Zinc in PDB 4z8l: Crystal Structure of DCAF1/Siv-Mnd Vpx/Mnd SAMHD1 Ntd Ternary Complex

All present enzymatic activity of Crystal Structure of DCAF1/Siv-Mnd Vpx/Mnd SAMHD1 Ntd Ternary Complex:
2.7.11.1;

The structure of Crystal Structure of DCAF1/Siv-Mnd Vpx/Mnd SAMHD1 Ntd Ternary Complex, PDB code: 4z8l was solved by L.M.Koharudin, Y.Wu, G.Calero, J.Ahn, A.M.Gronenborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.70 / 2.60
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	74.490, 74.490, 178.180, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 22.8

The binding sites of Zinc atom in the Crystal Structure of DCAF1/Siv-Mnd Vpx/Mnd SAMHD1 Ntd Ternary Complex (pdb code 4z8l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of DCAF1/Siv-Mnd Vpx/Mnd SAMHD1 Ntd Ternary Complex, PDB code: 4z8l:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of DCAF1/Siv-Mnd Vpx/Mnd SAMHD1 Ntd Ternary Complex


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 DCAF1/Siv-Mnd Vpx/Mnd SAMHD1 Ntd Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:68.9 occ:1.00 ND1 B:HIS38 2.0 63.5 1.0 NE2 B:HIS81 2.1 30.3 1.0 CB B:CYS86 2.5 51.3 1.0 CE1 B:HIS38 2.7 58.2 1.0 CE1 B:HIS81 3.0 40.7 1.0 SG B:CYS86 3.1 55.4 1.0 CD2 B:HIS81 3.2 30.6 1.0 CG B:HIS38 3.2 62.1 1.0 CB B:HIS38 3.8 59.5 1.0 NE2 B:HIS38 3.9 44.6 1.0 CA B:CYS86 3.9 47.5 1.0 CD2 B:HIS38 4.1 42.1 1.0 CA B:HIS38 4.1 58.1 1.0 ND1 B:HIS81 4.2 51.6 1.0 CG B:HIS81 4.3 48.2 1.0 SG B:CYS88 4.3 75.5 1.0 O B:LEU37 4.4 71.7 1.0 O B:HIS38 4.7 52.4 1.0 C B:CYS86 4.7 51.9 1.0 N B:CYS86 4.8 43.6 1.0 SD B:MET82 4.9 37.6 1.0 C B:HIS38 4.9 41.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of DCAF1/Siv-Mnd Vpx/Mnd SAMHD1 Ntd Ternary Complex


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 DCAF1/Siv-Mnd Vpx/Mnd SAMHD1 Ntd Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:56.3 occ:1.00 ND1 E:HIS38 2.0 33.2 1.0 CE1 E:HIS38 2.5 42.3 1.0 NE2 E:HIS81 2.5 39.1 1.0 CB E:CYS86 2.6 60.9 1.0 SG E:CYS86 3.1 81.9 1.0 CG E:HIS38 3.2 45.9 1.0 CD2 E:HIS81 3.5 53.2 1.0 CE1 E:HIS81 3.5 44.9 1.0 NE2 E:HIS38 3.8 46.7 1.0 CB E:HIS38 3.9 38.3 1.0 CA E:CYS86 4.0 54.1 1.0 CD2 E:HIS38 4.1 45.5 1.0 CA E:HIS38 4.2 33.0 1.0 O E:LEU37 4.2 56.9 1.0 SG E:CYS88 4.5 60.3 1.0 ND1 E:HIS81 4.6 53.6 1.0 CG E:HIS81 4.6 50.7 1.0 C E:CYS86 4.8 52.8 1.0 SD E:MET82 4.9 46.3 1.0 C E:LEU37 5.0 60.8 1.0 N E:CYS86 5.0 52.9 1.0

Y.Wu, L.M.Koharudin, J.Mehrens, M.Delucia, C.H.Byeon, I.J.Byeon, G.Calero, J.Ahn, A.M.Gronenborn. Structural Basis of Clade-Specific Engagement of SAMHD1 (Sterile Alpha Motif and Histidine/Aspartate-Containing Protein 1) Restriction Factors By Lentiviral Viral Protein X (Vpx) Virulence Factors. J.Biol.Chem. V. 290 17935 2015.
ISSN: ESSN 1083-351X
PubMed: 26045556
DOI: 10.1074/JBC.M115.665513