Zinc in PDB 6u6x: Human SAMHD1 Bound to Deoxyribo(C*G*C*C*T)-Oligonucleotide

Protein crystallography data

The structure of Human SAMHD1 Bound to Deoxyribo(C*G*C*C*T)-Oligonucleotide, PDB code: 6u6x 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) 61.66 / 2.58
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.360, 81.870, 106.000, 69.72, 76.30, 82.77
R / Rfree (%) 19.6 / 23.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Human SAMHD1 Bound to Deoxyribo(C*G*C*C*T)-Oligonucleotide (pdb code 6u6x). 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(C*G*C*C*T)-Oligonucleotide, PDB code: 6u6x:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6u6x

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

b:89.6
occ:0.77
NE2 A:HIS206 2.4 52.5 0.4
NE2 A:HIS167 2.5 53.0 1.0
OD2 A:ASP207 2.7 66.3 1.0
CD2 A:HIS167 3.1 35.6 1.0
OD1 A:ASP207 3.2 63.6 1.0
CE1 A:HIS206 3.2 50.0 0.4
CG A:ASP207 3.2 64.3 1.0
CD2 A:HIS206 3.3 56.4 0.4
CE1 A:HIS167 3.7 48.6 1.0
NH1 A:ARG164 3.8 41.8 1.0
ND1 A:HIS206 3.9 69.9 0.6
CB A:ALA311 4.1 47.3 1.0
ND1 A:HIS206 4.2 54.3 0.4
CG A:HIS206 4.3 58.5 0.4
CG A:HIS167 4.4 60.7 1.0
CE1 A:HIS206 4.4 69.0 0.6
CD2 A:TYR315 4.6 62.6 1.0
ND1 A:HIS167 4.6 55.2 1.0
CB A:ASP207 4.6 53.6 1.0
CG2 A:VAL171 4.8 51.2 1.0

Zinc binding site 2 out of 4 in 6u6x

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

b:99.5
occ:0.61
OD2 B:ASP207 2.5 96.7 1.0
NE2 B:HIS167 2.6 77.4 1.0
CG B:ASP207 3.1 97.0 1.0
OD1 B:ASP207 3.1 99.6 1.0
CD2 B:HIS167 3.2 76.5 1.0
NH1 B:ARG164 3.6 76.3 1.0
CE1 B:HIS167 3.8 77.8 1.0
ND1 B:HIS206 4.3 0.8 1.0
CB B:ALA311 4.4 86.9 1.0
CD2 B:TYR315 4.4 99.3 1.0
CG B:HIS167 4.4 73.0 1.0
CB B:ASP207 4.4 88.4 1.0
CE2 B:TYR315 4.6 0.3 1.0
ND1 B:HIS167 4.7 78.6 1.0
CG2 B:VAL171 4.7 70.3 1.0
NE2 B:GLN149 4.9 81.8 1.0
CE1 B:HIS206 4.9 0.6 1.0
CZ B:ARG164 4.9 77.6 1.0

Zinc binding site 3 out of 4 in 6u6x

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

b:0.7
occ:0.97
OD2 C:ASP207 2.5 80.1 1.0
NE2 C:HIS167 2.7 76.3 1.0
OD1 C:ASP207 2.9 80.3 1.0
CG C:ASP207 3.1 80.6 1.0
CD2 C:HIS167 3.4 72.5 1.0
NH1 C:ARG164 3.5 66.4 1.0
CE1 C:HIS167 3.9 76.6 1.0
ND1 C:HIS206 4.1 0.6 1.0
CE1 C:HIS206 4.4 0.2 1.0
CB C:ALA311 4.4 71.2 1.0
CB C:ASP207 4.5 79.6 1.0
CG C:HIS167 4.7 75.0 1.0
CD2 C:TYR315 4.7 79.0 1.0
CZ C:ARG164 4.8 74.9 1.0
ND1 C:HIS167 4.9 72.8 1.0

Zinc binding site 4 out of 4 in 6u6x

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

b:0.5
occ:0.87
NE2 D:HIS206 2.4 59.1 0.4
NE2 D:HIS167 2.6 56.4 1.0
OD2 D:ASP207 2.6 91.1 1.0
CG D:ASP207 3.2 88.3 1.0
OD1 D:ASP207 3.3 88.2 1.0
CD2 D:HIS167 3.3 50.9 1.0
CD2 D:HIS206 3.3 63.1 0.4
CE1 D:HIS206 3.3 62.2 0.4
CE1 D:HIS167 3.7 55.4 1.0
NH1 D:ARG164 3.8 41.7 1.0
CB D:ALA311 4.1 55.7 1.0
ND1 D:HIS206 4.3 64.6 0.4
CG D:HIS206 4.4 64.7 0.4
CD2 D:HIS206 4.5 63.2 0.6
CB D:ASP207 4.5 75.8 1.0
CG2 D:VAL171 4.5 55.5 1.0
CG D:HIS167 4.5 58.9 1.0
CD2 D:TYR315 4.7 60.4 1.0
ND1 D:HIS167 4.7 59.4 1.0
CA D:ALA311 4.9 58.1 1.0
NE2 D:GLN149 4.9 57.2 1.0
O D:ALA311 5.0 68.1 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 12:57:14 2020

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