Zinc in PDB 6u6x: Human SAMHD1 Bound to Deoxyribo(C*G*C*C*T)-Oligonucleotide

The structure of Human SAMHD1 Bound to Deoxyribo(C*G*C*C*T)-Oligonucleotide, PDB code: 6u6x was solved by A.B.Taylor, A.Bhattacharya, Z.Wang, D.N.Ivanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.66 / 2.58
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	69.360, 81.870, 106.000, 69.72, 76.30, 82.77
R / Rfree (%)	19.6 / 23.7

The binding sites of Zinc atom in the Human SAMHD1 Bound to Deoxyribo(C*G*C*C*T)-Oligonucleotide (pdb code 6u6x). 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(C*G*C*C*T)-Oligonucleotide, PDB code: 6u6x:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human SAMHD1 Bound to Deoxyribo(C*G*C*C*T)-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(C*G*C*C*T)-Oligonucleotide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:89.6 occ:0.77 NE2 A:HIS206 2.4 52.5 0.4 NE2 A:HIS167 2.5 53.0 1.0 OD2 A:ASP207 2.7 66.3 1.0 CD2 A:HIS167 3.1 35.6 1.0 OD1 A:ASP207 3.2 63.6 1.0 CE1 A:HIS206 3.2 50.0 0.4 CG A:ASP207 3.2 64.3 1.0 CD2 A:HIS206 3.3 56.4 0.4 CE1 A:HIS167 3.7 48.6 1.0 NH1 A:ARG164 3.8 41.8 1.0 ND1 A:HIS206 3.9 69.9 0.6 CB A:ALA311 4.1 47.3 1.0 ND1 A:HIS206 4.2 54.3 0.4 CG A:HIS206 4.3 58.5 0.4 CG A:HIS167 4.4 60.7 1.0 CE1 A:HIS206 4.4 69.0 0.6 CD2 A:TYR315 4.6 62.6 1.0 ND1 A:HIS167 4.6 55.2 1.0 CB A:ASP207 4.6 53.6 1.0 CG2 A:VAL171 4.8 51.2 1.0

Zinc binding site 2 out of 4 in the Human SAMHD1 Bound to Deoxyribo(C*G*C*C*T)-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(C*G*C*C*T)-Oligonucleotide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:99.5 occ:0.61 OD2 B:ASP207 2.5 96.7 1.0 NE2 B:HIS167 2.6 77.4 1.0 CG B:ASP207 3.1 97.0 1.0 OD1 B:ASP207 3.1 99.6 1.0 CD2 B:HIS167 3.2 76.5 1.0 NH1 B:ARG164 3.6 76.3 1.0 CE1 B:HIS167 3.8 77.8 1.0 ND1 B:HIS206 4.3 0.8 1.0 CB B:ALA311 4.4 86.9 1.0 CD2 B:TYR315 4.4 99.3 1.0 CG B:HIS167 4.4 73.0 1.0 CB B:ASP207 4.4 88.4 1.0 CE2 B:TYR315 4.6 0.3 1.0 ND1 B:HIS167 4.7 78.6 1.0 CG2 B:VAL171 4.7 70.3 1.0 NE2 B:GLN149 4.9 81.8 1.0 CE1 B:HIS206 4.9 0.6 1.0 CZ B:ARG164 4.9 77.6 1.0

Zinc binding site 3 out of 4 in the Human SAMHD1 Bound to Deoxyribo(C*G*C*C*T)-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(C*G*C*C*T)-Oligonucleotide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn701 b:0.7 occ:0.97 OD2 C:ASP207 2.5 80.1 1.0 NE2 C:HIS167 2.7 76.3 1.0 OD1 C:ASP207 2.9 80.3 1.0 CG C:ASP207 3.1 80.6 1.0 CD2 C:HIS167 3.4 72.5 1.0 NH1 C:ARG164 3.5 66.4 1.0 CE1 C:HIS167 3.9 76.6 1.0 ND1 C:HIS206 4.1 0.6 1.0 CE1 C:HIS206 4.4 0.2 1.0 CB C:ALA311 4.4 71.2 1.0 CB C:ASP207 4.5 79.6 1.0 CG C:HIS167 4.7 75.0 1.0 CD2 C:TYR315 4.7 79.0 1.0 CZ C:ARG164 4.8 74.9 1.0 ND1 C:HIS167 4.9 72.8 1.0

Zinc binding site 4 out of 4 in the Human SAMHD1 Bound to Deoxyribo(C*G*C*C*T)-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(C*G*C*C*T)-Oligonucleotide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:0.5 occ:0.87 NE2 D:HIS206 2.4 59.1 0.4 NE2 D:HIS167 2.6 56.4 1.0 OD2 D:ASP207 2.6 91.1 1.0 CG D:ASP207 3.2 88.3 1.0 OD1 D:ASP207 3.3 88.2 1.0 CD2 D:HIS167 3.3 50.9 1.0 CD2 D:HIS206 3.3 63.1 0.4 CE1 D:HIS206 3.3 62.2 0.4 CE1 D:HIS167 3.7 55.4 1.0 NH1 D:ARG164 3.8 41.7 1.0 CB D:ALA311 4.1 55.7 1.0 ND1 D:HIS206 4.3 64.6 0.4 CG D:HIS206 4.4 64.7 0.4 CD2 D:HIS206 4.5 63.2 0.6 CB D:ASP207 4.5 75.8 1.0 CG2 D:VAL171 4.5 55.5 1.0 CG D:HIS167 4.5 58.9 1.0 CD2 D:TYR315 4.7 60.4 1.0 ND1 D:HIS167 4.7 59.4 1.0 CA D:ALA311 4.9 58.1 1.0 NE2 D:GLN149 4.9 57.2 1.0 O D:ALA311 5.0 68.1 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.