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

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

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

Fluorine	(F)	8 atoms
Nickel	(Ni)	1 atom
Magnesium	(Mg)	10 atoms

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket, PDB code: 6dw5:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic 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 Gemcitabine-Tp in the Catalytic Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:Na706 b:37.3 occ:1.00 O A:TYR298 2.1 29.6 1.0 O A:SER302 2.1 36.7 1.0 O A:HOH858 2.3 28.6 1.0 O A:HOH914 2.4 37.3 1.0 C A:SER302 3.3 33.8 1.0 C A:TYR298 3.3 29.4 1.0 O A:GLN271 3.9 28.2 1.0 CA A:TYR298 4.0 29.1 1.0 CB A:TYR298 4.1 29.3 1.0 CA A:SER302 4.1 31.6 1.0 N A:SER302 4.1 26.3 1.0 N A:ASN303 4.2 34.9 1.0 CB A:SER302 4.2 34.8 1.0 CA A:ASN303 4.3 35.7 1.0 OH A:TYR287 4.3 38.3 1.0 N A:GLU299 4.3 30.6 1.0 CG A:LYS304 4.4 54.2 1.0 CA A:GLN271 4.6 26.2 1.0 CA A:GLU299 4.6 31.5 1.0 CE A:LYS304 4.6 58.5 1.0 C A:GLN271 4.6 25.6 1.0 N A:LYS304 4.6 40.5 1.0 CD A:LYS304 4.7 56.2 1.0 O A:HOH844 4.7 26.9 1.0 O A:GLU270 4.8 28.1 1.0 CD1 A:TYR298 4.8 29.7 1.0 CG A:TYR298 5.0 29.6 1.0

Sodium binding site 2 out of 4 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:Na705 b:40.8 occ:1.00 O B:SER302 2.1 39.7 1.0 O B:HOH834 2.2 28.3 1.0 O B:TYR298 2.3 37.5 1.0 O B:HOH913 2.3 38.0 1.0 O B:HOH865 2.4 33.1 1.0 C B:SER302 3.3 35.0 1.0 C B:TYR298 3.4 34.4 1.0 O B:GLN271 3.8 31.7 1.0 CB B:SER302 4.0 37.8 1.0 CA B:SER302 4.0 34.6 1.0 N B:SER302 4.0 31.6 1.0 CA B:TYR298 4.0 34.2 1.0 CB B:TYR298 4.1 35.4 1.0 N B:ASN303 4.2 34.7 1.0 CA B:ASN303 4.4 36.8 1.0 CE B:LYS304 4.5 49.4 1.0 OH B:TYR287 4.5 51.7 1.0 N B:GLU299 4.5 34.4 1.0 C B:GLN271 4.5 31.9 1.0 CG B:LYS304 4.5 51.6 1.0 CA B:GLN271 4.5 32.1 1.0 CD B:LYS304 4.6 50.7 1.0 CA B:GLU299 4.7 34.3 1.0 N B:LYS304 4.8 41.8 1.0 O B:GLU270 4.8 32.0 1.0 O B:HOH826 4.8 26.9 1.0 CD1 B:TYR298 4.9 35.6 1.0

Sodium binding site 3 out of 4 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket within 5.0Å range: probe atom residue distance (Å) B Occ C:Na706 b:56.5 occ:1.00 O C:HOH866 2.3 39.1 1.0 O C:HOH804 2.6 45.3 1.0 O C:TYR374 2.6 24.0 1.0 OD1 C:ASN380 2.6 25.9 1.0 OD2 C:ASP383 3.4 40.4 1.0 N3 C:GTF705 3.6 50.8 1.0 CG C:ASN380 3.7 26.5 1.0 C C:TYR374 3.9 23.3 1.0 OE1 C:GLN375 3.9 26.6 1.0 N4 C:GTF705 4.0 59.4 1.0 O C:HOH922 4.1 44.8 1.0 O C:HOH870 4.3 31.8 1.0 NE2 C:GLN375 4.3 31.9 1.0 ND2 C:ASN380 4.3 28.1 1.0 CD C:GLN375 4.4 28.1 1.0 C4 C:GTF705 4.4 50.5 1.0 CG C:ASP383 4.7 37.3 1.0 CA C:GLN375 4.7 23.3 1.0 N C:GLN375 4.7 22.3 1.0 NH1 C:ARG220 4.7 38.8 1.0 O2 C:GTF705 4.7 43.2 1.0 C2 C:GTF705 4.7 48.0 1.0 CA C:ASN380 4.8 26.4 1.0 CB C:ASN380 4.8 26.0 1.0 CA C:TYR374 4.9 23.2 1.0

Sodium binding site 4 out of 4 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket within 5.0Å range: probe atom residue distance (Å) B Occ C:Na707 b:39.5 occ:1.00 O C:TYR298 2.1 30.4 1.0 O C:HOH844 2.3 27.3 1.0 O C:SER302 2.3 38.1 1.0 O C:HOH841 2.4 33.6 1.0 O C:HOH898 2.5 41.5 1.0 C C:TYR298 3.2 28.5 1.0 C C:SER302 3.5 34.8 1.0 CA C:TYR298 3.8 27.1 1.0 CB C:TYR298 3.9 28.1 1.0 O C:GLN271 3.9 28.5 1.0 N C:SER302 4.2 28.3 1.0 CD C:LYS304 4.2 56.6 1.0 CA C:SER302 4.2 33.2 1.0 CB C:SER302 4.3 36.2 1.0 N C:GLU299 4.3 27.6 1.0 N C:ASN303 4.4 36.0 1.0 OH C:TYR287 4.4 40.2 1.0 CE C:LYS304 4.4 56.1 1.0 CA C:ASN303 4.5 36.5 1.0 CA C:GLN271 4.5 27.8 1.0 CA C:GLU299 4.6 29.3 1.0 C C:GLN271 4.6 28.9 1.0 CD1 C:TYR298 4.7 29.2 1.0 O C:HOH830 4.8 25.3 1.0 O C:GLU270 4.8 28.7 1.0 O C:HOH813 4.8 43.4 1.0 CG C:TYR298 4.8 28.3 1.0 N C:LYS304 4.9 41.7 1.0

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