Zinc in PDB 1k6y: Crystal Structure of A Two-Domain Fragment of Hiv-1 Integrase

All present enzymatic activity of Crystal Structure of A Two-Domain Fragment of Hiv-1 Integrase:
2.7.7.49;

The structure of Crystal Structure of A Two-Domain Fragment of Hiv-1 Integrase, PDB code: 1k6y was solved by J.Wang, H.Ling, W.Yang, R.Craigie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.40
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	102.710, 102.710, 280.560, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 26

The structure of Crystal Structure of A Two-Domain Fragment of Hiv-1 Integrase also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of A Two-Domain Fragment of Hiv-1 Integrase (pdb code 1k6y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A Two-Domain Fragment of Hiv-1 Integrase, PDB code: 1k6y:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A Two-Domain Fragment of Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Two-Domain Fragment of Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:50.2 occ:1.00 NE2 A:HIS12 2.3 24.9 1.0 ND1 A:HIS16 2.3 34.6 1.0 SG A:CYS40 2.4 50.2 1.0 SG A:CYS43 2.5 54.7 1.0 CD2 A:HIS12 3.1 23.3 1.0 CB A:CYS40 3.2 50.8 1.0 CE1 A:HIS12 3.2 22.2 1.0 CG A:HIS16 3.2 33.5 1.0 CE1 A:HIS16 3.3 33.9 1.0 CB A:CYS43 3.4 60.3 1.0 CB A:HIS16 3.4 28.9 1.0 CA A:HIS16 3.9 29.5 1.0 CG A:HIS12 4.2 22.9 1.0 ND1 A:HIS12 4.2 21.3 1.0 N A:CYS43 4.2 61.1 1.0 CD2 A:HIS16 4.3 33.9 1.0 NE2 A:HIS16 4.3 34.1 1.0 CA A:CYS43 4.4 61.9 1.0 C A:LYS42 4.4 60.4 1.0 O A:HIS12 4.5 31.8 1.0 CA A:CYS40 4.6 50.4 1.0 O A:LYS42 4.7 60.0 1.0 CB A:LYS42 4.7 59.3 1.0 C A:HIS16 4.7 29.3 1.0 O A:HIS16 4.8 27.7 1.0 CA A:LYS42 4.9 59.7 1.0 N A:LYS42 4.9 59.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Two-Domain Fragment of Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Two-Domain Fragment of Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:50.6 occ:1.00 ND1 B:HIS16 2.3 32.2 1.0 NE2 B:HIS12 2.3 21.6 1.0 SG B:CYS43 2.4 32.2 1.0 SG B:CYS40 2.6 33.2 1.0 CD2 B:HIS12 3.1 23.8 1.0 CG B:HIS16 3.2 33.2 1.0 CE1 B:HIS12 3.2 21.7 1.0 CB B:CYS40 3.3 34.3 1.0 CE1 B:HIS16 3.3 34.3 1.0 CB B:HIS16 3.3 28.7 1.0 CB B:CYS43 3.6 40.2 1.0 CA B:HIS16 3.7 28.0 1.0 CG B:HIS12 4.1 24.2 1.0 ND1 B:HIS12 4.2 23.4 1.0 N B:CYS43 4.2 43.6 1.0 O B:HIS12 4.3 28.3 1.0 CD2 B:HIS16 4.3 33.8 1.0 NE2 B:HIS16 4.4 36.4 1.0 CB B:LYS42 4.5 43.2 1.0 C B:LYS42 4.5 42.9 1.0 CA B:CYS43 4.5 45.0 1.0 C B:HIS16 4.5 28.3 1.0 O B:HIS16 4.8 29.6 1.0 CA B:CYS40 4.8 36.2 1.0 CA B:LYS42 4.8 43.0 1.0 N B:HIS16 4.9 26.5 1.0 N B:LYS42 4.9 43.3 1.0 O B:LYS42 4.9 42.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Two-Domain Fragment of Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Two-Domain Fragment of Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn403 b:41.5 occ:1.00 NE2 C:HIS12 2.2 18.1 1.0 ND1 C:HIS16 2.4 23.3 1.0 SG C:CYS43 2.5 41.5 1.0 SG C:CYS40 2.5 32.0 1.0 CD2 C:HIS12 2.9 19.5 1.0 CE1 C:HIS12 3.3 20.7 1.0 CB C:CYS43 3.3 47.0 1.0 CG C:HIS16 3.3 23.0 1.0 CB C:CYS40 3.3 30.5 1.0 CE1 C:HIS16 3.3 24.1 1.0 CB C:HIS16 3.5 19.4 1.0 CA C:HIS16 3.8 19.0 1.0 N C:CYS43 3.9 46.2 1.0 CG C:HIS12 4.1 22.8 1.0 ND1 C:HIS12 4.2 21.5 1.0 CA C:CYS43 4.2 49.1 1.0 C C:LYS42 4.3 44.1 1.0 O C:HIS12 4.4 26.5 1.0 CD2 C:HIS16 4.4 24.8 1.0 NE2 C:HIS16 4.5 27.1 1.0 CB C:LYS42 4.5 41.1 1.0 C C:HIS16 4.7 18.6 1.0 CA C:CYS40 4.7 32.3 1.0 CA C:LYS42 4.8 42.4 1.0 N C:LYS42 4.8 41.4 1.0 O C:LYS42 4.9 44.2 1.0 O C:HIS16 5.0 16.9 1.0 N C:HIS16 5.0 19.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Two-Domain Fragment of Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Two-Domain Fragment of Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn404 b:39.5 occ:1.00 NE2 D:HIS12 2.2 21.0 1.0 ND1 D:HIS16 2.3 19.3 1.0 SG D:CYS43 2.5 32.6 1.0 SG D:CYS40 2.5 26.5 1.0 CE1 D:HIS12 3.1 17.5 1.0 CD2 D:HIS12 3.1 19.3 1.0 CG D:HIS16 3.2 19.9 1.0 CB D:CYS40 3.3 26.9 1.0 CE1 D:HIS16 3.3 20.4 1.0 CB D:HIS16 3.4 17.0 1.0 CB D:CYS43 3.6 39.6 1.0 CA D:HIS16 3.9 19.5 1.0 N D:CYS43 4.1 40.8 1.0 ND1 D:HIS12 4.1 18.4 1.0 CG D:HIS12 4.1 20.2 1.0 CB D:LYS42 4.2 37.4 1.0 CD2 D:HIS16 4.4 20.5 1.0 C D:LYS42 4.4 39.6 1.0 NE2 D:HIS16 4.4 20.3 1.0 CA D:CYS43 4.5 43.1 1.0 O D:HIS12 4.6 20.3 1.0 CA D:LYS42 4.7 38.5 1.0 C D:HIS16 4.7 19.9 1.0 N D:LYS42 4.8 38.1 1.0 CA D:CYS40 4.8 28.5 1.0 O D:HIS16 4.8 19.6 1.0 CG D:LYS42 4.9 38.6 1.0 O D:LYS42 5.0 40.3 1.0

J.Y.Wang, H.Ling, W.Yang, R.Craigie. Structure of A Two-Domain Fragment of Hiv-1 Integrase: Implications For Domain Organization in the Intact Protein. Embo J. V. 20 7333 2001.
ISSN: ISSN 0261-4189
PubMed: 11743009
DOI: 10.1093/EMBOJ/20.24.7333