Zinc in PDB 6u6z: Human SAMHD1 Bound to Deoxyribo(Tg*Ttca)-Oligonucleotide

The structure of Human SAMHD1 Bound to Deoxyribo(Tg*Ttca)-Oligonucleotide, PDB code: 6u6z was solved by A.B.Taylor, C.H.Yu, D.N.Ivanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.27 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	81.610, 94.670, 96.320, 72.90, 70.95, 64.96
R / Rfree (%)	17.4 / 20.6

The binding sites of Zinc atom in the Human SAMHD1 Bound to Deoxyribo(Tg*Ttca)-Oligonucleotide (pdb code 6u6z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human SAMHD1 Bound to Deoxyribo(Tg*Ttca)-Oligonucleotide, PDB code: 6u6z:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human SAMHD1 Bound to Deoxyribo(Tg*Ttca)-Oligonucleotide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SAMHD1 Bound to Deoxyribo(Tg*Ttca)-Oligonucleotide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:42.0 occ:1.00 NE2 A:HIS206 2.0 39.0 1.0 NE2 A:HIS167 2.1 38.0 1.0 O A:HOH811 2.1 44.7 1.0 OD2 A:ASP207 2.2 39.2 1.0 OD1 A:ASP311 2.2 45.5 1.0 CE1 A:HIS206 2.9 42.7 1.0 CG A:ASP311 2.9 45.6 1.0 CE1 A:HIS167 3.0 35.5 1.0 CG A:ASP207 3.0 41.4 1.0 OD2 A:ASP311 3.0 46.9 1.0 CD2 A:HIS206 3.1 42.2 1.0 CD2 A:HIS167 3.1 36.2 1.0 OD1 A:ASP207 3.3 39.2 1.0 NH1 A:ARG164 3.9 40.5 1.0 O A:HOH868 4.0 44.6 1.0 ND1 A:HIS206 4.1 41.9 1.0 ND1 A:HIS167 4.1 34.7 1.0 CG A:HIS206 4.2 43.0 1.0 CG A:HIS167 4.2 40.4 1.0 CB A:ASP207 4.3 34.8 1.0 CB A:ASP311 4.3 42.1 1.0 CG2 A:VAL171 4.5 39.5 1.0 CD2 A:TYR315 4.6 43.8 1.0 CA A:ASP311 4.9 37.8 1.0 O A:HOH884 5.0 51.3 1.0 O A:ASP311 5.0 39.4 1.0

Zinc binding site 2 out of 4 in the Human SAMHD1 Bound to Deoxyribo(Tg*Ttca)-Oligonucleotide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human SAMHD1 Bound to Deoxyribo(Tg*Ttca)-Oligonucleotide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:48.4 occ:1.00 NE2 B:HIS206 2.0 48.4 1.0 O B:HOH847 2.1 46.2 1.0 NE2 B:HIS167 2.1 46.4 1.0 OD2 B:ASP207 2.3 42.8 1.0 OD1 B:ASP311 2.3 46.6 1.0 CE1 B:HIS206 3.0 48.9 1.0 CD2 B:HIS167 3.0 42.1 1.0 CG B:ASP207 3.0 48.7 1.0 CG B:ASP311 3.0 43.6 1.0 CD2 B:HIS206 3.1 46.8 1.0 CE1 B:HIS167 3.2 44.1 1.0 OD2 B:ASP311 3.2 52.1 1.0 OD1 B:ASP207 3.3 47.7 1.0 NH1 B:ARG164 3.6 42.3 1.0 ND1 B:HIS206 4.1 47.2 1.0 CG B:HIS206 4.2 47.4 1.0 CG B:HIS167 4.2 40.7 1.0 ND1 B:HIS167 4.2 40.4 1.0 CB B:ASP207 4.3 43.1 1.0 CB B:ASP311 4.4 49.0 1.0 CG2 B:VAL171 4.5 42.1 1.0 CD2 B:TYR315 4.7 50.9 1.0 CZ B:ARG164 4.9 43.5 1.0 O B:HOH846 5.0 52.9 1.0 CA B:ASP311 5.0 47.8 1.0

Zinc binding site 3 out of 4 in the Human SAMHD1 Bound to Deoxyribo(Tg*Ttca)-Oligonucleotide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human SAMHD1 Bound to Deoxyribo(Tg*Ttca)-Oligonucleotide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn701 b:44.7 occ:1.00 NE2 C:HIS206 2.0 44.2 1.0 NE2 C:HIS167 2.1 39.6 1.0 O C:HOH860 2.2 46.9 1.0 OD1 C:ASP311 2.3 44.9 1.0 OD2 C:ASP207 2.3 41.7 1.0 CE1 C:HIS206 2.8 44.1 1.0 CE1 C:HIS167 3.0 37.7 1.0 CG C:ASP311 3.0 43.3 1.0 CG C:ASP207 3.0 47.7 1.0 CD2 C:HIS167 3.1 40.0 1.0 CD2 C:HIS206 3.1 42.6 1.0 OD2 C:ASP311 3.2 48.9 1.0 OD1 C:ASP207 3.3 41.6 1.0 NH1 C:ARG164 3.8 35.4 1.0 ND1 C:HIS206 4.0 43.6 1.0 ND1 C:HIS167 4.1 36.7 1.0 CG C:HIS206 4.2 41.2 1.0 O C:HOH855 4.2 43.0 1.0 CG C:HIS167 4.2 42.9 1.0 CB C:ASP207 4.3 39.3 1.0 CB C:ASP311 4.4 38.1 1.0 CG2 C:VAL171 4.4 38.0 1.0 CD2 C:TYR315 4.6 40.1 1.0 O C:HOH886 4.7 51.6 1.0 CA C:ASP311 5.0 43.4 1.0 O C:ASP311 5.0 41.8 1.0

Zinc binding site 4 out of 4 in the Human SAMHD1 Bound to Deoxyribo(Tg*Ttca)-Oligonucleotide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human SAMHD1 Bound to Deoxyribo(Tg*Ttca)-Oligonucleotide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:46.7 occ:1.00 NE2 D:HIS206 2.0 43.5 1.0 NE2 D:HIS167 2.1 40.2 1.0 O D:HOH844 2.1 41.9 1.0 OD1 D:ASP311 2.2 42.9 1.0 OD2 D:ASP207 2.3 39.2 1.0 CE1 D:HIS206 3.0 42.6 1.0 CG D:ASP311 3.0 49.1 1.0 CE1 D:HIS167 3.0 39.1 1.0 CD2 D:HIS206 3.0 39.5 1.0 CG D:ASP207 3.1 40.4 1.0 CD2 D:HIS167 3.1 35.8 1.0 OD2 D:ASP311 3.2 51.0 1.0 OD1 D:ASP207 3.4 42.6 1.0 NH1 D:ARG164 3.8 36.6 1.0 ND1 D:HIS206 4.1 43.9 1.0 CG D:HIS206 4.1 45.2 1.0 ND1 D:HIS167 4.1 36.2 1.0 CG D:HIS167 4.2 37.3 1.0 CB D:ASP207 4.3 39.7 1.0 CB D:ASP311 4.3 46.3 1.0 CG2 D:VAL171 4.4 39.6 1.0 CD2 D:TYR315 4.6 52.4 1.0 CA D:ASP311 4.9 42.6 1.0

C.H.Yu, A.Bhattacharya, Z.Wang, A.B.Taylor, M.Persaud, A.Bulnes-Ramos, J.Xu, A.Selyutina, A.Martinez-Lopez, B.Demeler, B.Kim, F.Diaz-Griffero, D.N.Ivanov. The Gpsn Modification Enhances Affinity of Nucleic Acid Binding By SAMHD1 To Be Published.