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Sodium in PDB 6dw4: SAMHD1 Bound to Cladribine-Tp in the Catalytic Pocket and Allosteric Pocket

Protein crystallography data

The structure of SAMHD1 Bound to Cladribine-Tp in the Catalytic Pocket and Allosteric Pocket, PDB code: 6dw4 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) 89.87 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.324, 142.272, 98.438, 90.00, 114.08, 90.00
R / Rfree (%) 16.9 / 20.2

Other elements in 6dw4:

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

Magnesium (Mg) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the SAMHD1 Bound to Cladribine-Tp in the Catalytic Pocket and Allosteric Pocket (pdb code 6dw4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the SAMHD1 Bound to Cladribine-Tp in the Catalytic Pocket and Allosteric Pocket, PDB code: 6dw4:

Sodium binding site 1 out of 1 in 6dw4

Go back to Sodium Binding Sites List in 6dw4
Sodium binding site 1 out of 1 in the SAMHD1 Bound to Cladribine-Tp in the Catalytic Pocket and Allosteric Pocket


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of SAMHD1 Bound to Cladribine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na707

b:93.8
occ:1.00
O C:ALA373 3.0 16.9 1.0
O C:HOH981 3.3 38.8 1.0
C C:ALA373 3.4 17.2 1.0
CA C:GLY153 3.5 17.1 1.0
CL2 C:HF7701 3.7 25.1 1.0
CA C:TYR374 3.7 16.6 1.0
N C:TYR374 3.8 16.7 1.0
CB C:LEU150 3.9 19.5 1.0
CD1 C:LEU150 4.0 20.2 1.0
CB C:ALA373 4.1 16.9 1.0
CA C:ALA373 4.2 17.6 1.0
CD1 C:TYR374 4.2 16.2 1.0
O C:LEU150 4.3 22.0 1.0
N C:GLY153 4.3 18.8 1.0
CG C:LEU150 4.4 20.1 1.0
C C:GLY153 4.4 16.1 1.0
C C:TYR374 4.5 17.1 1.0
O C:TYR374 4.6 18.1 1.0
CD1 C:PHE157 4.6 15.0 1.0
CD2 C:LEU323 4.7 14.3 1.0
O C:GLY153 4.7 15.8 1.0
CD2 C:LEU150 4.8 20.0 1.0
CE1 C:PHE157 4.8 15.5 1.0
CB C:TYR374 4.8 16.5 1.0
O C:HOH814 4.8 42.0 1.0
C2 C:HF7701 4.8 25.8 1.0
CA C:LEU150 5.0 18.7 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: Tue Dec 15 12:08:46 2020

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