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Magnesium 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:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 8 binding sites of Magnesium where determined in the SAMHD1 Bound to Cladribine-Tp in the Catalytic Pocket and Allosteric Pocket, PDB code: 6dw4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6dw4

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Magnesium binding site 1 out of 8 in the SAMHD1 Bound to Cladribine-Tp in the Catalytic Pocket and Allosteric 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 Cladribine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg704

b:24.4
occ:1.00
 O1B D:HF7701 2.0 28.1 1.0
O2G D:HF7701 2.0 28.6 1.0
O D:HOH943 2.0 23.0 1.0
O D:HOH915 2.0 23.6 1.0
O D:HOH914 2.1 26.4 1.0
O D:HOH845 2.2 19.9 1.0
PB D:HF7701 3.2 30.7 1.0
PG D:HF7701 3.2 26.3 1.0
O D:HOH804 3.4 36.9 1.0
O3B D:HF7701 3.6 28.9 1.0
NZ D:LYS312 3.7 19.3 1.0
O3G D:HF7701 3.8 26.0 1.0
NH2 D:ARG206 4.0 22.3 1.0
OD2 D:ASP309 4.0 17.7 1.0
O D:HOH857 4.0 28.7 1.0
NH1 D:ARG206 4.1 21.7 1.0
O2B D:HF7701 4.1 27.4 1.0
O3A D:HF7701 4.2 31.7 1.0
O D:HOH885 4.3 38.1 1.0
O1G D:HF7701 4.3 26.3 1.0
O D:HOH846 4.3 27.7 1.0
OD1 D:ASP309 4.5 17.3 1.0
CZ D:ARG206 4.6 22.9 1.0
CG D:ASP309 4.7 16.8 1.0
OG D:SER302 4.8 25.2 1.0
O D:HOH920 4.8 27.8 1.0
OD2 D:ASP311 4.9 23.7 1.0
CE D:LYS312 4.9 17.5 1.0

Magnesium binding site 2 out of 8 in 6dw4

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Magnesium binding site 2 out of 8 in the SAMHD1 Bound to Cladribine-Tp in the Catalytic Pocket and Allosteric 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 Cladribine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:20.3
occ:1.00
 O3G C:GTP703 1.9 21.8 1.0
O1G D:HF7702 2.1 17.9 1.0
O2A C:GTP703 2.1 17.7 1.0
O C:HOH924 2.1 15.7 1.0
O2B D:HF7702 2.1 16.4 1.0
O2B C:GTP703 2.2 20.0 1.0
PG C:GTP703 3.1 22.8 1.0
PB C:GTP703 3.2 20.4 1.0
PG D:HF7702 3.3 18.0 1.0
PB D:HF7702 3.3 16.6 1.0
PA C:GTP703 3.4 17.7 1.0
O3B C:GTP703 3.4 21.4 1.0
O3B D:HF7702 3.6 17.0 1.0
NZ C:LYS116 3.7 28.4 1.0
O3A C:GTP703 3.7 19.0 1.0
NZ D:LYS523 3.8 33.1 1.0
O C:HOH933 3.9 30.6 1.0
O3' C:GTP703 3.9 16.0 1.0
O2G D:HF7702 4.0 17.7 1.0
O1G C:GTP703 4.1 23.8 1.0
O2G C:GTP703 4.1 24.1 1.0
O1B D:HF7702 4.1 15.4 1.0
O D:HOH816 4.2 35.4 1.0
C5' C:GTP703 4.2 15.8 1.0
O5' C:GTP703 4.3 16.4 1.0
O C:HOH967 4.4 18.5 1.0
O3G D:HF7702 4.4 18.5 1.0
O3A D:HF7702 4.5 16.2 1.0
O1B C:GTP703 4.5 21.6 1.0
O1A C:GTP703 4.6 17.4 1.0
C3' C:GTP703 4.7 15.6 1.0
C4' C:GTP703 4.9 15.2 1.0
CE C:LYS116 4.9 27.2 1.0

Magnesium binding site 3 out of 8 in 6dw4

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Magnesium binding site 3 out of 8 in the SAMHD1 Bound to Cladribine-Tp in the Catalytic Pocket and Allosteric 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 Cladribine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg705

b:15.2
occ:1.00
 O1G D:GTP703 2.0 17.1 1.0
O3G C:HF7704 2.1 16.0 1.0
O1A D:GTP703 2.1 14.4 1.0
O D:HOH941 2.1 8.8 1.0
O2B C:HF7704 2.1 13.8 1.0
O1B D:GTP703 2.2 15.4 1.0
PG C:HF7704 3.2 16.4 1.0
PB C:HF7704 3.2 13.8 1.0
PB D:GTP703 3.3 15.6 1.0
PG D:GTP703 3.3 17.7 1.0
O3B C:HF7704 3.4 14.7 1.0
PA D:GTP703 3.5 13.9 1.0
O3B D:GTP703 3.5 16.4 1.0
NZ C:LYS523 3.6 26.1 1.0
O3A D:GTP703 3.8 14.5 1.0
O C:HOH998 3.8 29.7 1.0
NZ D:LYS116 3.8 20.1 1.0
O3' D:GTP703 3.9 13.4 1.0
O1B C:HF7704 4.1 12.9 1.0
O1G C:HF7704 4.1 16.3 1.0
O D:HOH945 4.1 26.7 1.0
O3G D:GTP703 4.2 17.7 1.0
O2G D:GTP703 4.2 18.6 1.0
C5' D:GTP703 4.3 12.9 1.0
O D:HOH921 4.3 11.9 1.0
O2G C:HF7704 4.4 16.7 1.0
O5' D:GTP703 4.4 13.0 1.0
O3A C:HF7704 4.4 13.5 1.0
C3' D:GTP703 4.6 12.9 1.0
O2A D:GTP703 4.6 14.2 1.0
O2B D:GTP703 4.6 16.2 1.0
O C:HOH966 4.8 18.0 1.0
CE C:LYS523 4.9 26.5 1.0
O D:HOH858 4.9 33.9 1.0
C4' D:GTP703 4.9 12.4 1.0
CE D:LYS116 5.0 19.9 1.0

Magnesium binding site 4 out of 8 in 6dw4

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Magnesium binding site 4 out of 8 in the SAMHD1 Bound to Cladribine-Tp in the Catalytic Pocket and Allosteric 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 Cladribine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg706

b:36.0
occ:1.00
 O2B C:HF7701 1.9 31.5 1.0
O C:HOH829 2.1 22.9 1.0
O C:HOH843 2.1 26.3 1.0
O C:HOH928 2.2 26.5 1.0
O3G C:HF7701 2.2 27.7 1.0
O C:HOH926 2.2 31.3 1.0
PB C:HF7701 3.3 30.0 1.0
PG C:HF7701 3.3 28.4 1.0
O3B C:HF7701 3.6 31.0 1.0
O1G C:HF7701 3.8 28.2 1.0
NZ C:LYS312 3.9 20.8 1.0
OD2 C:ASP309 4.0 20.0 1.0
NH2 C:ARG206 4.0 23.7 1.0
NH1 C:ARG206 4.1 24.5 1.0
O1B C:HF7701 4.2 32.1 1.0
O3A C:HF7701 4.2 32.0 1.0
O C:HOH875 4.2 29.1 1.0
O C:HOH830 4.3 26.3 1.0
O2G C:HF7701 4.4 29.5 1.0
OD1 C:ASP309 4.4 20.2 1.0
CZ C:ARG206 4.6 23.9 1.0
CG C:ASP309 4.6 19.6 1.0
OD2 C:ASP311 4.8 24.9 1.0
OG C:SER302 4.8 25.9 1.0
O C:HOH906 5.0 29.6 1.0

Magnesium binding site 5 out of 8 in 6dw4

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Magnesium binding site 5 out of 8 in the SAMHD1 Bound to Cladribine-Tp in the Catalytic Pocket and Allosteric 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 Cladribine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg704

b:35.7
occ:1.00
 O B:HOH944 2.0 29.6 1.0
O2B B:HF7703 2.1 32.1 1.0
O3G B:HF7703 2.1 30.2 1.0
O B:HOH818 2.1 21.5 1.0
O B:HOH930 2.2 25.6 1.0
O B:HOH851 2.2 33.5 1.0
PB B:HF7703 3.3 32.6 1.0
PG B:HF7703 3.4 30.4 1.0
NZ B:LYS312 3.7 24.9 1.0
O3B B:HF7703 3.7 34.1 1.0
O1G B:HF7703 3.9 29.4 1.0
OD2 B:ASP309 3.9 24.0 1.0
NH2 B:ARG206 4.2 28.1 1.0
O3A B:HF7703 4.3 37.4 1.0
NH1 B:ARG206 4.3 27.0 1.0
O B:HOH834 4.3 35.2 1.0
O1B B:HF7703 4.4 35.4 1.0
O2G B:HF7703 4.4 30.4 1.0
OD1 B:ASP309 4.5 22.5 1.0
CG B:ASP309 4.7 21.5 1.0
CZ B:ARG206 4.8 26.9 1.0
OG B:SER302 4.9 31.7 1.0
OD2 B:ASP311 4.9 27.9 1.0
CE B:LYS312 5.0 23.5 1.0

Magnesium binding site 6 out of 8 in 6dw4

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Magnesium binding site 6 out of 8 in the SAMHD1 Bound to Cladribine-Tp in the Catalytic Pocket and Allosteric 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 Cladribine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:16.4
occ:1.00
 O1G A:GTP702 1.9 22.1 1.0
O3G B:HF7701 2.1 16.6 1.0
O1A A:GTP702 2.1 17.9 1.0
O1B B:HF7701 2.1 16.5 1.0
O A:HOH926 2.2 14.5 1.0
O1B A:GTP702 2.2 19.4 1.0
PG A:GTP702 3.2 24.4 1.0
PB A:GTP702 3.2 21.2 1.0
PG B:HF7701 3.3 17.6 1.0
PB B:HF7701 3.3 16.8 1.0
PA A:GTP702 3.4 19.2 1.0
O3B A:GTP702 3.4 21.8 1.0
O3B B:HF7701 3.6 17.4 1.0
O3A A:GTP702 3.6 19.0 1.0
NZ A:LYS116 3.8 30.3 1.0
O3' A:GTP702 4.0 15.9 1.0
NZ B:LYS523 4.0 35.6 1.0
O3G A:GTP702 4.1 24.6 1.0
O2G A:GTP702 4.1 23.6 1.0
O2B B:HF7701 4.1 16.7 1.0
O1G B:HF7701 4.1 16.5 1.0
C5' A:GTP702 4.2 15.6 1.0
O5' A:GTP702 4.2 16.3 1.0
O3A B:HF7701 4.4 16.9 1.0
O A:HOH872 4.4 30.2 1.0
O2G B:HF7701 4.4 17.8 1.0
O A:HOH964 4.5 20.5 1.0
O2B A:GTP702 4.5 21.5 1.0
O2A A:GTP702 4.6 17.8 1.0
C3' A:GTP702 4.6 15.3 1.0
CE B:LYS523 4.6 35.2 1.0
C4' A:GTP702 4.9 14.8 1.0
CE A:LYS116 4.9 29.0 1.0
O B:HOH858 4.9 25.3 1.0

Magnesium binding site 7 out of 8 in 6dw4

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Magnesium binding site 7 out of 8 in the SAMHD1 Bound to Cladribine-Tp in the Catalytic Pocket and Allosteric 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 Cladribine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg704

b:18.3
occ:1.00
 O3G B:GTP702 2.0 23.4 1.0
O B:HOH869 2.0 15.8 1.0
O2B B:GTP702 2.1 22.4 1.0
O1B A:HF7703 2.1 17.7 1.0
O1G A:HF7703 2.1 18.6 1.0
O2A B:GTP702 2.1 19.6 1.0
PB B:GTP702 3.2 24.0 1.0
PG A:HF7703 3.2 19.0 1.0
PG B:GTP702 3.3 24.5 1.0
PB A:HF7703 3.3 17.6 1.0
PA B:GTP702 3.4 20.3 1.0
O3B B:GTP702 3.5 23.5 1.0
O3B A:HF7703 3.6 18.0 1.0
NZ B:LYS116 3.7 31.3 1.0
O3A B:GTP702 3.7 21.5 1.0
O3' B:GTP702 3.8 17.1 1.0
NZ A:LYS523 3.9 37.0 1.0
O2G A:HF7703 4.1 17.6 1.0
O2B A:HF7703 4.1 17.1 1.0
O2G B:GTP702 4.2 25.0 1.0
O1G B:GTP702 4.2 24.2 1.0
C5' B:GTP702 4.3 17.9 1.0
O3G A:HF7703 4.3 19.7 1.0
O3A A:HF7703 4.3 17.1 1.0
O5' B:GTP702 4.4 18.6 1.0
O B:HOH866 4.4 18.3 1.0
O B:HOH902 4.5 30.2 1.0
C3' B:GTP702 4.5 17.7 1.0
O1B B:GTP702 4.5 23.8 1.0
O1A B:GTP702 4.6 21.1 1.0
C4' B:GTP702 4.8 17.3 1.0
CE B:LYS116 4.9 30.9 1.0
O A:HOH821 4.9 33.4 1.0
CE A:LYS523 5.0 36.7 1.0

Magnesium binding site 8 out of 8 in 6dw4

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Magnesium binding site 8 out of 8 in the SAMHD1 Bound to Cladribine-Tp in the Catalytic Pocket and Allosteric 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 Cladribine-Tp in the Catalytic Pocket and Allosteric Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg706

b:30.1
occ:1.00
 O1B A:HF7705 2.0 23.0 1.0
O2G A:HF7705 2.1 27.5 1.0
O A:HOH935 2.1 22.4 1.0
O A:HOH882 2.1 23.9 1.0
O A:HOH896 2.1 29.2 1.0
O A:HOH865 2.2 24.3 1.0
PB A:HF7705 3.3 26.5 1.0
PG A:HF7705 3.3 26.7 1.0
O3B A:HF7705 3.7 26.7 1.0
NZ A:LYS312 3.8 20.8 1.0
O3G A:HF7705 3.9 26.0 1.0
OD2 A:ASP309 4.0 20.9 1.0
NH2 A:ARG206 4.1 23.0 1.0
O A:HOH895 4.1 28.4 1.0
O A:HOH883 4.2 22.8 1.0
O2B A:HF7705 4.2 25.9 1.0
NH1 A:ARG206 4.2 21.8 1.0
O3A A:HF7705 4.2 27.7 1.0
O A:HOH938 4.3 33.0 1.0
O1G A:HF7705 4.5 26.2 1.0
OD1 A:ASP309 4.5 20.2 1.0
CZ A:ARG206 4.6 22.6 1.0
CG A:ASP309 4.7 20.1 1.0
OG A:SER302 4.7 32.8 1.0
OD2 A:ASP311 4.9 27.8 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 Sep 30 23:32:19 2024

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