Zinc in PDB 6u6z: Human SAMHD1 Bound to Deoxyribo(Tg*Ttca)-Oligonucleotide

Protein crystallography data

The structure of Human SAMHD1 Bound to Deoxyribo(Tg*Ttca)-Oligonucleotide, PDB code: 6u6z was solved by A.B.Taylor, C.H.Yu, D.N.Ivanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.27 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 81.610, 94.670, 96.320, 72.90, 70.95, 64.96
R / Rfree (%) 17.4 / 20.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Human SAMHD1 Bound to Deoxyribo(Tg*Ttca)-Oligonucleotide (pdb code 6u6z). 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(Tg*Ttca)-Oligonucleotide, PDB code: 6u6z:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6u6z

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Zinc binding site 1 out of 4 in the Human SAMHD1 Bound to Deoxyribo(Tg*Ttca)-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(Tg*Ttca)-Oligonucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:42.0
occ:1.00
NE2 A:HIS206 2.0 39.0 1.0
NE2 A:HIS167 2.1 38.0 1.0
O A:HOH811 2.1 44.7 1.0
OD2 A:ASP207 2.2 39.2 1.0
OD1 A:ASP311 2.2 45.5 1.0
CE1 A:HIS206 2.9 42.7 1.0
CG A:ASP311 2.9 45.6 1.0
CE1 A:HIS167 3.0 35.5 1.0
CG A:ASP207 3.0 41.4 1.0
OD2 A:ASP311 3.0 46.9 1.0
CD2 A:HIS206 3.1 42.2 1.0
CD2 A:HIS167 3.1 36.2 1.0
OD1 A:ASP207 3.3 39.2 1.0
NH1 A:ARG164 3.9 40.5 1.0
O A:HOH868 4.0 44.6 1.0
ND1 A:HIS206 4.1 41.9 1.0
ND1 A:HIS167 4.1 34.7 1.0
CG A:HIS206 4.2 43.0 1.0
CG A:HIS167 4.2 40.4 1.0
CB A:ASP207 4.3 34.8 1.0
CB A:ASP311 4.3 42.1 1.0
CG2 A:VAL171 4.5 39.5 1.0
CD2 A:TYR315 4.6 43.8 1.0
CA A:ASP311 4.9 37.8 1.0
O A:HOH884 5.0 51.3 1.0
O A:ASP311 5.0 39.4 1.0

Zinc binding site 2 out of 4 in 6u6z

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Zinc binding site 2 out of 4 in the Human SAMHD1 Bound to Deoxyribo(Tg*Ttca)-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(Tg*Ttca)-Oligonucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:48.4
occ:1.00
NE2 B:HIS206 2.0 48.4 1.0
O B:HOH847 2.1 46.2 1.0
NE2 B:HIS167 2.1 46.4 1.0
OD2 B:ASP207 2.3 42.8 1.0
OD1 B:ASP311 2.3 46.6 1.0
CE1 B:HIS206 3.0 48.9 1.0
CD2 B:HIS167 3.0 42.1 1.0
CG B:ASP207 3.0 48.7 1.0
CG B:ASP311 3.0 43.6 1.0
CD2 B:HIS206 3.1 46.8 1.0
CE1 B:HIS167 3.2 44.1 1.0
OD2 B:ASP311 3.2 52.1 1.0
OD1 B:ASP207 3.3 47.7 1.0
NH1 B:ARG164 3.6 42.3 1.0
ND1 B:HIS206 4.1 47.2 1.0
CG B:HIS206 4.2 47.4 1.0
CG B:HIS167 4.2 40.7 1.0
ND1 B:HIS167 4.2 40.4 1.0
CB B:ASP207 4.3 43.1 1.0
CB B:ASP311 4.4 49.0 1.0
CG2 B:VAL171 4.5 42.1 1.0
CD2 B:TYR315 4.7 50.9 1.0
CZ B:ARG164 4.9 43.5 1.0
O B:HOH846 5.0 52.9 1.0
CA B:ASP311 5.0 47.8 1.0

Zinc binding site 3 out of 4 in 6u6z

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Zinc binding site 3 out of 4 in the Human SAMHD1 Bound to Deoxyribo(Tg*Ttca)-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(Tg*Ttca)-Oligonucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn701

b:44.7
occ:1.00
NE2 C:HIS206 2.0 44.2 1.0
NE2 C:HIS167 2.1 39.6 1.0
O C:HOH860 2.2 46.9 1.0
OD1 C:ASP311 2.3 44.9 1.0
OD2 C:ASP207 2.3 41.7 1.0
CE1 C:HIS206 2.8 44.1 1.0
CE1 C:HIS167 3.0 37.7 1.0
CG C:ASP311 3.0 43.3 1.0
CG C:ASP207 3.0 47.7 1.0
CD2 C:HIS167 3.1 40.0 1.0
CD2 C:HIS206 3.1 42.6 1.0
OD2 C:ASP311 3.2 48.9 1.0
OD1 C:ASP207 3.3 41.6 1.0
NH1 C:ARG164 3.8 35.4 1.0
ND1 C:HIS206 4.0 43.6 1.0
ND1 C:HIS167 4.1 36.7 1.0
CG C:HIS206 4.2 41.2 1.0
O C:HOH855 4.2 43.0 1.0
CG C:HIS167 4.2 42.9 1.0
CB C:ASP207 4.3 39.3 1.0
CB C:ASP311 4.4 38.1 1.0
CG2 C:VAL171 4.4 38.0 1.0
CD2 C:TYR315 4.6 40.1 1.0
O C:HOH886 4.7 51.6 1.0
CA C:ASP311 5.0 43.4 1.0
O C:ASP311 5.0 41.8 1.0

Zinc binding site 4 out of 4 in 6u6z

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Zinc binding site 4 out of 4 in the Human SAMHD1 Bound to Deoxyribo(Tg*Ttca)-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(Tg*Ttca)-Oligonucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn701

b:46.7
occ:1.00
NE2 D:HIS206 2.0 43.5 1.0
NE2 D:HIS167 2.1 40.2 1.0
O D:HOH844 2.1 41.9 1.0
OD1 D:ASP311 2.2 42.9 1.0
OD2 D:ASP207 2.3 39.2 1.0
CE1 D:HIS206 3.0 42.6 1.0
CG D:ASP311 3.0 49.1 1.0
CE1 D:HIS167 3.0 39.1 1.0
CD2 D:HIS206 3.0 39.5 1.0
CG D:ASP207 3.1 40.4 1.0
CD2 D:HIS167 3.1 35.8 1.0
OD2 D:ASP311 3.2 51.0 1.0
OD1 D:ASP207 3.4 42.6 1.0
NH1 D:ARG164 3.8 36.6 1.0
ND1 D:HIS206 4.1 43.9 1.0
CG D:HIS206 4.1 45.2 1.0
ND1 D:HIS167 4.1 36.2 1.0
CG D:HIS167 4.2 37.3 1.0
CB D:ASP207 4.3 39.7 1.0
CB D:ASP311 4.3 46.3 1.0
CG2 D:VAL171 4.4 39.6 1.0
CD2 D:TYR315 4.6 52.4 1.0
CA D:ASP311 4.9 42.6 1.0

Reference:

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.
Page generated: Wed Dec 16 12:57:29 2020

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