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Nickel in PDB 6dw5: SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket

Protein crystallography data

The structure of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket, PDB code: 6dw5 was solved by K.M.Knecht, O.Buzovetsky, C.Schneider, D.Thomas, V.Srikanth, L.Kaderali, F.Tofoleanu, K.Reiss, N.Ferreiros, G.Geisslinger, V.S.Batista, X.Ji, J.Cinatl, O.T.Keppler, Y.Xiong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 90.41 / 1.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.686, 142.901, 98.907, 90.00, 113.92, 90.00
R / Rfree (%) 17.3 / 20.5

Other elements in 6dw5:

The structure of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Magnesium (Mg) 10 atoms
Sodium (Na) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket (pdb code 6dw5). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket, PDB code: 6dw5:

Nickel binding site 1 out of 1 in 6dw5

Go back to Nickel Binding Sites List in 6dw5
Nickel binding site 1 out of 1 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni701

b:0.1
occ:1.00
ND1 C:HIS322 2.6 35.2 1.0
CD2 B:HIS321 2.8 21.6 1.0
NE2 B:HIS321 2.8 21.4 1.0
CE1 B:HIS322 2.9 32.7 1.0
CE1 C:HIS322 3.0 37.9 1.0
CG C:HIS322 3.2 26.6 1.0
NE2 B:HIS322 3.3 27.8 1.0
CD2 C:HIS321 3.4 22.4 1.0
CA C:HIS322 3.4 21.0 1.0
ND1 B:HIS322 3.5 31.4 1.0
O C:HIS321 3.6 21.9 1.0
CB C:HIS322 3.7 23.9 1.0
NE2 C:HIS322 3.8 28.7 1.0
NE2 C:HIS321 3.8 23.2 1.0
N C:HIS322 3.9 18.2 1.0
CD2 C:HIS322 3.9 27.7 1.0
C C:HIS321 3.9 20.3 1.0
CD2 B:HIS322 4.1 28.5 1.0
CG B:HIS321 4.1 20.4 1.0
CE1 B:HIS321 4.1 23.1 1.0
CG B:HIS322 4.1 26.3 1.0
CG C:HIS321 4.3 22.2 1.0
O C:GLY159 4.3 19.9 1.0
C C:HIS322 4.5 22.5 1.0
CG B:PRO121 4.6 24.3 1.0
O C:HIS322 4.6 21.4 1.0
CB B:PRO121 4.7 24.5 1.0
ND1 B:HIS321 4.8 20.2 1.0
CE1 C:HIS321 4.9 23.4 1.0
O B:HOH872 4.9 22.9 1.0
CB C:HIS321 5.0 20.7 1.0

Reference:

K.M.Knecht, O.Buzovetsky, C.Schneider, D.Thomas, V.Srikanth, L.Kaderali, F.Tofoleanu, K.Reiss, N.Ferreiros, G.Geisslinger, V.S.Batista, X.Ji, J.Cinatl Jr., O.T.Keppler, Y.Xiong. The Structural Basis For Cancer Drug Interactions with the Catalytic and Allosteric Sites of SAMHD1. Proc. Natl. Acad. Sci. V. 115 10022 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30305425
DOI: 10.1073/PNAS.1805593115
Page generated: Wed Dec 16 01:50:46 2020

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