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Zinc in PDB 3u1n: Structure of the Catalytic Core of Human SAMHD1

Protein crystallography data

The structure of Structure of the Catalytic Core of Human SAMHD1, PDB code: 3u1n was solved by D.C.Goldstone, V.Ennis-Adeniran, P.A.Walker, L.F.Haire, M.Webb, I.A.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.56 / 3.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 81.516, 95.818, 96.661, 91.18, 109.24, 115.20
R / Rfree (%) 19.6 / 22.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Catalytic Core of Human SAMHD1 (pdb code 3u1n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the Catalytic Core of Human SAMHD1, PDB code: 3u1n:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3u1n

Go back to Zinc Binding Sites List in 3u1n
Zinc binding site 1 out of 4 in the Structure of the Catalytic Core of Human SAMHD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Catalytic Core of Human SAMHD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn627

b:53.9
occ:1.00
NE2 A:HIS167 2.1 31.2 1.0
O2 A:PO41 2.2 70.7 1.0
NE2 A:HIS206 2.2 40.4 1.0
OD1 A:ASP311 2.4 52.9 1.0
OD2 A:ASP207 2.7 54.7 1.0
CD2 A:HIS167 3.1 31.4 1.0
CE1 A:HIS167 3.1 31.4 1.0
CG A:ASP311 3.2 53.7 1.0
CD2 A:HIS206 3.2 40.6 1.0
P A:PO41 3.2 70.7 1.0
CE1 A:HIS206 3.2 40.7 1.0
OD2 A:ASP311 3.3 53.6 1.0
CG A:ASP207 3.4 55.0 1.0
O3 A:PO41 3.5 70.7 1.0
OD1 A:ASP207 3.6 55.1 1.0
O1 A:PO41 3.6 70.7 1.0
NH1 A:ARG164 4.0 32.4 1.0
ND1 A:HIS167 4.2 31.6 1.0
CG A:HIS167 4.2 31.5 1.0
CG A:HIS206 4.3 41.1 1.0
ND1 A:HIS206 4.3 41.2 1.0
CD2 A:TYR315 4.5 31.6 1.0
O4 A:PO41 4.5 70.7 1.0
CB A:ASP311 4.6 54.8 1.0
CG2 A:VAL171 4.6 32.9 1.0
CB A:ASP207 4.6 55.3 1.0

Zinc binding site 2 out of 4 in 3u1n

Go back to Zinc Binding Sites List in 3u1n
Zinc binding site 2 out of 4 in the Structure of the Catalytic Core of Human SAMHD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Catalytic Core of Human SAMHD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4

b:50.0
occ:1.00
NE2 B:HIS167 2.2 32.0 1.0
NE2 B:HIS206 2.2 41.6 1.0
O3 B:PO42 2.3 71.1 1.0
OD1 B:ASP311 2.3 49.8 1.0
OD2 B:ASP207 2.8 48.8 1.0
CG B:ASP311 3.1 50.5 1.0
CD2 B:HIS206 3.1 41.8 1.0
CD2 B:HIS167 3.1 32.2 1.0
CE1 B:HIS167 3.2 32.2 1.0
CE1 B:HIS206 3.2 42.1 1.0
OD2 B:ASP311 3.2 50.5 1.0
P B:PO42 3.3 71.1 1.0
CG B:ASP207 3.4 49.1 1.0
O4 B:PO42 3.4 71.1 1.0
OD1 B:ASP207 3.5 49.1 1.0
O2 B:PO42 3.7 71.1 1.0
NH1 B:ARG164 4.1 27.1 1.0
ND1 B:HIS167 4.3 32.5 1.0
CG B:HIS206 4.3 42.5 1.0
ND1 B:HIS206 4.3 42.7 1.0
CG B:HIS167 4.3 32.5 1.0
CB B:ASP311 4.5 51.6 1.0
CB B:ASP207 4.6 49.6 1.0
CG2 B:VAL171 4.6 23.7 1.0
CD2 B:TYR315 4.6 34.6 1.0
O1 B:PO42 4.6 71.1 1.0
CA B:ASP311 5.0 51.5 1.0
O B:ASP311 5.0 49.8 1.0

Zinc binding site 3 out of 4 in 3u1n

Go back to Zinc Binding Sites List in 3u1n
Zinc binding site 3 out of 4 in the Structure of the Catalytic Core of Human SAMHD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Catalytic Core of Human SAMHD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn627

b:53.4
occ:1.00
O2 C:PO43 2.1 63.3 1.0
NE2 C:HIS167 2.3 35.9 1.0
NE2 C:HIS206 2.3 49.2 1.0
OD1 C:ASP311 2.5 59.0 1.0
OD2 C:ASP207 2.6 49.0 1.0
O1 C:PO43 3.0 63.3 1.0
P C:PO43 3.0 63.3 1.0
CD2 C:HIS206 3.2 49.8 1.0
CG C:ASP311 3.2 59.6 1.0
CD2 C:HIS167 3.2 35.8 1.0
CG C:ASP207 3.3 49.4 1.0
OD2 C:ASP311 3.3 60.2 1.0
CE1 C:HIS167 3.3 35.8 1.0
CE1 C:HIS206 3.3 49.0 1.0
OD1 C:ASP207 3.4 49.9 1.0
O3 C:PO43 3.7 63.3 1.0
NH1 C:ARG164 3.9 36.3 1.0
O4 C:PO43 4.3 63.3 1.0
CG C:HIS206 4.4 49.9 1.0
ND1 C:HIS167 4.4 35.6 1.0
CG C:HIS167 4.4 35.5 1.0
ND1 C:HIS206 4.4 49.4 1.0
CB C:ASP207 4.5 49.3 1.0
CD2 C:TYR315 4.6 41.1 1.0
O C:HOH7 4.6 46.4 1.0
CB C:ASP311 4.7 59.9 1.0
CG2 C:VAL171 4.8 35.9 1.0

Zinc binding site 4 out of 4 in 3u1n

Go back to Zinc Binding Sites List in 3u1n
Zinc binding site 4 out of 4 in the Structure of the Catalytic Core of Human SAMHD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Catalytic Core of Human SAMHD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2

b:51.7
occ:1.00
O4 D:PO44 2.2 64.8 1.0
NE2 D:HIS167 2.2 38.6 1.0
NE2 D:HIS206 2.3 46.2 1.0
OD1 D:ASP311 2.4 53.0 1.0
OD2 D:ASP207 2.8 52.9 1.0
O1 D:PO44 2.9 64.8 1.0
P D:PO44 3.0 64.8 1.0
CG D:ASP311 3.1 53.8 1.0
CE1 D:HIS167 3.2 38.8 1.0
CD2 D:HIS206 3.2 46.5 1.0
CD2 D:HIS167 3.2 38.4 1.0
OD2 D:ASP311 3.2 54.4 1.0
CE1 D:HIS206 3.3 45.8 1.0
CG D:ASP207 3.4 52.9 1.0
OD1 D:ASP207 3.5 53.3 1.0
O2 D:PO44 3.6 64.8 1.0
NH1 D:ARG164 4.0 36.1 1.0
ND1 D:HIS167 4.3 38.7 1.0
CG D:HIS167 4.3 38.4 1.0
CG D:HIS206 4.3 46.3 1.0
O3 D:PO44 4.4 64.8 1.0
ND1 D:HIS206 4.4 45.9 1.0
CD2 D:TYR315 4.5 37.0 1.0
CB D:ASP311 4.6 54.4 1.0
O D:HOH11 4.6 44.5 1.0
CB D:ASP207 4.6 52.5 1.0
CG2 D:VAL171 4.7 30.9 1.0

Reference:

D.C.Goldstone, V.Ennis-Adeniran, J.J.Hedden, H.C.Groom, G.I.Rice, E.Christodoulou, P.A.Walker, G.Kelly, L.F.Haire, M.W.Yap, L.P.De Carvalho, J.P.Stoye, Y.J.Crow, I.A.Taylor, M.Webb. Hiv-1 Restriction Factor SAMHD1 Is A Deoxynucleoside Triphosphate Triphosphohydrolase Nature V. 480 379 2011.
ISSN: ISSN 0028-0836
PubMed: 22056990
DOI: 10.1038/NATURE10623
Page generated: Wed Dec 16 04:53:16 2020

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