Zinc in PDB 6xqi: Structure of Hiv-1 Vpr in Complex with the Human Nucleotide Excision Repair Protein HHR23A

The structure of Structure of Hiv-1 Vpr in Complex with the Human Nucleotide Excision Repair Protein HHR23A, PDB code: 6xqi was solved by G.C.Calero, Y.Wu, S.C.Weiss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.78 / 2.34
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.165, 130.165, 81.305, 90, 90, 120
R / Rfree (%)	20.2 / 22

The binding sites of Zinc atom in the Structure of Hiv-1 Vpr in Complex with the Human Nucleotide Excision Repair Protein HHR23A (pdb code 6xqi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Hiv-1 Vpr in Complex with the Human Nucleotide Excision Repair Protein HHR23A, PDB code: 6xqi:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Hiv-1 Vpr in Complex with the Human Nucleotide Excision Repair Protein HHR23A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Hiv-1 Vpr in Complex with the Human Nucleotide Excision Repair Protein HHR23A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:69.8 occ:1.00 ND1 A:HIS78 1.9 79.2 1.0 ND1 A:HIS33 2.0 68.2 1.0 NE2 A:HIS71 2.1 65.6 1.0 SG A:CYS76 2.3 70.8 1.0 CE1 A:HIS78 2.5 83.5 1.0 CE1 A:HIS33 3.0 68.8 1.0 CG A:HIS33 3.1 71.9 1.0 CD2 A:HIS71 3.1 61.5 1.0 CE1 A:HIS71 3.1 63.2 1.0 CG A:HIS78 3.2 88.8 1.0 CB A:CYS76 3.3 73.3 1.0 CB A:HIS33 3.4 68.8 1.0 NE2 A:HIS78 3.8 87.8 1.0 CB A:HIS78 3.9 103.8 1.0 CA A:CYS76 3.9 82.3 1.0 CA A:HIS33 4.0 67.8 1.0 CD2 A:HIS78 4.1 89.5 1.0 NE2 A:HIS33 4.1 68.1 1.0 CD2 A:HIS33 4.2 72.1 1.0 ND1 A:HIS71 4.2 63.0 1.0 CG A:HIS71 4.2 63.5 1.0 N A:HIS78 4.4 112.8 1.0 C A:CYS76 4.5 96.3 1.0 CE1 A:PHE72 4.6 52.7 1.0 N A:SER77 4.6 106.7 1.0 O A:ARG32 4.7 76.7 1.0 CA A:HIS78 4.8 111.0 1.0 O A:HIS33 4.8 71.8 1.0 O A:HOH206 4.9 89.3 1.0 N A:HIS33 4.9 65.2 1.0 C A:HIS33 4.9 68.8 1.0

Zinc binding site 2 out of 4 in the Structure of Hiv-1 Vpr in Complex with the Human Nucleotide Excision Repair Protein HHR23A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Hiv-1 Vpr in Complex with the Human Nucleotide Excision Repair Protein HHR23A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:57.0 occ:1.00 ND1 B:HIS33 2.1 56.5 1.0 NE2 B:HIS71 2.1 55.5 1.0 ND1 B:HIS78 2.2 57.9 1.0 SG B:CYS76 2.2 60.7 1.0 CD2 B:HIS71 3.0 55.6 1.0 O B:HOH201 3.0 110.0 1.0 CE1 B:HIS33 3.0 48.0 1.0 CE1 B:HIS78 3.1 57.6 1.0 CG B:HIS33 3.1 57.9 1.0 CB B:CYS76 3.2 50.0 1.0 CE1 B:HIS71 3.2 53.6 1.0 CG B:HIS78 3.3 65.8 1.0 CB B:HIS33 3.4 63.9 1.0 CB B:HIS78 3.6 55.1 1.0 CA B:CYS76 3.8 59.1 1.0 CA B:HIS33 4.1 57.2 1.0 O B:HOH204 4.1 68.2 1.0 NE2 B:HIS33 4.1 54.1 1.0 CG B:HIS71 4.2 56.0 1.0 CD2 B:HIS33 4.2 52.4 1.0 N B:HIS78 4.2 58.1 1.0 NE2 B:HIS78 4.2 67.4 1.0 ND1 B:HIS71 4.2 60.9 1.0 CD2 B:HIS78 4.3 57.7 1.0 C B:CYS76 4.5 63.0 1.0 N B:SER77 4.5 65.7 1.0 CA B:HIS78 4.5 59.8 1.0 CE1 B:PHE72 4.6 58.5 1.0 O B:ARG32 4.7 69.3 1.0 O B:HIS33 4.8 65.5 1.0

Zinc binding site 3 out of 4 in the Structure of Hiv-1 Vpr in Complex with the Human Nucleotide Excision Repair Protein HHR23A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Hiv-1 Vpr in Complex with the Human Nucleotide Excision Repair Protein HHR23A within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:56.5 occ:1.00 ND1 C:HIS78 2.0 62.0 1.0 NE2 C:HIS71 2.1 59.2 1.0 ND1 C:HIS33 2.1 58.1 1.0 SG C:CYS76 2.3 55.3 1.0 CE1 C:HIS78 2.9 56.1 1.0 CE1 C:HIS33 3.0 61.9 1.0 CD2 C:HIS71 3.0 59.0 1.0 CE1 C:HIS71 3.1 57.3 1.0 CG C:HIS33 3.1 63.4 1.0 CG C:HIS78 3.1 64.0 1.0 CB C:CYS76 3.2 50.0 1.0 CB C:HIS33 3.4 51.7 1.0 CB C:HIS78 3.6 57.5 1.0 CA C:CYS76 3.9 56.8 1.0 NE2 C:HIS78 4.1 64.6 1.0 NE2 C:HIS33 4.1 62.0 1.0 CA C:HIS33 4.1 60.5 1.0 CD2 C:HIS33 4.1 62.3 1.0 N C:HIS78 4.1 61.2 1.0 ND1 C:HIS71 4.2 64.1 1.0 CG C:HIS71 4.2 57.5 1.0 O C:HOH202 4.2 72.5 1.0 CD2 C:HIS78 4.2 52.7 1.0 C C:CYS76 4.4 60.0 1.0 N C:SER77 4.5 57.3 1.0 CA C:HIS78 4.5 66.7 1.0 CE2 C:PHE72 4.7 60.0 1.0 O C:ARG32 4.7 68.2 1.0 O C:HIS33 4.9 66.5 1.0

Zinc binding site 4 out of 4 in the Structure of Hiv-1 Vpr in Complex with the Human Nucleotide Excision Repair Protein HHR23A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Hiv-1 Vpr in Complex with the Human Nucleotide Excision Repair Protein HHR23A within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:67.8 occ:1.00 ND1 D:HIS78 2.0 71.1 1.0 ND1 D:HIS33 2.1 58.8 1.0 NE2 D:HIS71 2.1 66.8 1.0 SG D:CYS76 2.3 74.8 1.0 CE1 D:HIS78 2.8 77.2 1.0 CD2 D:HIS71 3.0 65.1 1.0 CG D:HIS33 3.0 70.6 1.0 CE1 D:HIS33 3.1 70.6 1.0 CG D:HIS78 3.1 85.2 1.0 CE1 D:HIS71 3.1 67.6 1.0 CB D:CYS76 3.2 78.5 1.0 CB D:HIS33 3.3 63.0 1.0 CB D:HIS78 3.6 99.9 1.0 CA D:CYS76 3.9 84.6 1.0 CA D:HIS33 4.0 67.6 1.0 NE2 D:HIS78 4.0 78.8 1.0 CD2 D:HIS78 4.1 84.7 1.0 NE2 D:HIS33 4.2 66.4 1.0 CG D:HIS71 4.2 63.8 1.0 CD2 D:HIS33 4.2 68.4 1.0 ND1 D:HIS71 4.2 74.2 1.0 N D:HIS78 4.2 110.6 1.0 C D:CYS76 4.5 89.8 1.0 N D:SER77 4.5 100.6 1.0 CA D:HIS78 4.6 111.3 1.0 CE2 D:PHE72 4.6 60.7 1.0 O D:HIS33 4.7 69.2 1.0 O D:ARG32 4.8 75.3 1.0 C D:HIS33 4.9 68.5 1.0 N D:HIS33 4.9 65.3 1.0

I.-J.L.Byeon, G.C.Calero, Y.Wu, C.H.Byeon, J.Jung, M.Delucia, X.Zhou, S.C.Weiss, J.Ahn, C.Hao, J.Skowronski, A.M.Gronenborn. Structure of Hiv-1 Vpr in Complex with the Human Nucleotide Excision Repair Protein HHR23A To Be Published.