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Sodium in PDB 6dwd: SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket

Protein crystallography data

The structure of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket, PDB code: 6dwd 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) 50.00 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.477, 142.233, 98.790, 90.00, 114.10, 90.00
R / Rfree (%) 17.6 / 20.2

Other elements in 6dwd:

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

Fluorine (F) 8 atoms
Magnesium (Mg) 10 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Sodium atom in the SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket (pdb code 6dwd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 23 binding sites of Sodium where determined in the SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket, PDB code: 6dwd:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 23 in 6dwd

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Sodium binding site 1 out of 23 in the SAMHD1 Bound to Clofarabine-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 Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na707

b:52.2
occ:1.00
 O D:HOH1025 1.9 27.9 1.0
OE1 D:GLU355 2.5 26.4 1.0
O D:HOH1049 2.9 34.5 1.0
CG D:GLU355 3.1 21.9 1.0
CD D:GLU355 3.2 23.6 1.0
CB D:GLU355 3.4 18.0 1.0
CA D:PHE334 3.5 14.6 1.0
O D:ARG333 3.6 14.2 1.0
CB D:PHE337 3.6 22.1 1.0
N D:PHE334 3.8 12.9 1.0
CD1 D:PHE337 3.8 19.5 1.0
C D:ARG333 3.8 13.5 1.0
CG D:ARG333 3.8 13.6 1.0
O D:HOH966 3.9 19.7 1.0
CG D:PHE337 3.9 22.3 1.0
O D:HOH923 4.1 24.3 1.0
NE D:ARG333 4.2 14.2 1.0
ND2 D:ASN358 4.2 19.8 1.0
CD D:ARG333 4.3 14.5 1.0
CB D:PHE334 4.4 15.4 1.0
OE2 D:GLU355 4.4 23.0 1.0
O D:PHE334 4.4 13.9 1.0
C D:PHE334 4.5 15.0 1.0
CB D:ARG333 4.6 14.9 1.0
CD2 D:PHE334 4.6 21.8 1.0
CA D:GLU355 4.7 18.0 1.0
CE1 D:PHE337 4.8 20.3 1.0
CA D:PHE337 4.8 21.8 1.0
CG D:PHE334 4.8 16.2 1.0
CA D:ARG333 4.8 14.7 1.0
CD2 D:PHE337 4.9 23.0 1.0
N D:PHE337 5.0 18.9 1.0

Sodium binding site 2 out of 23 in 6dwd

Go back to Sodium Binding Sites List in 6dwd
Sodium binding site 2 out of 23 in the SAMHD1 Bound to Clofarabine-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 2 of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na708

b:48.6
occ:1.00
 O D:HOH1062 2.2 30.0 1.0
OD2 D:ASP361 3.0 25.3 1.0
OD1 D:ASN358 3.1 20.8 1.0
NE B:ARG372 3.5 28.1 1.0
C D:GLY357 3.5 15.9 1.0
N D:ASN358 3.6 14.2 1.0
O D:HOH943 3.7 34.1 1.0
CG B:ARG372 3.7 20.4 1.0
O D:GLY357 3.7 16.0 1.0
CG D:ASP361 4.0 22.0 1.0
CA D:ASN358 4.0 14.6 1.0
O D:HOH950 4.0 24.5 1.0
CA D:GLY357 4.1 14.8 1.0
CG D:ASN358 4.1 18.2 1.0
CD B:ARG372 4.2 24.6 1.0
NH1 B:ARG372 4.3 43.8 1.0
CZ B:ARG372 4.4 38.5 1.0
CB B:ARG371 4.5 21.9 1.0
O D:HOH912 4.5 33.3 1.0
OD1 D:ASP361 4.7 27.5 1.0
CB D:ASP361 4.7 16.4 1.0
CB D:ASN358 4.7 14.7 1.0
O B:SER368 4.8 16.3 1.0
CB B:SER368 4.9 19.3 1.0
N6 D:HDV703 5.0 20.8 1.0
CA B:SER368 5.0 15.3 1.0

Sodium binding site 3 out of 23 in 6dwd

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Sodium binding site 3 out of 23 in the SAMHD1 Bound to Clofarabine-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 3 of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na709

b:48.7
occ:1.00
 OD2 D:ASP583 2.4 35.8 1.0
O D:VAL457 2.8 21.7 1.0
CG D:ASP583 3.3 32.0 1.0
OD1 D:ASP583 3.5 31.3 1.0
O D:HOH958 3.7 35.9 1.0
C D:VAL457 3.7 20.3 1.0
CE2 D:TYR456 3.8 28.4 1.0
CA D:GLY458 3.9 17.9 1.0
O D:HOH1001 4.1 41.8 1.0
N D:GLY458 4.1 16.9 1.0
CG2 D:ILE587 4.2 32.0 1.0
CD2 D:TYR456 4.2 25.0 1.0
CD1 D:ILE587 4.4 24.4 1.0
CB D:ASP583 4.6 30.2 1.0
CZ D:TYR456 4.7 25.7 1.0
CA D:VAL457 4.8 20.5 1.0
NE D:ARG566 4.9 42.7 1.0
O D:TYR456 4.9 19.3 1.0
OH D:TYR456 5.0 36.3 1.0

Sodium binding site 4 out of 23 in 6dwd

Go back to Sodium Binding Sites List in 6dwd
Sodium binding site 4 out of 23 in the SAMHD1 Bound to Clofarabine-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 4 of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na710

b:50.0
occ:1.00
 OH D:TYR473 2.6 46.1 1.0
O D:ILE468 2.7 44.9 1.0
ND2 D:ASN504 3.2 30.7 1.0
NE2 D:GLN548 3.4 25.5 1.0
CZ D:TYR473 3.5 37.0 1.0
CE1 D:TYR473 3.7 35.0 1.0
N D:ARG470 3.8 47.0 1.0
C D:ILE468 3.9 50.6 1.0
OD1 D:ASN504 4.0 29.9 1.0
NZ D:LYS467 4.0 81.1 1.0
NZ D:LYS469 4.0 83.5 1.0
CA D:LYS469 4.0 55.3 1.0
CG D:ASN504 4.0 27.4 1.0
C D:LYS469 4.1 50.8 1.0
N D:LYS469 4.4 53.7 1.0
CA D:ARG470 4.6 49.6 1.0
CE D:LYS467 4.7 78.8 1.0
CE2 D:TYR473 4.7 40.4 1.0
CG1 D:VAL502 4.7 22.0 1.0
CD D:GLN548 4.7 28.3 1.0
CB D:ARG470 4.9 53.5 1.0
O D:LYS469 4.9 44.8 1.0
CE D:LYS469 5.0 83.0 1.0

Sodium binding site 5 out of 23 in 6dwd

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Sodium binding site 5 out of 23 in the SAMHD1 Bound to Clofarabine-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 5 of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na711

b:47.9
occ:1.00
 O2 D:SIN714 2.2 59.2 1.0
O1 D:SIN714 3.0 45.1 1.0
C1 D:SIN714 3.1 48.1 1.0
O D:HOH994 3.6 34.4 1.0
NA D:NA712 3.7 49.3 1.0
CG D:GLN447 3.9 21.9 1.0
CB D:GLN447 4.1 20.6 1.0
CG1 D:ILE444 4.1 19.2 1.0
CA D:ILE444 4.2 16.1 1.0
CE1 D:PHE454 4.5 25.5 1.0
C2 D:SIN714 4.5 50.0 1.0
CE D:MET385 4.6 21.1 1.0
CB D:ILE444 4.6 18.5 1.0
CZ D:PHE454 4.8 26.9 1.0
O D:GLU443 4.8 17.7 1.0
CG2 D:ILE444 4.8 16.0 1.0
N D:ILE444 5.0 15.9 1.0
O D:ILE444 5.0 15.2 1.0

Sodium binding site 6 out of 23 in 6dwd

Go back to Sodium Binding Sites List in 6dwd
Sodium binding site 6 out of 23 in the SAMHD1 Bound to Clofarabine-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 6 of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na712

b:49.3
occ:1.00
 O2 D:SIN714 2.4 59.2 1.0
O D:HOH881 3.1 40.2 1.0
C1 D:SIN714 3.4 48.1 1.0
C2 D:SIN714 3.7 50.0 1.0
NA D:NA711 3.7 47.9 1.0
O D:HOH994 3.8 34.4 1.0
O1 D:SIN714 4.4 45.1 1.0
C3 D:SIN714 4.5 44.5 1.0
CE1 D:PHE454 4.5 25.5 1.0
C4 D:SIN714 4.7 48.3 1.0
O D:LYS555 4.7 28.8 1.0
O3 D:SIN714 4.8 55.5 1.0

Sodium binding site 7 out of 23 in 6dwd

Go back to Sodium Binding Sites List in 6dwd
Sodium binding site 7 out of 23 in the SAMHD1 Bound to Clofarabine-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 7 of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na708

b:38.7
occ:1.00
 OE1 C:GLU355 2.5 25.6 1.0
O C:HOH970 2.6 18.5 1.0
CD C:GLU355 3.4 27.1 1.0
CA C:PHE334 3.5 14.7 1.0
CB C:GLU355 3.5 16.3 1.0
CG C:GLU355 3.5 19.5 1.0
ND2 C:ASN358 3.7 18.4 1.0
CB C:PHE334 3.7 17.1 1.0
N C:PHE334 3.8 13.0 1.0
CB C:ASN358 3.9 13.1 1.0
CD2 C:PHE334 3.9 22.0 1.0
O C:HOH937 4.1 37.1 1.0
CG C:PHE334 4.3 16.9 1.0
C C:ARG333 4.3 12.6 1.0
CG C:ASN358 4.3 17.8 1.0
CD1 C:LEU359 4.4 26.4 1.0
CA C:GLU355 4.4 13.7 1.0
CG C:ARG333 4.5 11.3 1.0
OE2 C:GLU355 4.5 39.2 1.0
O C:GLU355 4.6 13.2 1.0
O C:ARG333 4.6 12.4 1.0
CD C:ARG333 4.7 11.2 1.0
NE C:ARG333 4.7 11.8 1.0
CB C:ARG333 4.8 10.8 1.0
C C:PHE334 4.8 15.7 1.0
O C:ASP330 4.8 10.3 1.0

Sodium binding site 8 out of 23 in 6dwd

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Sodium binding site 8 out of 23 in the SAMHD1 Bound to Clofarabine-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 8 of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na709

b:34.5
occ:1.00
 O C:HOH1040 2.1 29.4 1.0
O C:HOH1036 2.3 28.2 1.0
OD2 C:ASP361 2.8 26.9 1.0
OD1 C:ASN358 3.1 19.0 1.0
NE A:ARG372 3.3 25.8 1.0
O C:HOH961 3.5 32.9 1.0
C C:GLY357 3.5 12.4 1.0
N C:ASN358 3.6 12.5 1.0
O C:GLY357 3.6 12.3 1.0
CG A:ARG372 3.7 17.6 1.0
CG C:ASP361 3.8 22.2 1.0
NH1 A:ARG372 3.9 36.1 1.0
CA C:ASN358 4.0 12.9 1.0
CZ A:ARG372 4.1 36.9 1.0
OG A:SER368 4.1 28.3 1.0
CG C:ASN358 4.1 17.8 1.0
CA C:GLY357 4.1 12.7 1.0
CD A:ARG372 4.1 22.2 1.0
O C:HOH835 4.2 24.5 1.0
O C:HOH980 4.5 25.8 1.0
CB C:ASP361 4.5 16.4 1.0
OD1 C:ASP361 4.5 23.5 1.0
CB C:ASN358 4.7 13.1 1.0
CB A:ARG371 4.7 19.4 1.0
N6 C:HDV704 4.9 16.3 1.0
O A:SER368 4.9 13.3 1.0
CB A:SER368 5.0 18.8 1.0

Sodium binding site 9 out of 23 in 6dwd

Go back to Sodium Binding Sites List in 6dwd
Sodium binding site 9 out of 23 in the SAMHD1 Bound to Clofarabine-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 9 of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na710

b:48.8
occ:1.00
 O C:HOH947 2.4 38.2 1.0
OH B:TYR450 2.8 29.1 1.0
OD1 C:ASN248 2.9 27.9 1.0
O C:SER247 3.4 31.2 1.0
CG C:ASN248 3.5 27.3 1.0
CZ B:TYR450 3.7 24.4 1.0
ND2 C:ASN248 3.7 24.3 1.0
CE1 B:TYR450 3.8 21.8 1.0
CG C:PRO139 3.9 23.7 1.0
CD C:PRO139 3.9 23.8 1.0
CB C:SER247 3.9 30.3 1.0
C C:SER247 4.1 31.3 1.0
OE1 C:GLN140 4.2 23.8 1.0
NE2 C:GLN140 4.3 28.6 1.0
CA C:SER247 4.7 29.5 1.0
CD C:GLN140 4.7 22.5 1.0
CB C:ASN248 4.8 26.6 1.0
O B:HOH981 4.8 37.0 1.0
N C:ASN248 4.8 27.8 1.0
CA C:ASN248 4.8 27.4 1.0
CE2 B:TYR450 5.0 25.1 1.0

Sodium binding site 10 out of 23 in 6dwd

Go back to Sodium Binding Sites List in 6dwd
Sodium binding site 10 out of 23 in the SAMHD1 Bound to Clofarabine-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 10 of SAMHD1 Bound to Clofarabine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na711

b:47.9
occ:1.00
 OE1 C:GLU292 2.5 55.0 1.0
O C:HOH1021 2.6 22.7 1.0
CD C:GLU292 3.5 57.0 1.0
CB C:GLU292 3.8 38.8 1.0
CB C:TRP285 3.9 31.5 1.0
CG C:GLU292 4.2 50.2 1.0
OE2 C:GLU292 4.3 57.1 1.0
CG C:TRP285 4.5 28.4 1.0
CD1 C:TRP285 4.7 27.0 1.0
N C:GLU292 4.8 26.9 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 Oct 8 08:11:11 2024

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