Manganese in PDB 1y90: Hiv-1 Dis(Mal) Duplex Mn-Soaked

The structure of Hiv-1 Dis(Mal) Duplex Mn-Soaked, PDB code: 1y90 was solved by E.Ennifar, P.Walter, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 3.08
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.080, 59.080, 63.659, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 24.4

The structure of Hiv-1 Dis(Mal) Duplex Mn-Soaked also contains other interesting chemical elements:

Bromine

(Br)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Manganese atom in the Hiv-1 Dis(Mal) Duplex Mn-Soaked (pdb code 1y90). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Hiv-1 Dis(Mal) Duplex Mn-Soaked, PDB code: 1y90:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in the Hiv-1 Dis(Mal) Duplex Mn-Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Hiv-1 Dis(Mal) Duplex Mn-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn101 b:60.2 occ:1.00 O6 A:G7 4.4 41.0 1.0 O4 A:U6 4.6 46.0 1.0 N7 A:G7 4.8 43.4 1.0

Manganese binding site 2 out of 12 in the Hiv-1 Dis(Mal) Duplex Mn-Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Hiv-1 Dis(Mal) Duplex Mn-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn102 b:50.9 occ:0.48 OP1 B:G9 2.3 36.6 0.5 OP2 B:G9 2.5 43.5 0.5 OP1 A:G9 2.5 51.5 1.0 P B:G9 3.4 42.3 0.5 O2' B:A8 3.7 49.8 0.5 OP1 B:G9 3.7 41.9 0.5 P B:G9 3.7 36.1 0.5 O3' B:A8 3.8 44.4 0.5 P A:G9 3.8 50.4 1.0 O3' A:A8 4.0 49.9 1.0 C5' B:G9 4.2 35.8 0.5 O5' B:G9 4.3 36.2 0.5 OP1 B:G10 4.3 42.4 1.0 O3' B:A8 4.4 38.3 0.5 C2' B:A8 4.7 48.7 0.5 O2' A:A8 4.7 52.7 1.0 OP2 B:G9 4.8 35.9 0.5 OP2 A:G9 4.8 50.6 1.0 O5' A:G9 4.8 49.6 1.0 O5' B:G9 4.8 42.0 0.5 C3' B:A8 4.8 46.6 0.5 O3' B:G9 4.9 39.4 0.5 C5' A:G9 4.9 48.2 1.0

Manganese binding site 3 out of 12 in the Hiv-1 Dis(Mal) Duplex Mn-Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Hiv-1 Dis(Mal) Duplex Mn-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn103 b:58.8 occ:0.91 N4 B:C20 3.8 50.0 1.0 N7 B:A18 3.9 41.8 1.0 N7 B:G19 4.1 47.4 1.0 O6 B:G19 4.3 48.3 1.0 C8 B:A18 4.4 41.1 1.0 OP2 B:A18 4.4 46.7 1.0 C5 B:A18 4.6 42.2 1.0 OP2 B:G19 4.9 45.6 1.0 C5 B:G19 4.9 47.3 1.0 C4 B:C20 5.0 47.4 1.0 N6 B:A18 5.0 40.8 1.0 C6 B:G19 5.0 46.3 1.0

Manganese binding site 4 out of 12 in the Hiv-1 Dis(Mal) Duplex Mn-Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Hiv-1 Dis(Mal) Duplex Mn-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn104 b:51.7 occ:0.53 O6 B:G4 2.7 39.2 1.0 O4 B:U3 3.0 45.0 1.0 C6 B:G4 3.8 37.2 1.0 N4 A:C20 3.9 40.3 1.0 C4 B:U3 4.0 42.3 1.0 MN A:MN111 4.2 60.8 0.5 N7 B:G4 4.3 36.2 1.0 C5 B:G4 4.5 35.3 1.0 C5 B:U3 4.6 40.3 1.0 BR B:5BU2 4.6 62.8 0.7 N6 A:A21 4.6 31.6 1.0 N4 B:C5 4.9 33.0 1.0 O4 B:5BU2 5.0 52.1 1.0 N1 B:G4 5.0 36.4 1.0

Manganese binding site 5 out of 12 in the Hiv-1 Dis(Mal) Duplex Mn-Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Hiv-1 Dis(Mal) Duplex Mn-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn105 b:59.9 occ:0.73 O6 B:G7 3.3 33.0 0.5 O4 B:U6 3.7 37.7 1.0 N7 B:G7 3.9 35.0 0.5 O6 B:G7 4.0 35.7 0.5 C6 B:G7 4.2 33.8 0.5 C4 B:U6 4.2 37.1 1.0 C5 B:G7 4.4 34.4 0.5 C5 B:U6 4.4 35.9 1.0 N7 B:G7 4.8 35.2 0.5 C6 B:G7 5.0 35.3 0.5

Manganese binding site 6 out of 12 in the Hiv-1 Dis(Mal) Duplex Mn-Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Hiv-1 Dis(Mal) Duplex Mn-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn106 b:38.9 occ:1.00 N7 B:G9 2.2 39.3 0.5 OP2 B:A8 2.3 39.8 0.5 N7 B:G9 2.3 39.8 0.5 OP2 B:A8 2.6 39.5 0.5 C5 B:G9 3.0 39.0 0.5 O6 B:G9 3.1 39.4 0.5 O6 B:G9 3.2 39.6 0.5 C5 B:G9 3.2 39.7 0.5 C8 B:G9 3.3 38.5 0.5 C6 B:G9 3.3 38.6 0.5 C8 B:G9 3.4 39.2 0.5 P B:A8 3.5 38.1 0.5 C6 B:G9 3.5 39.4 0.5 P B:A8 3.7 38.2 0.5 OP1 B:A8 3.8 38.6 0.5 OP1 B:A8 3.9 38.3 0.5 OP2 B:G9 4.0 35.9 0.5 C4 B:G9 4.2 38.3 0.5 O3' B:G7 4.3 37.9 0.5 N9 B:G9 4.3 37.9 0.5 C2' B:G7 4.4 37.2 0.5 C3' B:G7 4.4 37.3 0.5 C4 B:G9 4.5 39.1 0.5 O6 B:G10 4.5 41.4 1.0 N9 B:G9 4.6 39.1 0.5 N7 B:G10 4.7 37.5 1.0 N1 B:G9 4.7 38.0 0.5 C2' B:G7 4.7 35.8 0.5 O5' B:A8 4.7 38.9 0.5 O3' B:G7 4.8 37.1 0.5 O5' B:A8 4.8 40.6 0.5 C3' B:G7 4.8 35.7 0.5 C5' B:A8 4.9 43.5 0.5 N1 B:G9 4.9 38.7 0.5 C5' B:A8 5.0 39.3 0.5 O5' B:G9 5.0 36.2 0.5

Manganese binding site 7 out of 12 in the Hiv-1 Dis(Mal) Duplex Mn-Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Hiv-1 Dis(Mal) Duplex Mn-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn107 b:46.7 occ:1.00 OP2 A:A8 2.4 43.2 1.0 N7 A:G9 2.6 45.5 1.0 O6 A:G9 3.4 43.3 1.0 C5 A:G9 3.4 43.5 1.0 C8 A:G9 3.6 42.5 1.0 C6 A:G9 3.8 42.3 1.0 P A:A8 3.8 43.7 1.0 OP1 A:A8 4.4 43.0 1.0 O3' A:G7 4.5 42.5 1.0 C3' A:G7 4.6 43.0 1.0 C2' A:G7 4.6 43.5 1.0 OP2 A:G9 4.6 50.6 1.0 C4 A:G9 4.7 42.8 1.0 N9 A:G9 4.7 42.6 1.0 O5' A:A8 4.9 45.6 1.0 N7 A:G10 5.0 50.3 1.0

Manganese binding site 8 out of 12 in the Hiv-1 Dis(Mal) Duplex Mn-Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Hiv-1 Dis(Mal) Duplex Mn-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn108 b:61.4 occ:0.51 O6 B:G12 3.4 46.9 1.0 O4 B:U11 3.8 36.0 1.0 N7 B:G12 4.1 48.3 1.0 C4 B:U11 4.3 35.6 1.0 C6 B:G12 4.3 48.1 1.0 N4 B:C13 4.5 55.3 1.0 C5 B:G12 4.6 48.4 1.0 C5 B:U11 4.7 35.8 1.0 O6 A:G12 4.9 62.3 1.0

Manganese binding site 9 out of 12 in the Hiv-1 Dis(Mal) Duplex Mn-Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Hiv-1 Dis(Mal) Duplex Mn-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn109 b:64.3 occ:0.64 C4 A:A8 4.3 45.0 1.0 O4' A:A8 4.4 48.3 1.0 C5 A:A8 4.5 43.6 1.0 N3 A:A8 4.5 46.4 1.0 N9 A:A8 4.6 45.2 1.0 C2 A:A8 4.7 47.8 1.0 C6 A:A8 4.8 44.3 1.0 N7 A:A8 4.9 42.9 1.0 O5' A:A8 4.9 45.6 1.0 C8 A:A8 4.9 44.4 1.0 N1 A:A8 4.9 46.5 1.0

Manganese binding site 10 out of 12 in the Hiv-1 Dis(Mal) Duplex Mn-Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Hiv-1 Dis(Mal) Duplex Mn-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn110 b:63.8 occ:0.64 N7 A:A22 3.6 31.0 1.0 N6 A:A22 4.3 28.1 1.0 O6 A:G23 4.5 42.4 1.0 C8 A:A22 4.5 30.9 1.0 OP2 A:A22 4.5 43.0 1.0 C5 A:A22 4.5 28.7 1.0 N7 A:G23 4.6 40.3 1.0 C6 A:A22 4.9 28.6 1.0

E.Ennifar, P.Walter, P.Dumas. A Crystallographic Study of the Binding of 13 Metal Ions to Two Related Rna Duplexes Nucleic Acids Res. V. 31 2671 2003.
ISSN: ISSN 0305-1048
PubMed: 12736317
DOI: 10.1093/NAR/GKG350