Zinc in PDB 4q7h: Crystal Structure of SAMHD1 Catalytic Core with Gtp

The structure of Crystal Structure of SAMHD1 Catalytic Core with Gtp, PDB code: 4q7h was solved by Q.Xiaohong, L.Yanhong, K.Jia, Y.Xiaofang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.57 / 2.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.943, 142.765, 199.501, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 24.8

The binding sites of Zinc atom in the Crystal Structure of SAMHD1 Catalytic Core with Gtp (pdb code 4q7h). 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 SAMHD1 Catalytic Core with Gtp, PDB code: 4q7h:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of SAMHD1 Catalytic Core with Gtp


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 SAMHD1 Catalytic Core with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:34.3 occ:1.00 NE2 A:HIS206 2.1 30.1 1.0 NE2 A:HIS167 2.2 27.8 1.0 OD1 A:ASP311 2.2 38.5 1.0 OD2 A:ASP207 2.4 32.5 1.0 CG A:ASP311 2.9 35.3 1.0 CD2 A:HIS206 3.0 29.1 1.0 CG A:ASP207 3.1 33.3 1.0 OD2 A:ASP311 3.1 34.4 1.0 CE1 A:HIS206 3.1 30.3 1.0 CD2 A:HIS167 3.1 30.7 1.0 CE1 A:HIS167 3.2 34.4 1.0 OD1 A:ASP207 3.3 30.1 1.0 NH1 A:ARG164 3.9 28.1 1.0 CG A:HIS206 4.2 32.0 1.0 ND1 A:HIS206 4.2 30.2 1.0 ND1 A:HIS167 4.3 30.2 1.0 CG A:HIS167 4.3 31.9 1.0 CB A:ASP311 4.3 33.7 1.0 CB A:ASP207 4.4 32.9 1.0 CG2 A:VAL171 4.5 30.9 1.0 CD2 A:TYR315 4.5 25.9 1.0 O A:HOH1007 4.7 26.2 1.0 O A:ASP311 4.9 35.5 1.0 CE2 A:TYR315 4.9 27.2 1.0 CA A:ASP311 5.0 32.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of SAMHD1 Catalytic Core with Gtp


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 SAMHD1 Catalytic Core with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:39.2 occ:1.00 NE2 B:HIS206 2.2 37.1 1.0 OD1 B:ASP311 2.2 40.8 1.0 NE2 B:HIS167 2.2 37.1 1.0 OD2 B:ASP207 2.4 32.5 1.0 CG B:ASP311 2.9 39.5 1.0 OD2 B:ASP311 2.9 38.2 1.0 CD2 B:HIS206 3.1 34.4 1.0 CE1 B:HIS167 3.1 36.5 1.0 CE1 B:HIS206 3.2 35.9 1.0 CD2 B:HIS167 3.2 35.6 1.0 CG B:ASP207 3.2 37.3 1.0 OD1 B:ASP207 3.5 33.4 1.0 NH1 B:ARG164 3.7 28.1 1.0 ND1 B:HIS206 4.3 36.4 1.0 ND1 B:HIS167 4.3 35.7 1.0 CG B:HIS206 4.3 34.4 1.0 CG B:HIS167 4.3 36.6 1.0 CB B:ASP311 4.3 37.2 1.0 CB B:ASP207 4.5 37.5 1.0 O B:HOH1006 4.5 23.0 1.0 CG2 B:VAL171 4.5 34.9 1.0 CD2 B:TYR315 4.5 32.8 1.0 CA B:ASP311 4.9 39.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of SAMHD1 Catalytic Core with Gtp


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 SAMHD1 Catalytic Core with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn901 b:42.6 occ:1.00 NE2 C:HIS206 2.1 44.7 1.0 OD2 C:ASP207 2.2 42.6 1.0 OD1 C:ASP311 2.2 39.3 1.0 NE2 C:HIS167 2.2 40.9 1.0 CG C:ASP311 2.9 39.1 1.0 OD2 C:ASP311 2.9 42.7 1.0 CE1 C:HIS206 3.1 42.9 1.0 CG C:ASP207 3.1 42.0 1.0 CD2 C:HIS206 3.1 36.0 1.0 CD2 C:HIS167 3.1 35.9 1.0 CE1 C:HIS167 3.3 40.7 1.0 OD1 C:ASP207 3.4 37.1 1.0 NH1 C:ARG164 3.9 31.4 1.0 ND1 C:HIS206 4.2 40.1 1.0 CG C:HIS206 4.2 37.4 1.0 CB C:ASP311 4.3 36.1 1.0 CG C:HIS167 4.3 39.9 1.0 ND1 C:HIS167 4.3 36.6 1.0 CB C:ASP207 4.4 44.4 1.0 CD2 C:TYR315 4.6 42.8 1.0 CG2 C:VAL171 4.7 34.4 1.0 O C:HOH1004 4.7 31.5 1.0 CA C:ASP311 5.0 40.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of SAMHD1 Catalytic Core with Gtp


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 SAMHD1 Catalytic Core with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn901 b:39.5 occ:1.00 NE2 D:HIS206 2.0 37.6 1.0 NE2 D:HIS167 2.1 37.6 1.0 OD1 D:ASP311 2.3 46.2 1.0 OD2 D:ASP207 2.6 36.9 1.0 OD2 D:ASP311 2.9 44.3 1.0 CG D:ASP311 2.9 41.8 1.0 CD2 D:HIS206 2.9 37.0 1.0 CE1 D:HIS206 3.0 40.0 1.0 CE1 D:HIS167 3.0 41.5 1.0 CG D:ASP207 3.2 39.3 1.0 CD2 D:HIS167 3.2 34.3 1.0 OD1 D:ASP207 3.3 38.8 1.0 NH1 D:ARG164 3.8 37.1 1.0 ND1 D:HIS206 4.1 40.8 1.0 CG D:HIS206 4.1 37.2 1.0 ND1 D:HIS167 4.2 38.8 1.0 CG D:HIS167 4.3 36.3 1.0 CB D:ASP311 4.3 42.4 1.0 CB D:ASP207 4.4 38.9 1.0 CG2 D:VAL171 4.5 40.9 1.0 CD2 D:TYR315 4.6 39.7 1.0 O D:HOH1001 4.7 29.0 1.0 CA D:ASP311 5.0 44.9 1.0

Q.Xiaohong, L.Yanhong, K.Jia, Y.Xiaofang. Structural Insight Into Activation Mechanism of SAMHD1 To Be Published.