Zinc in PDB 4qg4: Crystal Structure of the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) Mutant Catalytic Core

The structure of Crystal Structure of the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) Mutant Catalytic Core, PDB code: 4qg4 was solved by L.M.I.Koharudin, Y.Wu, M.Delucia, J.Mehrens, A.M.Gronenborn, J.Ahn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.74 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.799, 147.120, 99.211, 90.00, 114.00, 90.00
R / Rfree (%)	22.3 / 24.5

The structure of Crystal Structure of the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) Mutant Catalytic Core also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) Mutant Catalytic Core (pdb code 4qg4). 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 the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) Mutant Catalytic Core, PDB code: 4qg4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) Mutant Catalytic Core


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 the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn705 b:42.3 occ:1.00 NE2 A:HIS206 2.0 20.0 1.0 OD1 A:ASP311 2.3 45.6 1.0 NE2 A:HIS167 2.3 35.4 1.0 OD2 A:ASP207 2.8 20.0 1.0 CE1 A:HIS206 3.0 20.0 1.0 CG A:ASP311 3.0 44.5 1.0 CD2 A:HIS206 3.0 20.0 1.0 O A:HOH898 3.0 34.0 1.0 OD2 A:ASP311 3.0 46.0 1.0 CD2 A:HIS167 3.2 36.6 1.0 CE1 A:HIS167 3.3 34.8 1.0 CG A:ASP207 3.5 20.0 1.0 OD1 A:ASP207 3.8 20.0 1.0 NH1 A:ARG164 4.0 31.2 1.0 ND1 A:HIS206 4.1 20.0 1.0 CG A:HIS206 4.1 20.0 1.0 CB A:ASP311 4.4 37.6 1.0 CG A:HIS167 4.4 32.8 1.0 ND1 A:HIS167 4.4 33.8 1.0 CG2 A:VAL171 4.5 34.6 1.0 CD2 A:TYR315 4.6 45.5 1.0 CB A:ASP207 4.7 20.0 1.0 CA A:ASP311 4.9 39.8 1.0 NE2 A:GLN149 5.0 31.2 0.9

Zinc binding site 2 out of 4 in the Crystal Structure of the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) Mutant Catalytic Core


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 the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn705 b:39.9 occ:1.00 NE2 B:HIS206 1.8 20.0 1.0 OD1 B:ASP311 2.2 37.5 0.9 NE2 B:HIS167 2.3 31.4 1.0 CE1 B:HIS206 2.7 20.0 1.0 CG B:ASP311 3.0 40.5 0.9 CD2 B:HIS206 3.0 20.0 1.0 OD2 B:ASP311 3.0 44.6 0.9 OD2 B:ASP207 3.1 20.0 1.0 CD2 B:HIS167 3.2 31.5 1.0 CE1 B:HIS167 3.3 31.6 1.0 OD1 B:ASP207 3.6 20.0 1.0 CG B:ASP207 3.6 20.0 1.0 NH1 B:ARG164 3.8 33.6 1.0 ND1 B:HIS206 3.9 20.0 1.0 CG B:HIS206 4.0 20.0 1.0 CB B:ASP311 4.4 35.4 0.9 CG B:HIS167 4.4 35.0 1.0 ND1 B:HIS167 4.4 34.8 1.0 CD2 B:TYR315 4.5 38.2 0.9 CG2 B:VAL171 4.5 32.7 1.0 CB B:ASP207 4.9 20.0 1.0 CE2 B:TYR315 4.9 39.5 0.9 CA B:ASP311 4.9 31.8 0.9 O B:ASP311 5.0 33.0 0.9 NE2 B:GLN149 5.0 32.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) Mutant Catalytic Core


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 the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn703 b:42.9 occ:1.00 NE2 C:HIS206 2.4 20.0 1.0 OD1 C:ASP311 2.4 40.1 0.9 NE2 C:HIS167 2.4 37.4 0.9 OD2 C:ASP311 2.8 46.0 0.9 CD2 C:HIS206 2.9 20.0 1.0 CG C:ASP311 2.9 43.1 0.9 OD2 C:ASP207 2.9 20.0 1.0 O C:HOH884 2.9 33.6 1.0 CD2 C:HIS167 3.2 35.1 0.9 CE1 C:HIS167 3.5 31.7 0.9 CG C:ASP207 3.5 20.0 1.0 OD1 C:ASP207 3.5 20.0 1.0 CE1 C:HIS206 3.6 20.0 1.0 NH1 C:ARG164 4.0 37.9 1.0 CG C:HIS206 4.2 20.0 1.0 CB C:ASP311 4.3 37.3 0.9 CG C:HIS167 4.4 32.4 0.9 ND1 C:HIS206 4.5 20.0 1.0 ND1 C:HIS167 4.5 33.0 0.9 CD2 C:TYR315 4.6 42.9 0.8 CG2 C:VAL171 4.8 36.4 1.0 CB C:ASP207 4.8 20.0 1.0 CA C:ASP311 5.0 36.5 0.9

Zinc binding site 4 out of 4 in the Crystal Structure of the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) Mutant Catalytic Core


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 the Tetrameric Gtp/Datp/Atp-Bound SAMHD1 (H210A) Mutant Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn703 b:40.8 occ:1.00 NE2 D:HIS206 2.1 20.0 1.0 OD1 D:ASP311 2.3 33.5 1.0 NE2 D:HIS167 2.3 29.6 1.0 OD2 D:ASP207 2.8 20.0 1.0 CG D:ASP311 2.9 33.8 1.0 OD2 D:ASP311 2.9 41.7 1.0 CE1 D:HIS206 3.0 20.0 1.0 CD2 D:HIS206 3.1 20.0 1.0 CD2 D:HIS167 3.2 28.8 1.0 CE1 D:HIS167 3.3 30.4 1.0 CG D:ASP207 3.4 20.0 1.0 OD1 D:ASP207 3.5 20.0 1.0 NH1 D:ARG164 3.8 31.6 1.0 ND1 D:HIS206 4.1 20.0 1.0 CG D:HIS206 4.2 20.0 1.0 CG D:HIS167 4.4 27.3 1.0 CB D:ASP311 4.4 34.1 1.0 ND1 D:HIS167 4.4 32.0 1.0 CD2 D:TYR315 4.5 38.6 1.0 CG2 D:VAL171 4.6 33.7 1.0 CB D:ASP207 4.7 20.0 1.0 NE2 D:GLN149 4.9 32.7 1.0 CE2 D:TYR315 5.0 39.6 1.0 CA D:ASP311 5.0 35.2 1.0

L.M.Koharudin, Y.Wu, M.Delucia, J.Mehrens, A.M.Gronenborn, J.Ahn. Structural Basis of Allosteric Activation of Sterile Alpha Motif and Histidine-Aspartate Domain Containing Protein 1 (SAMHD1) By Nucleoside Triphosphates. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25288794
DOI: 10.1074/JBC.M114.591958