Zinc in PDB 6u6y: Human SAMHD1 Bound to Ribo(Cgccu)-Oligonucleotide

Protein crystallography data

The structure of Human SAMHD1 Bound to Ribo(Cgccu)-Oligonucleotide, PDB code: 6u6y was solved by A.B.Taylor, A.Bhattacharya, Z.Wang, D.N.Ivanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.96 / 2.47
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.340, 183.620, 81.560, 90.00, 100.85, 90.00
R / Rfree (%) 18 / 23.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Human SAMHD1 Bound to Ribo(Cgccu)-Oligonucleotide (pdb code 6u6y). 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 Ribo(Cgccu)-Oligonucleotide, PDB code: 6u6y:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6u6y

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

b:61.8
occ:0.74
NE2 A:HIS206 2.1 36.6 0.6
OD2 A:ASP207 2.5 47.0 1.0
NE2 A:HIS167 2.5 37.2 1.0
CD2 A:HIS206 3.0 29.4 0.6
CG A:ASP207 3.1 43.2 1.0
O1A A:DTP702 3.1 88.8 0.8
CE1 A:HIS206 3.2 34.1 0.6
CD2 A:HIS167 3.3 35.5 1.0
OD1 A:ASP207 3.3 42.2 1.0
CE1 A:HIS167 3.6 39.6 1.0
PA A:DTP702 3.8 94.2 0.8
ND1 A:HIS206 3.9 32.7 0.4
O2A A:DTP702 3.9 84.3 0.8
CB A:ALA311 3.9 36.3 1.0
NH1 A:ARG164 4.0 29.1 1.0
O5' A:DTP702 4.0 74.4 0.8
CG A:HIS206 4.2 33.4 0.6
ND1 A:HIS206 4.2 32.4 0.6
CE1 A:HIS206 4.3 36.2 0.4
CB A:ASP207 4.4 35.3 1.0
CG A:HIS167 4.5 40.1 1.0
C5' A:DTP702 4.5 65.0 0.8
ND1 A:HIS167 4.6 40.4 1.0
CG2 A:VAL171 4.6 29.7 1.0
CD2 A:TYR315 4.7 42.2 1.0
CE2 A:TYR315 5.0 38.6 1.0

Zinc binding site 2 out of 4 in 6u6y

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

b:52.2
occ:0.67
NE2 B:HIS206 2.3 48.1 1.0
OD2 B:ASP207 2.4 45.4 1.0
NE2 B:HIS167 2.5 38.1 1.0
O3A B:DTP702 3.1 62.0 0.8
CD2 B:HIS206 3.1 51.1 1.0
CG B:ASP207 3.3 49.0 1.0
CD2 B:HIS167 3.3 40.9 1.0
CE1 B:HIS206 3.4 49.5 1.0
CE1 B:HIS167 3.5 36.1 1.0
OD1 B:ASP207 3.6 50.5 1.0
PA B:DTP702 3.7 85.7 0.8
O2A B:DTP702 3.9 79.8 0.8
O5' B:DTP702 3.9 73.3 0.8
CB B:ALA311 3.9 33.8 1.0
NH1 B:ARG164 3.9 39.2 1.0
CG B:HIS206 4.3 46.3 1.0
ND1 B:HIS206 4.4 51.6 1.0
CB B:ASP207 4.5 41.5 1.0
CG B:HIS167 4.5 35.8 1.0
C5' B:DTP702 4.6 63.6 0.8
ND1 B:HIS167 4.6 39.5 1.0
CD2 B:TYR315 4.6 40.2 1.0
CG2 B:VAL171 4.8 41.1 1.0
CA B:ALA311 5.0 40.4 1.0

Zinc binding site 3 out of 4 in 6u6y

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

b:64.9
occ:0.87
NE2 C:HIS206 2.3 24.1 0.5
NE2 C:HIS167 2.5 34.7 1.0
OD2 C:ASP207 2.8 43.6 1.0
O1A C:DTP702 2.9 79.3 0.6
CD2 C:HIS206 3.0 18.6 0.5
CG C:ASP207 3.3 36.5 1.0
CE1 C:HIS206 3.3 23.7 0.5
CD2 C:HIS167 3.3 27.1 1.0
OD1 C:ASP207 3.4 45.5 1.0
CE1 C:HIS167 3.5 27.4 1.0
PA C:DTP702 3.6 87.7 0.6
O2A C:DTP702 3.8 74.6 0.6
CB C:ALA311 3.9 24.0 1.0
O5' C:DTP702 4.0 71.6 0.6
NH1 C:ARG164 4.0 39.6 1.0
CG C:HIS206 4.2 21.2 0.5
ND1 C:HIS206 4.3 19.4 0.5
CG C:HIS167 4.5 30.2 1.0
ND1 C:HIS167 4.6 29.4 1.0
ND1 C:HIS206 4.6 24.6 0.5
CB C:ASP207 4.6 41.2 1.0
CG2 C:VAL171 4.6 22.0 1.0
CD2 C:TYR315 4.7 28.0 1.0
C5' C:DTP702 4.8 64.3 0.6
CA C:ALA311 5.0 32.3 1.0

Zinc binding site 4 out of 4 in 6u6y

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

b:54.4
occ:0.69
NE2 D:HIS206 2.2 53.0 1.0
NE2 D:HIS167 2.5 44.6 1.0
OD2 D:ASP207 2.7 40.2 1.0
O3A D:DTP702 2.8 77.2 0.8
CD2 D:HIS206 3.2 56.9 1.0
CE1 D:HIS206 3.2 57.7 1.0
CG D:ASP207 3.2 36.6 1.0
OD1 D:ASP207 3.3 37.5 1.0
CE1 D:HIS167 3.4 48.4 1.0
CD2 D:HIS167 3.5 45.7 1.0
PA D:DTP702 3.6 94.0 0.8
O2A D:DTP702 3.8 79.2 0.8
NH1 D:ARG164 3.8 34.6 1.0
O5' D:DTP702 3.8 85.4 0.8
CB D:ALA311 4.2 34.6 1.0
ND1 D:HIS206 4.3 58.2 1.0
CG D:HIS206 4.3 54.1 1.0
C5' D:DTP702 4.4 78.6 0.8
CD2 D:TYR315 4.5 46.9 1.0
CB D:ASP207 4.5 34.7 1.0
ND1 D:HIS167 4.5 49.0 1.0
CG D:HIS167 4.6 37.6 1.0
CG2 D:VAL171 4.8 38.6 1.0
CE2 D:TYR315 4.8 41.5 1.0
NE2 D:GLN149 5.0 33.3 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 12:57:24 2020

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