Magnesium in PDB 6dw3: SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket

Protein crystallography data

The structure of SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket, PDB code: 6dw3 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 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.340, 147.325, 98.537, 90.00, 114.64, 90.00
R / Rfree (%) 19 / 22.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket (pdb code 6dw3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket, PDB code: 6dw3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6dw3

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Magnesium binding site 1 out of 8 in the SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg703

b:25.2
occ:1.00
O2B C:DTP704 1.9 24.4 1.0
O3G C:DTP704 1.9 27.0 1.0
O C:HOH809 2.0 19.7 1.0
O1G D:GTP704 2.1 27.8 1.0
O1B D:GTP704 2.1 27.1 1.0
O1A D:GTP704 2.1 24.2 1.0
PB D:GTP704 3.1 27.3 1.0
PB C:DTP704 3.1 24.5 1.0
PG C:DTP704 3.3 28.2 1.0
PG D:GTP704 3.3 29.5 1.0
PA D:GTP704 3.4 24.6 1.0
O3B D:GTP704 3.4 27.4 1.0
O3B C:DTP704 3.5 26.4 1.0
O3A D:GTP704 3.5 25.8 1.0
O3' D:GTP704 3.9 21.8 1.0
NZ D:LYS116 3.9 35.9 1.0
O1B C:DTP704 4.0 24.0 1.0
NZ C:LYS523 4.0 41.3 1.0
O1G C:DTP704 4.1 27.1 1.0
C5' D:GTP704 4.1 22.6 1.0
O5' D:GTP704 4.2 22.8 1.0
O2G D:GTP704 4.3 31.2 1.0
O3A C:DTP704 4.3 24.0 1.0
O3G D:GTP704 4.4 28.6 1.0
O2G C:DTP704 4.4 28.2 1.0
O2B D:GTP704 4.5 27.6 1.0
O2A D:GTP704 4.6 24.8 1.0
C3' D:GTP704 4.6 22.3 1.0
CE D:LYS116 4.7 33.8 1.0
C4' D:GTP704 4.9 21.9 1.0
CD D:LYS116 5.0 32.8 1.0

Magnesium binding site 2 out of 8 in 6dw3

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Magnesium binding site 2 out of 8 in the SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg705

b:66.9
occ:1.00
O D:HOH819 1.8 31.5 1.0
O D:HOH822 2.0 36.2 1.0
O2G D:HF4701 2.2 30.9 1.0
O2B D:HF4701 2.5 35.5 1.0
O D:HOH807 2.8 30.9 1.0
NZ D:LYS312 3.6 24.6 1.0
OD2 D:ASP309 3.7 23.0 1.0
PG D:HF4701 3.7 29.2 1.0
PB D:HF4701 3.9 34.8 1.0
O1G D:HF4701 4.2 30.8 1.0
O3B D:HF4701 4.3 31.5 1.0
OD1 D:ASP309 4.4 22.2 1.0
CG D:ASP309 4.4 23.0 1.0
NH1 D:ARG206 4.4 31.2 1.0
O1B D:HF4701 4.5 34.8 1.0
O3G D:HF4701 4.6 30.0 1.0
NH2 D:ARG206 4.7 31.9 1.0
O D:HOH887 4.8 42.3 1.0
CE D:LYS312 4.9 23.9 1.0
O3A D:HF4701 5.0 40.9 1.0

Magnesium binding site 3 out of 8 in 6dw3

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Magnesium binding site 3 out of 8 in the SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:35.8
occ:1.00
O C:HOH802 1.9 25.0 1.0
O2A C:GTP703 1.9 30.6 1.0
O3G C:GTP703 1.9 31.8 1.0
O2B C:GTP703 2.2 31.6 1.0
O2B D:DTP702 2.2 26.2 1.0
O1G D:DTP702 2.3 28.8 1.0
PB C:GTP703 3.0 31.4 1.0
PG C:GTP703 3.0 33.5 1.0
PA C:GTP703 3.1 30.5 1.0
O3B C:GTP703 3.3 31.7 1.0
O3A C:GTP703 3.3 31.0 1.0
NZ C:LYS116 3.3 44.5 1.0
PB D:DTP702 3.4 26.4 1.0
PG D:DTP702 3.6 28.5 1.0
O1G C:GTP703 3.8 33.5 1.0
O3B D:DTP702 3.9 27.1 1.0
O3' C:GTP703 3.9 25.2 1.0
C5' C:GTP703 3.9 28.1 1.0
O5' C:GTP703 3.9 28.8 1.0
O1B D:DTP702 4.1 25.3 1.0
O2G C:GTP703 4.2 34.9 1.0
O1A C:GTP703 4.2 30.4 1.0
O1B C:GTP703 4.3 32.2 1.0
O3G D:DTP702 4.4 28.1 1.0
C3' C:GTP703 4.4 26.9 1.0
NZ D:LYS523 4.4 45.4 1.0
CE C:LYS116 4.5 42.5 1.0
O3A D:DTP702 4.6 25.6 1.0
O2G D:DTP702 4.7 29.1 1.0
C4' C:GTP703 4.7 26.9 1.0

Magnesium binding site 4 out of 8 in 6dw3

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Magnesium binding site 4 out of 8 in the SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg705

b:79.9
occ:1.00
O C:HOH818 2.1 35.0 1.0
O1B C:HF4701 2.2 45.6 1.0
O C:HOH827 3.0 29.8 1.0
O2G C:HF4701 3.2 37.3 1.0
PB C:HF4701 3.7 46.5 1.0
NH2 C:ARG206 3.7 31.6 1.0
NH1 C:ARG206 3.8 34.4 1.0
OG C:SER302 4.0 45.4 1.0
OD2 C:ASP309 4.0 37.2 1.0
O2B C:HF4701 4.2 44.3 1.0
CZ C:ARG206 4.2 32.9 1.0
PG C:HF4701 4.4 36.6 1.0
O3B C:HF4701 4.6 42.9 1.0
O3A C:HF4701 4.7 54.4 1.0
NZ C:LYS312 4.7 32.0 1.0
CG C:ASP309 4.9 34.7 1.0
O3G C:HF4701 4.9 37.3 1.0
OD1 C:ASP309 4.9 32.5 1.0

Magnesium binding site 5 out of 8 in 6dw3

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Magnesium binding site 5 out of 8 in the SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg704

b:58.6
occ:1.00
O B:HOH814 1.8 37.9 1.0
O2G B:HF4703 1.8 29.5 1.0
O1B B:HF4703 2.1 38.5 1.0
O B:HOH809 2.2 35.9 1.0
O B:HOH829 2.4 30.0 1.0
O B:HOH838 2.4 29.1 1.0
PG B:HF4703 3.1 31.9 1.0
PB B:HF4703 3.3 39.5 1.0
NZ B:LYS312 3.5 28.3 1.0
O3B B:HF4703 3.7 36.3 1.0
OD2 B:ASP311 3.9 32.6 1.0
OD2 B:ASP309 4.0 29.9 1.0
O1G B:HF4703 4.0 30.7 1.0
NH2 B:ARG206 4.1 32.5 1.0
O3A B:HF4703 4.1 41.2 1.0
O3G B:HF4703 4.1 32.5 1.0
OD1 B:ASP309 4.1 31.1 1.0
NH1 B:ARG206 4.2 33.0 1.0
O2B B:HF4703 4.4 40.1 1.0
CG B:ASP309 4.5 30.5 1.0
CG B:LYS312 4.5 25.0 1.0
CZ B:ARG206 4.6 33.0 1.0
CE B:LYS312 4.7 27.5 1.0
CG B:ASP311 4.8 31.5 1.0

Magnesium binding site 6 out of 8 in 6dw3

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Magnesium binding site 6 out of 8 in the SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:26.5
occ:1.00
O A:HOH833 2.0 23.8 1.0
O1G A:GTP702 2.0 28.6 1.0
O1B A:GTP702 2.0 26.6 1.0
O3G B:DTP701 2.1 25.2 1.0
O1A A:GTP702 2.1 23.8 1.0
O1B B:DTP701 2.3 23.4 1.0
PB A:GTP702 3.1 27.1 1.0
PG A:GTP702 3.1 29.7 1.0
PA A:GTP702 3.3 24.1 1.0
O3B A:GTP702 3.3 27.6 1.0
PG B:DTP701 3.4 24.3 1.0
PB B:DTP701 3.5 21.4 1.0
NZ A:LYS116 3.5 35.0 1.0
O3A A:GTP702 3.6 24.8 1.0
O3B B:DTP701 3.7 22.4 1.0
O3G A:GTP702 3.9 33.2 1.0
NZ B:LYS523 3.9 38.5 1.0
O3' A:GTP702 4.0 20.2 1.0
O2G A:GTP702 4.1 31.8 1.0
O5' A:GTP702 4.2 22.9 1.0
O1G B:DTP701 4.2 24.3 1.0
C5' A:GTP702 4.3 21.5 1.0
O2B B:DTP701 4.3 21.9 1.0
O A:HOH846 4.5 19.0 1.0
O2G B:DTP701 4.5 25.1 1.0
O3A B:DTP701 4.5 21.7 1.0
O2B A:GTP702 4.5 26.5 1.0
O2A A:GTP702 4.6 25.0 1.0
CE B:LYS523 4.7 38.0 1.0
C3' A:GTP702 4.7 20.7 1.0
O B:HOH824 4.8 35.5 1.0
CE A:LYS116 4.9 34.5 1.0

Magnesium binding site 7 out of 8 in 6dw3

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Magnesium binding site 7 out of 8 in the SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg704

b:26.1
occ:1.00
O2B B:GTP702 1.9 28.2 1.0
O1G A:DTP703 1.9 24.2 1.0
O3G B:GTP702 2.0 27.8 1.0
O A:HOH820 2.0 20.1 1.0
O1B A:DTP703 2.2 23.7 1.0
O2A B:GTP702 2.3 25.9 1.0
PB B:GTP702 3.0 29.4 1.0
PG B:GTP702 3.1 28.8 1.0
O3B B:GTP702 3.3 28.2 1.0
PG A:DTP703 3.3 24.7 1.0
PB A:DTP703 3.4 23.2 1.0
PA B:GTP702 3.5 26.1 1.0
NZ A:LYS523 3.6 45.9 1.0
O3A B:GTP702 3.7 26.7 1.0
O3B A:DTP703 3.7 24.2 1.0
O2G B:GTP702 3.9 30.2 1.0
O3' B:GTP702 4.1 24.1 1.0
NZ B:LYS116 4.1 35.4 1.0
O2G A:DTP703 4.2 24.3 1.0
O2B A:DTP703 4.2 22.4 1.0
C5' B:GTP702 4.2 24.1 1.0
O1G B:GTP702 4.2 29.1 1.0
O5' B:GTP702 4.3 24.8 1.0
O1B B:GTP702 4.4 29.8 1.0
O3G A:DTP703 4.4 25.9 1.0
O3A A:DTP703 4.5 23.4 1.0
O1A B:GTP702 4.6 28.1 1.0
C3' B:GTP702 4.7 24.1 1.0
O B:HOH836 4.7 24.0 1.0
CE A:LYS523 4.8 45.5 1.0
CE B:LYS116 4.9 34.5 1.0
C4' B:GTP702 4.9 23.9 1.0

Magnesium binding site 8 out of 8 in 6dw3

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Magnesium binding site 8 out of 8 in the SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of SAMHD1 Bound to Cytarabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg706

b:64.8
occ:1.00
O A:HOH826 1.6 43.5 1.0
O A:HOH844 1.9 32.8 1.0
O2G A:HF4705 2.3 42.7 1.0
O2B A:HF4705 2.4 46.7 1.0
O A:HOH842 2.4 33.5 1.0
PG A:HF4705 3.7 44.4 1.0
OD2 A:ASP309 3.7 33.4 1.0
NZ A:LYS312 3.8 31.3 1.0
PB A:HF4705 3.8 46.0 1.0
O3B A:HF4705 4.2 46.0 1.0
NH1 A:ARG206 4.3 32.5 1.0
NH2 A:ARG206 4.3 32.2 1.0
O1G A:HF4705 4.4 40.4 1.0
OD1 A:ASP309 4.4 30.7 1.0
CG A:ASP309 4.5 31.6 1.0
O1B A:HF4705 4.6 47.0 1.0
O3G A:HF4705 4.6 41.4 1.0
O3A A:HF4705 4.7 53.2 1.0
CZ A:ARG206 4.8 32.2 1.0
OD2 A:ASP311 4.9 34.8 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: Mon Dec 14 22:37:23 2020

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