8.3 occ:1.00 OP1 A:A9 2.0 10.3 1.0 O A:HOH133 2.1 10.6 1.0 O A:HOH132 2.1 11.1 1.0 O A:HOH134 2.2 11.4 1.0 P A:A9 3.4 9.9 1.0 H5'' A:A9 3.5 12.4 1.0 O A:HOH52 4.0 20.4 1.0 OP2 A:A9 4.1 10.7 1.0 O A:HOH87 4.2 14.6 1.0 O5' A:A9 4.2 10.3 1.0 C5' A:A9 4.3 10.3 1.0 O A:HOH142 4.4 11.6 1.0 O3' A:A8 4.4 10.3 1.0 OP2 A:G10 4.4 9.9 1.0 H5' A:A9 4.8 12.4 1.0 OP1 A:G10 5.0 10.2 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of An Rna/Dna Hybrid of Hiv-1 Ppt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of An Rna/Dna Hybrid of Hiv-1 Ppt within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg32 b:16.6 occ:1.00 O A:HOH137 2.0 23.9 1.0 O A:HOH136 2.0 17.7 1.0 O A:HOH138 2.0 16.1 1.0 O A:HOH140 2.0 22.3 1.0 O A:HOH139 2.1 24.3 1.0 OP2 A:G5 2.1 16.0 1.0 O A:HOH125 2.8 36.3 0.5 P A:G5 3.5 15.9 1.0 H3' A:A4 3.5 16.9 1.0 O A:HOH29 4.0 13.2 1.0 O5' A:G5 4.0 14.4 1.0 N7 A:G5 4.0 13.7 1.0 O A:HOH75 4.0 27.5 0.5 OP2 A:A6 4.2 17.0 1.0 O A:HOH62 4.3 31.3 1.0 C3' A:A4 4.3 14.1 1.0 H2' A:A4 4.3 15.7 1.0 N7 A:A6 4.3 13.7 1.0 H8 A:G5 4.4 15.8 1.0 O3' A:A4 4.4 15.2 1.0 H62 A:A6 4.4 14.7 1.0 C8 A:G5 4.4 13.2 1.0 O A:HOH107 4.4 44.0 1.0 H3' A:G5 4.5 16.8 1.0 OP1 A:G5 4.5 17.5 1.0 C5 A:G5 4.8 12.0 1.0 O A:HOH49 4.8 30.7 1.0 C2' A:A4 4.9 13.1 1.0 H8 A:A6 5.0 15.9 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of An Rna/Dna Hybrid of Hiv-1 Ppt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of An Rna/Dna Hybrid of Hiv-1 Ppt within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg33 b:8.8 occ:1.00 OP2 A:A9 2.0 10.7 1.0 O A:HOH144 2.0 14.9 1.0 O A:HOH142 2.0 11.6 1.0 O A:HOH141 2.1 12.5 1.0 O A:HOH143 2.1 11.6 1.0 O A:HOH145 2.1 13.7 1.0 P A:A9 3.4 9.9 1.0 H3' A:A8 3.5 13.1 1.0 O5' A:A9 4.0 10.3 1.0 O A:HOH55 4.0 25.6 1.0 O A:HOH64 4.1 35.1 1.0 H8 A:A9 4.2 13.8 1.0 O A:HOH128 4.2 12.3 1.0 N7 A:A9 4.2 10.9 1.0 OP2 A:G10 4.3 9.9 1.0 C3' A:A8 4.3 10.9 1.0 O3' A:A8 4.3 10.3 1.0 O A:HOH134 4.4 11.4 1.0 OP1 A:A9 4.4 10.3 1.0 C8 A:A9 4.4 11.5 1.0 H3' A:A9 4.6 12.6 1.0 N7 A:G10 4.7 9.9 1.0 O A:HOH44 4.7 18.7 1.0 H2' A:A8 4.8 13.7 1.0 O A:HOH52 4.9 20.4 1.0 H5' A:A8 5.0 18.1 1.0 O A:HOH132 5.0 11.1 1.0 H5'' A:A8 5.0 18.1 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of An Rna/Dna Hybrid of Hiv-1 Ppt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of An Rna/Dna Hybrid of Hiv-1 Ppt within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg35 b:21.7 occ:0.70 O B:HOH155 1.9 36.1 0.7 O A:HOH150 1.9 24.4 0.7 O A:HOH154 1.9 27.6 0.7 O B:HOH153 2.0 31.8 0.7 O A:HOH151 2.1 34.4 0.7 O A:HOH152 2.2 22.5 0.7 H61 A:A3 3.7 15.8 1.0 H62 A:A4 3.8 13.9 1.0 O B:HOH97 4.1 42.3 1.0 O B:HOH84 4.1 39.9 1.0 O A:HOH103 4.1 49.3 1.0 O A:HOH116 4.1 38.6 1.0 O A:HOH48 4.2 26.2 1.0 O B:HOH129 4.3 16.1 1.0 O A:HOH79 4.4 35.7 1.0 N7 A:A3 4.4 13.6 1.0 N6 A:A4 4.4 11.6 1.0 O B:HOH127 4.5 14.8 1.0 H61 A:A4 4.5 13.9 1.0 O B:HOH121 4.5 41.1 1.0 N6 A:A3 4.5 13.2 1.0 O B:HOH53 4.7 19.6 1.0 H71 B:DT15 4.8 18.6 1.0 H72 B:DT15 4.9 18.6 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of An Rna/Dna Hybrid of Hiv-1 Ppt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of An Rna/Dna Hybrid of Hiv-1 Ppt within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg36 b:32.3 occ:0.30 O A:HOH156 1.9 35.8 0.3 OP1 A:A7 2.0 21.6 1.0 O A:HOH160 2.0 40.0 0.3 O A:HOH159 2.2 30.5 0.3 O A:HOH157 2.2 27.8 0.3 O A:HOH158 2.4 42.9 0.3 O A:HOH101 3.5 23.6 0.3 P A:A7 3.5 18.6 1.0 H5'' A:A7 3.7 21.6 1.0 O5' A:A7 4.2 17.6 1.0 C5' A:A7 4.3 18.0 1.0 O3' A:A6 4.3 17.1 1.0 H5' A:A7 4.3 21.6 1.0 OP2 A:A7 4.4 20.8 1.0 O A:HOH66 4.6 27.0 1.0 O A:HOH118 5.0 38.3 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of An Rna/Dna Hybrid of Hiv-1 Ppt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of An Rna/Dna Hybrid of Hiv-1 Ppt within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg34 b:11.6 occ:1.00 O B:HOH146 1.9 17.0 1.0 OP1 B:DT18 2.0 10.7 1.0 H5'' B:DT18 3.2 11.3 1.0 P B:DT18 3.5 10.0 1.0 C5' B:DT18 3.9 9.4 1.0 H5' B:DT18 4.0 11.3 1.0 O5' B:DT18 4.0 9.7 1.0 O3' B:DT17 4.3 10.0 1.0 OP2 B:DT18 4.5 10.3 1.0

M.L.Kopka, L.Lavelle, G.W.Han, H.-L.Ng, R.E.Dickerson. An Unusual Sugar Conformation in the Structure of An Rna/Dna Decamer of the Polypurine Tract May Affect Recognition By Rnase H J.Mol.Biol. V. 334 653 2003.
ISSN: ISSN 0022-2836
PubMed: 14636594
DOI: 10.1016/J.JMB.2003.09.057