Zinc in PDB 4rxo: The Structure of Gtp-Bound SAMHD1

The structure of The Structure of Gtp-Bound SAMHD1, PDB code: 4rxo was solved by C.F.Zhu, W.Wei, X.Peng, Y.H.Dong, Y.Gong, X.F.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.219, 183.187, 81.275, 90.00, 100.62, 90.00
R / Rfree (%)	18.3 / 22.2

The binding sites of Zinc atom in the The Structure of Gtp-Bound SAMHD1 (pdb code 4rxo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Structure of Gtp-Bound SAMHD1, PDB code: 4rxo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Structure of Gtp-Bound SAMHD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of Gtp-Bound SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:58.3 occ:1.00 O2 A:PO4702 1.8 54.0 1.0 NE2 A:HIS206 2.3 47.7 1.0 OD1 A:ASP311 2.4 56.5 1.0 NE2 A:HIS167 2.4 38.2 1.0 OD2 A:ASP207 2.5 46.1 1.0 P A:PO4702 2.9 63.2 1.0 CG A:ASP311 3.0 50.2 1.0 OD2 A:ASP311 3.1 58.1 1.0 O1 A:PO4702 3.1 57.7 1.0 CG A:ASP207 3.1 49.5 1.0 CD2 A:HIS206 3.2 46.1 1.0 OD1 A:ASP207 3.2 51.0 1.0 CD2 A:HIS167 3.3 41.9 1.0 CE1 A:HIS206 3.3 47.4 1.0 CE1 A:HIS167 3.5 40.4 1.0 NH1 A:ARG164 3.7 40.6 1.0 O4 A:PO4702 3.7 63.2 1.0 O3 A:PO4702 4.0 60.4 1.0 CG A:HIS206 4.3 45.5 1.0 ND1 A:HIS206 4.4 45.7 1.0 CB A:ASP207 4.4 47.0 1.0 CB A:ASP311 4.4 49.7 1.0 CG A:HIS167 4.5 41.4 1.0 ND1 A:HIS167 4.6 41.6 1.0 CD2 A:TYR315 4.6 51.5 1.0 CG2 A:VAL171 4.8 47.9 1.0 O A:HOH847 4.9 60.6 1.0 CZ A:ARG164 5.0 38.1 1.0

Zinc binding site 2 out of 4 in the The Structure of Gtp-Bound SAMHD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of Gtp-Bound SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:57.0 occ:1.00 O2 B:PO4804 1.8 66.0 1.0 NE2 B:HIS206 2.2 45.4 1.0 NE2 B:HIS167 2.3 35.0 1.0 OD1 B:ASP311 2.3 50.3 1.0 OD2 B:ASP207 2.5 42.4 1.0 CG B:ASP311 3.0 46.6 1.0 OD2 B:ASP311 3.1 50.6 1.0 CD2 B:HIS167 3.1 34.6 1.0 P B:PO4804 3.1 67.2 1.0 CD2 B:HIS206 3.2 46.9 1.0 CG B:ASP207 3.2 43.3 1.0 CE1 B:HIS206 3.2 46.8 1.0 CE1 B:HIS167 3.3 35.6 1.0 OD1 B:ASP207 3.3 45.6 1.0 O1 B:PO4804 3.5 63.2 1.0 NH1 B:ARG164 3.7 39.4 1.0 O4 B:PO4804 4.1 73.0 1.0 O3 B:PO4804 4.1 65.8 1.0 ND1 B:HIS206 4.3 46.9 1.0 CG B:HIS167 4.3 34.0 1.0 CG B:HIS206 4.3 45.6 1.0 ND1 B:HIS167 4.4 35.7 1.0 CB B:ASP311 4.4 42.9 1.0 CB B:ASP207 4.5 40.8 1.0 CG2 B:VAL171 4.6 39.4 1.0 CD2 B:TYR315 4.6 39.0 1.0 O B:HOH930 4.8 59.2 1.0 CA B:ASP311 5.0 40.6 1.0

Zinc binding site 3 out of 4 in the The Structure of Gtp-Bound SAMHD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of Gtp-Bound SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn701 b:62.7 occ:1.00 O2 C:PO4703 1.9 62.4 1.0 NE2 C:HIS167 2.2 33.5 1.0 NE2 C:HIS206 2.2 52.1 1.0 OD1 C:ASP311 2.4 52.8 1.0 OD2 C:ASP207 2.4 48.2 1.0 CD2 C:HIS167 3.0 35.6 1.0 CG C:ASP207 3.1 48.2 1.0 CG C:ASP311 3.1 48.9 1.0 P C:PO4703 3.2 74.0 1.0 CE1 C:HIS206 3.2 50.3 1.0 CD2 C:HIS206 3.2 49.7 1.0 OD2 C:ASP311 3.2 51.2 1.0 CE1 C:HIS167 3.3 35.4 1.0 OD1 C:ASP207 3.3 49.4 1.0 O1 C:PO4703 3.6 66.4 1.0 NH1 C:ARG164 3.7 44.4 1.0 O4 C:PO4703 4.0 81.8 1.0 O3 C:PO4703 4.2 75.7 1.0 CG C:HIS167 4.2 34.8 1.0 ND1 C:HIS206 4.3 51.6 1.0 ND1 C:HIS167 4.3 35.7 1.0 CG C:HIS206 4.3 49.9 1.0 CB C:ASP207 4.4 44.1 1.0 CB C:ASP311 4.5 48.0 1.0 CG2 C:VAL171 4.6 44.2 1.0 CD2 C:TYR315 4.7 43.1 1.0 O C:HOH863 4.8 64.3 1.0 CZ C:ARG164 5.0 44.8 1.0

Zinc binding site 4 out of 4 in the The Structure of Gtp-Bound SAMHD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of Gtp-Bound SAMHD1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:64.3 occ:1.00 O2 D:PO4703 1.8 74.5 1.0 OD1 D:ASP311 2.3 63.1 1.0 NE2 D:HIS206 2.4 50.0 1.0 NE2 D:HIS167 2.4 43.6 1.0 OD2 D:ASP207 2.6 56.9 1.0 CG D:ASP311 3.0 55.1 1.0 OD2 D:ASP311 3.0 60.5 1.0 P D:PO4703 3.0 75.2 1.0 CG D:ASP207 3.2 55.8 1.0 CD2 D:HIS206 3.2 49.5 1.0 OD1 D:ASP207 3.3 55.2 1.0 O1 D:PO4703 3.3 66.0 1.0 CD2 D:HIS167 3.3 43.6 1.0 CE1 D:HIS206 3.4 52.3 1.0 CE1 D:HIS167 3.5 45.4 1.0 NH1 D:ARG164 3.7 39.7 1.0 O4 D:PO4703 3.9 75.8 1.0 O3 D:PO4703 4.1 69.7 1.0 CG D:HIS206 4.4 49.9 1.0 CB D:ASP311 4.4 52.7 1.0 ND1 D:HIS206 4.4 54.4 1.0 CG D:HIS167 4.5 42.4 1.0 CB D:ASP207 4.5 54.0 1.0 CD2 D:TYR315 4.5 53.4 1.0 ND1 D:HIS167 4.5 46.0 1.0 CG2 D:VAL171 4.8 39.5 1.0 CE2 D:TYR315 4.9 54.5 1.0 O D:HOH846 5.0 57.9 1.0

C.F.Zhu, W.Wei, X.Peng, Y.H.Dong, Y.Gong, X.F.Yu. The Mechanism of Substrate-Controlled Allosteric Regulation of SAMHD1 Activated By Gtp Acta Crystallogr.,Sect.D 2015.
ISSN: ESSN 1399-0047
DOI: 10.1107/S1399004714027527