Fluorine 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:

Nickel (Ni) 1 atom
Magnesium (Mg) 10 atoms
Sodium (Na) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 8 binding sites of Fluorine where determined in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket, PDB code: 6dw5:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 6dw5

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Fluorine binding site 1 out of 8 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F701

b:60.6
occ:1.00
F1 A:GTF701 0.0 60.6 1.0
C2' A:GTF701 1.4 46.7 1.0
C1' A:GTF701 2.0 45.5 1.0
F2 A:GTF701 2.4 57.3 1.0
C3' A:GTF701 2.5 42.0 1.0
CE1 A:TYR374 2.5 17.2 1.0
CZ A:TYR374 2.7 17.8 1.0
CD1 A:TYR374 2.8 18.0 1.0
N1 A:GTF701 2.9 47.5 1.0
O3' A:GTF701 2.9 23.9 1.0
CE2 A:TYR374 3.0 18.5 1.0
CG A:TYR374 3.1 17.6 1.0
CD2 A:LEU150 3.2 18.4 1.0
CD2 A:TYR374 3.2 17.9 1.0
O4' A:GTF701 3.4 44.4 1.0
OH A:TYR374 3.4 21.7 1.0
OD2 A:ASP319 3.5 18.2 1.0
O2 A:GTF701 3.5 34.4 1.0
C2 A:GTF701 3.6 45.4 1.0
C4' A:GTF701 3.7 42.6 1.0
C6 A:GTF701 3.9 44.4 1.0
CB A:TYR374 4.2 17.7 1.0
C5' A:GTF701 4.5 50.7 1.0
CG A:ASP319 4.6 17.0 1.0
CG A:LEU150 4.7 18.3 1.0
CE1 A:TYR315 4.7 20.1 1.0
CD1 A:TYR315 4.7 18.4 1.0
N3 A:GTF701 4.9 47.0 1.0

Fluorine binding site 2 out of 8 in 6dw5

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Fluorine binding site 2 out of 8 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
A:F701

b:57.3
occ:1.00
F2 A:GTF701 0.0 57.3 1.0
C2' A:GTF701 1.5 46.7 1.0
C1' A:GTF701 2.3 45.5 1.0
C3' A:GTF701 2.4 42.0 1.0
F1 A:GTF701 2.4 60.6 1.0
N1 A:GTF701 2.7 47.5 1.0
C6 A:GTF701 2.7 44.4 1.0
C5' A:GTF701 2.8 50.7 1.0
C4' A:GTF701 2.9 42.6 1.0
O4' A:GTF701 3.1 44.4 1.0
MG A:MG707 3.2 62.5 1.0
CE2 A:TYR374 3.5 18.5 1.0
O3' A:GTF701 3.7 23.9 1.0
CD2 A:TYR374 3.7 17.9 1.0
CZ A:TYR315 3.8 21.7 1.0
O5' A:GTF701 3.8 64.3 1.0
CE1 A:TYR315 3.9 20.1 1.0
OH A:TYR315 3.9 22.5 1.0
CZ A:TYR374 4.0 17.8 1.0
C5 A:GTF701 4.0 44.2 1.0
C2 A:GTF701 4.1 45.4 1.0
CE2 A:TYR315 4.2 20.6 1.0
NE2 A:HIS370 4.2 26.7 1.0
CG A:TYR374 4.3 17.6 1.0
CE1 A:HIS370 4.4 28.5 1.0
CD1 A:TYR315 4.4 18.4 1.0
CE1 A:TYR374 4.5 17.2 1.0
OH A:TYR374 4.6 21.7 1.0
O1G A:GTF701 4.6 56.2 1.0
CD1 A:TYR374 4.6 18.0 1.0
CD2 A:TYR315 4.7 18.7 1.0
O2 A:GTF701 4.7 34.4 1.0
NE2 A:HIS215 4.8 41.1 1.0
CG A:TYR315 4.8 17.5 1.0
CD2 A:HIS215 4.9 36.9 1.0
C4 A:GTF701 5.0 45.3 1.0

Fluorine binding site 3 out of 8 in 6dw5

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Fluorine binding site 3 out of 8 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
B:F701

b:64.8
occ:1.00
F1 B:GTF701 0.0 64.8 1.0
C2' B:GTF701 1.4 56.1 1.0
C1' B:GTF701 2.1 55.5 1.0
F2 B:GTF701 2.3 66.2 1.0
C3' B:GTF701 2.5 49.5 1.0
CE1 B:TYR374 2.5 24.4 1.0
CZ B:TYR374 2.7 25.7 1.0
CD1 B:TYR374 2.7 24.9 1.0
O3' B:GTF701 2.8 30.7 1.0
N1 B:GTF701 2.9 57.4 1.0
CG B:TYR374 3.0 23.9 1.0
CE2 B:TYR374 3.0 26.2 1.0
CD2 B:LEU150 3.1 23.0 1.0
CD2 B:TYR374 3.2 25.3 1.0
C2 B:GTF701 3.4 53.5 1.0
O2 B:GTF701 3.5 44.4 1.0
O4' B:GTF701 3.5 51.9 1.0
OH B:TYR374 3.5 25.5 1.0
OD2 B:ASP319 3.5 18.8 1.0
C4' B:GTF701 3.7 51.2 1.0
C6 B:GTF701 4.0 56.7 1.0
CB B:TYR374 4.1 23.8 1.0
C5' B:GTF701 4.6 58.7 1.0
CG B:LEU150 4.6 23.0 1.0
CG B:ASP319 4.6 19.4 1.0
N3 B:GTF701 4.7 54.1 1.0
CD1 B:TYR315 4.8 20.6 1.0
CE1 B:TYR315 4.8 22.4 1.0

Fluorine binding site 4 out of 8 in 6dw5

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Fluorine binding site 4 out of 8 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
B:F701

b:66.2
occ:1.00
F2 B:GTF701 0.0 66.2 1.0
C2' B:GTF701 1.4 56.1 1.0
F1 B:GTF701 2.3 64.8 1.0
C1' B:GTF701 2.3 55.5 1.0
N1 B:GTF701 2.5 57.4 1.0
C3' B:GTF701 2.5 49.5 1.0
C6 B:GTF701 2.6 56.7 1.0
C4' B:GTF701 3.1 51.2 1.0
C5' B:GTF701 3.2 58.7 1.0
O4' B:GTF701 3.2 51.9 1.0
CE2 B:TYR374 3.3 26.2 1.0
CD2 B:TYR374 3.4 25.3 1.0
O3' B:GTF701 3.7 30.7 1.0
C2 B:GTF701 3.7 53.5 1.0
C5 B:GTF701 3.8 54.1 1.0
CZ B:TYR374 3.8 25.7 1.0
CG B:TYR374 3.9 23.9 1.0
NE2 B:HIS370 4.0 29.3 1.0
CE1 B:HIS370 4.1 32.7 1.0
O5' B:GTF701 4.1 76.0 1.0
O2G B:GTF701 4.1 70.3 1.0
CZ B:TYR315 4.2 23.9 1.0
CE1 B:TYR315 4.2 22.4 1.0
CE1 B:TYR374 4.3 24.4 1.0
CD1 B:TYR374 4.3 24.9 1.0
OH B:TYR315 4.3 26.4 1.0
O2 B:GTF701 4.4 44.4 1.0
OH B:TYR374 4.5 25.5 1.0
N3 B:GTF701 4.6 54.1 1.0
C4 B:GTF701 4.6 54.6 1.0
CE2 B:TYR315 4.7 23.2 1.0
CB B:TYR374 4.7 23.8 1.0
CD1 B:TYR315 4.7 20.6 1.0
CD2 B:HIS370 4.9 28.8 1.0
CD2 B:HIS215 4.9 41.4 1.0
NE2 B:HIS215 5.0 42.1 1.0
ND1 B:HIS370 5.0 31.8 1.0

Fluorine binding site 5 out of 8 in 6dw5

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Fluorine binding site 5 out of 8 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F705

b:65.6
occ:1.00
F1 C:GTF705 0.0 65.6 1.0
C2' C:GTF705 1.4 54.6 1.0
C1' C:GTF705 2.2 51.0 1.0
F2 C:GTF705 2.4 65.7 1.0
C3' C:GTF705 2.4 51.0 1.0
CE1 C:TYR374 2.5 25.7 1.0
CZ C:TYR374 2.5 25.9 1.0
O3' C:GTF705 2.7 32.9 1.0
CD1 C:TYR374 2.8 24.3 1.0
CE2 C:TYR374 3.0 25.4 1.0
CD2 C:LEU150 3.1 23.9 1.0
CG C:TYR374 3.2 24.0 1.0
N1 C:GTF705 3.2 50.8 1.0
OD2 C:ASP319 3.2 20.3 1.0
CD2 C:TYR374 3.2 25.2 1.0
OH C:TYR374 3.3 24.6 1.0
O4' C:GTF705 3.6 49.2 1.0
C4' C:GTF705 3.7 49.0 1.0
O2 C:GTF705 3.9 43.2 1.0
C2 C:GTF705 3.9 48.0 1.0
C6 C:GTF705 4.2 49.6 1.0
CG C:ASP319 4.3 20.3 1.0
CB C:TYR374 4.3 24.1 1.0
C5' C:GTF705 4.5 57.1 1.0
CD1 C:TYR315 4.5 21.9 1.0
CG C:LEU150 4.6 22.9 1.0
CE1 C:TYR315 4.6 22.7 1.0
OD1 C:ASP319 5.0 19.5 1.0
CD1 C:LEU150 5.0 23.1 1.0

Fluorine binding site 6 out of 8 in 6dw5

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Fluorine binding site 6 out of 8 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F705

b:65.7
occ:1.00
F2 C:GTF705 0.0 65.7 1.0
C2' C:GTF705 1.4 54.6 1.0
C1' C:GTF705 2.4 51.0 1.0
C3' C:GTF705 2.4 51.0 1.0
F1 C:GTF705 2.4 65.6 1.0
N1 C:GTF705 2.8 50.8 1.0
C5' C:GTF705 2.9 57.1 1.0
C6 C:GTF705 2.9 49.6 1.0
C4' C:GTF705 2.9 49.0 1.0
O4' C:GTF705 3.2 49.2 1.0
CE2 C:TYR374 3.3 25.4 1.0
CD2 C:TYR374 3.5 25.2 1.0
O3' C:GTF705 3.6 32.9 1.0
CZ C:TYR374 3.8 25.9 1.0
CZ C:TYR315 3.8 24.1 1.0
CE1 C:TYR315 3.8 22.7 1.0
OH C:TYR315 4.0 25.3 1.0
CG C:TYR374 4.1 24.0 1.0
NE2 C:HIS370 4.1 34.1 1.0
O5' C:GTF705 4.1 66.5 1.0
CE2 C:TYR315 4.2 23.4 1.0
C2 C:GTF705 4.2 48.0 1.0
C5 C:GTF705 4.3 49.3 1.0
CD1 C:TYR315 4.3 21.9 1.0
CE1 C:HIS370 4.3 35.5 1.0
CE1 C:TYR374 4.3 25.7 1.0
OH C:TYR374 4.3 24.6 1.0
CD1 C:TYR374 4.5 24.3 1.0
CD2 C:TYR315 4.6 22.7 1.0
CG C:TYR315 4.7 20.2 1.0
O2 C:GTF705 4.8 43.2 1.0
OD2 C:ASP319 4.8 20.3 1.0
CD2 C:HIS370 5.0 32.2 1.0
CB C:TYR374 5.0 24.1 1.0

Fluorine binding site 7 out of 8 in 6dw5

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Fluorine binding site 7 out of 8 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F702

b:51.6
occ:1.00
F1 D:GTF702 0.0 51.6 1.0
C2' D:GTF702 1.4 43.4 1.0
C1' D:GTF702 2.2 43.2 1.0
F2 D:GTF702 2.3 52.7 1.0
C3' D:GTF702 2.4 39.2 1.0
CE1 D:TYR374 2.5 19.9 1.0
O3' D:GTF702 2.6 25.5 1.0
CZ D:TYR374 2.7 20.8 1.0
CD1 D:TYR374 2.8 19.2 1.0
CD2 D:LEU150 2.9 20.4 1.0
N1 D:GTF702 3.1 44.6 1.0
CE2 D:TYR374 3.2 22.1 1.0
OD2 D:ASP319 3.2 17.9 1.0
CG D:TYR374 3.2 20.0 1.0
CD2 D:TYR374 3.4 22.1 1.0
OH D:TYR374 3.4 19.0 1.0
O4' D:GTF702 3.5 44.4 1.0
C4' D:GTF702 3.7 40.6 1.0
O2 D:GTF702 3.7 35.7 1.0
C2 D:GTF702 3.8 44.1 1.0
C6 D:GTF702 4.2 44.6 1.0
CG D:ASP319 4.3 16.4 1.0
CB D:TYR374 4.3 19.3 1.0
CG D:LEU150 4.4 19.4 1.0
C5' D:GTF702 4.6 42.2 1.0
CD1 D:TYR315 4.7 18.6 1.0
CD1 D:LEU150 4.8 19.3 1.0
CE1 D:TYR315 4.9 21.4 1.0
OD1 D:ASP319 4.9 17.9 1.0

Fluorine binding site 8 out of 8 in 6dw5

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Fluorine binding site 8 out of 8 in the SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of SAMHD1 Bound to Gemcitabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F702

b:52.7
occ:1.00
F2 D:GTF702 0.0 52.7 1.0
C2' D:GTF702 1.4 43.4 1.0
F1 D:GTF702 2.3 51.6 1.0
C1' D:GTF702 2.4 43.2 1.0
C3' D:GTF702 2.4 39.2 1.0
N1 D:GTF702 2.7 44.6 1.0
C6 D:GTF702 2.9 44.6 1.0
C4' D:GTF702 3.1 40.6 1.0
O4' D:GTF702 3.1 44.4 1.0
C5' D:GTF702 3.1 42.2 1.0
CE2 D:TYR374 3.2 22.1 1.0
CD2 D:TYR374 3.3 22.1 1.0
MG D:MG705 3.4 57.1 1.0
O3' D:GTF702 3.5 25.5 1.0
CZ D:TYR374 3.6 20.8 1.0
O5' D:GTF702 3.8 50.2 1.0
CG D:TYR374 3.8 20.0 1.0
CE1 D:TYR315 3.9 21.4 1.0
CZ D:TYR315 3.9 23.3 1.0
C2 D:GTF702 4.1 44.1 1.0
CE1 D:TYR374 4.1 19.9 1.0
NE2 D:HIS370 4.1 28.1 1.0
C5 D:GTF702 4.1 42.1 1.0
CD1 D:TYR374 4.2 19.2 1.0
OH D:TYR374 4.2 19.0 1.0
OH D:TYR315 4.2 26.8 1.0
CD1 D:TYR315 4.3 18.6 1.0
CE1 D:HIS370 4.4 29.4 1.0
CE2 D:TYR315 4.4 22.1 1.0
O2 D:GTF702 4.6 35.7 1.0
OD2 D:ASP319 4.7 17.9 1.0
CB D:TYR374 4.7 19.3 1.0
CD2 D:TYR315 4.7 20.2 1.0
CG D:TYR315 4.8 18.8 1.0
O2G D:GTF702 4.9 53.8 1.0
CD2 D:HIS370 5.0 27.7 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: Sun Dec 13 12:48:29 2020

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