Zinc in PDB 1nlc: Hiv-1 Dis(Mal) Duplex Zn-Soaked

The structure of Hiv-1 Dis(Mal) Duplex Zn-Soaked, PDB code: 1nlc 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)	8.00 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.333, 59.333, 63.683, 90.00, 90.00, 120.00
R / Rfree (%)	21.8 / 21.9

The binding sites of Zinc atom in the Hiv-1 Dis(Mal) Duplex Zn-Soaked (pdb code 1nlc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Hiv-1 Dis(Mal) Duplex Zn-Soaked, PDB code: 1nlc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Hiv-1 Dis(Mal) Duplex Zn-Soaked


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hiv-1 Dis(Mal) Duplex Zn-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn54 b:39.3 occ:0.88 O A:HOH156 2.0 39.4 1.0 OP2 A:A8 2.2 33.5 1.0 O A:HOH137 2.2 21.7 0.6 O A:HOH241 2.3 39.3 0.9 O A:HOH256 2.4 32.8 0.8 N7 A:G9 2.5 37.3 1.0 C8 A:G9 3.4 37.2 1.0 C5 A:G9 3.5 37.3 1.0 P A:A8 3.6 33.6 1.0 O6 A:G9 3.7 37.3 1.0 O A:HOH198 4.0 32.4 0.9 C6 A:G9 4.0 37.3 1.0 OP1 A:A8 4.2 33.5 1.0 O B:HOH155 4.3 36.8 0.8 O3' A:G7 4.4 33.3 1.0 OP2 A:G9 4.4 35.9 1.0 C3' A:G7 4.5 32.9 1.0 C2' A:G7 4.5 32.9 1.0 O A:HOH331 4.6 31.9 0.7 O5' A:A8 4.7 33.9 1.0 N9 A:G9 4.7 37.3 1.0 C4 A:G9 4.7 37.3 1.0 N7 A:G10 4.9 39.6 1.0 O A:HOH135 4.9 49.9 0.8 C5' A:A8 5.0 34.4 1.0 O6 A:G10 5.0 39.6 1.0

Zinc binding site 2 out of 6 in the Hiv-1 Dis(Mal) Duplex Zn-Soaked


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hiv-1 Dis(Mal) Duplex Zn-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn50 b:43.9 occ:0.70 O A:HOH386 2.0 33.0 0.9 O A:HOH168 2.0 61.5 1.0 O A:HOH387 2.1 37.4 1.0 O A:HOH388 2.2 31.1 0.9 O A:HOH319 2.3 35.5 0.6 O A:HOH347 4.0 36.0 0.8 O A:HOH290 4.2 39.0 0.7 O B:HOH317 4.2 37.1 0.9 O6 A:G7 4.3 32.5 1.0 O4 A:U6 4.4 31.9 1.0 O A:HOH311 4.5 36.9 0.8 N7 A:G7 4.5 32.6 1.0 O A:HOH198 4.6 32.4 0.9 O B:HOH259 4.6 49.0 0.8 O B:HOH321 4.8 32.2 0.6 C5 A:U6 4.8 32.1 1.0 C4 A:U6 4.9 32.0 1.0 O B:HOH258 5.0 44.5 0.8

Zinc binding site 3 out of 6 in the Hiv-1 Dis(Mal) Duplex Zn-Soaked


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Hiv-1 Dis(Mal) Duplex Zn-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn53 b:23.9 occ:0.78 O B:HOH378 2.1 49.0 1.0 OP2 B:A8 2.1 23.6 0.5 O B:HOH354 2.2 32.4 1.0 N7 B:G9 2.2 26.2 0.5 N7 B:G9 2.2 23.0 0.5 O B:HOH355 2.2 26.6 0.9 O B:HOH353 2.3 31.4 0.8 OP2 B:A8 2.4 23.8 0.5 C8 B:G9 3.1 26.2 0.5 C5 B:G9 3.1 26.2 0.5 C8 B:G9 3.1 23.0 0.5 C5 B:G9 3.3 23.0 0.5 P B:A8 3.3 23.7 0.5 O6 B:G9 3.4 26.2 0.5 C6 B:G9 3.6 26.2 0.5 O6 B:G9 3.6 23.0 0.5 P B:A8 3.6 23.9 0.5 C6 B:G9 3.8 23.0 0.5 OP1 B:A8 3.9 23.6 0.5 OP1 B:A8 4.0 23.9 0.5 C2' B:G7 4.0 23.4 0.5 O A:HOH223 4.2 53.4 0.5 O B:HOH296 4.2 25.7 0.9 O3' B:G7 4.2 23.6 0.5 C3' B:G7 4.2 23.4 0.5 N9 B:G9 4.2 26.2 0.5 C4 B:G9 4.3 26.2 0.5 OP2 B:G9 4.3 25.1 0.5 N9 B:G9 4.4 23.0 0.5 C4 B:G9 4.4 23.0 0.5 O5' B:A8 4.5 23.9 0.5 C2' B:G7 4.6 24.0 0.5 O B:HOH391 4.6 38.1 0.5 O3' B:G7 4.6 24.0 0.5 O5' B:A8 4.7 23.9 0.5 C5' B:A8 4.7 24.2 0.5 C3' B:G7 4.7 24.1 0.5 C5' B:A8 4.7 23.9 0.5 O B:HOH324 4.8 37.4 0.6 N7 B:G10 4.8 28.6 1.0 OP2 B:G9 4.8 23.6 0.5 O2' B:G7 4.9 23.4 0.5 O5' B:G9 4.9 25.4 0.5 O6 B:G10 4.9 28.7 1.0 N1 B:G9 4.9 26.2 0.5 N9 B:G7 4.9 23.4 0.5 O5' B:G9 5.0 23.5 0.5

Zinc binding site 4 out of 6 in the Hiv-1 Dis(Mal) Duplex Zn-Soaked


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Hiv-1 Dis(Mal) Duplex Zn-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn55 b:45.3 occ:0.33 N7 B:A22 2.5 36.2 1.0 O B:HOH174 2.7 56.2 0.9 O B:HOH215 3.2 42.9 0.9 C8 B:A22 3.3 36.2 1.0 C5 B:A22 3.7 36.1 1.0 OP2 B:A22 3.7 35.9 1.0 O B:HOH160 3.8 32.4 0.5 N6 B:A22 3.9 36.1 1.0 O B:HOH152 4.0 60.1 0.5 N7 B:A21 4.1 35.2 1.0 C6 B:A22 4.2 36.1 1.0 C8 B:A21 4.4 35.2 1.0 N7 B:G23 4.5 35.9 1.0 C5 B:A21 4.6 35.2 1.0 N9 B:A22 4.6 36.2 1.0 OP2 B:A21 4.7 34.2 1.0 C4 B:A22 4.8 36.2 1.0 O6 B:G23 4.8 35.9 1.0 P B:A22 5.0 35.8 1.0

Zinc binding site 5 out of 6 in the Hiv-1 Dis(Mal) Duplex Zn-Soaked


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Hiv-1 Dis(Mal) Duplex Zn-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn51 b:40.3 occ:0.74 O B:HOH385 2.1 50.1 1.0 O A:HOH389 2.1 49.5 0.7 O B:HOH390 2.2 52.7 0.9 O B:HOH384 2.2 53.4 1.0 O B:HOH376 2.3 23.5 0.6 O B:HOH330 2.4 39.3 0.6 O B:HOH342 3.7 25.2 0.7 O A:HOH218 3.9 35.5 0.7 O B:HOH128 4.0 30.9 0.9 O A:HOH299 4.1 41.3 0.3 O6 B:G4 4.3 30.2 1.0 O4 B:U3 4.4 31.7 1.0 O B:HOH301 4.4 32.8 0.7 O B:HOH309 4.4 36.1 0.8 O B:HOH235 4.4 29.2 0.6 O A:HOH216 4.5 48.4 0.6 N7 B:G4 4.5 30.2 1.0 C5 B:U3 4.7 31.8 1.0 C4 B:U3 4.8 31.8 1.0 O A:HOH370 5.0 46.0 0.9

Zinc binding site 6 out of 6 in the Hiv-1 Dis(Mal) Duplex Zn-Soaked


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Hiv-1 Dis(Mal) Duplex Zn-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn52 b:46.2 occ:0.68 O B:HOH392 2.0 37.4 0.5 O B:HOH391 2.1 51.8 0.5 O B:HOH393 2.2 37.3 0.6 O B:HOH380 2.3 47.4 1.0 O B:HOH381 2.5 39.9 1.0 O B:HOH391 3.2 38.1 0.5 O A:HOH300 3.9 26.4 0.8 O6 B:G7 3.9 23.4 0.5 O B:HOH302 4.1 19.4 0.6 O6 B:G7 4.2 23.9 0.5 O A:HOH228 4.2 42.0 0.7 O4 B:U6 4.3 25.7 1.0 O B:HOH375 4.4 67.6 0.9 N7 B:G7 4.4 23.3 0.5 O B:HOH334 4.5 44.5 0.6 O B:HOH178 4.5 28.3 1.0 O A:HOH271 4.6 43.4 0.4 C5 B:U6 4.8 25.8 1.0 C4 B:U6 4.8 25.9 1.0 C6 B:G7 4.8 23.3 0.5 N7 B:G7 4.8 23.9 0.5

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