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Magnesium in PDB 6dwk: SAMHD1 Bound to Fludarabine-Tp in the Catalytic Pocket

Protein crystallography data

The structure of SAMHD1 Bound to Fludarabine-Tp in the Catalytic Pocket, PDB code: 6dwk 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 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.691, 146.671, 99.131, 90.00, 114.53, 90.00
R / Rfree (%) 17.6 / 21.2

Other elements in 6dwk:

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

Fluorine (F) 4 atoms
Sodium (Na) 23 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 9 in 6dwk

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Magnesium binding site 1 out of 9 in the SAMHD1 Bound to Fludarabine-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 Fludarabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg704

b:31.5
occ:1.00
 O1G A:DTP703 2.0 35.2 1.0
O2G C:GTP705 2.0 32.9 1.0
O1B A:DTP703 2.1 29.9 1.0
O C:HOH816 2.1 23.6 1.0
O3A C:GTP705 2.1 38.1 1.0
O2B C:GTP705 2.3 37.6 1.0
PB C:GTP705 2.8 36.2 1.0
PG C:GTP705 3.1 33.7 1.0
PB A:DTP703 3.2 28.9 1.0
PG A:DTP703 3.3 34.9 1.0
O3B C:GTP705 3.4 35.5 1.0
O3B A:DTP703 3.5 31.4 1.0
PA C:GTP705 3.5 33.0 1.0
O5' C:GTP705 3.6 34.2 1.0
NZ B:LYS116 3.9 39.5 1.0
NZ A:LYS523 3.9 54.9 1.0
O3' C:GTP705 4.0 27.6 1.0
O1G C:GTP705 4.1 35.5 1.0
O3G C:GTP705 4.1 36.1 1.0
O1B C:GTP705 4.1 35.9 1.0
O2B A:DTP703 4.1 29.5 1.0
O2G A:DTP703 4.1 34.9 1.0
O1A C:GTP705 4.3 39.2 1.0
O3G A:DTP703 4.3 38.4 1.0
O3A A:DTP703 4.4 27.9 1.0
C5' C:GTP705 4.4 30.2 1.0
O2A C:GTP705 4.5 37.5 1.0
O A:HOH833 4.5 52.9 1.0
O B:HOH870 4.6 30.4 1.0
C3' C:GTP705 4.8 27.5 1.0
C4' C:GTP705 5.0 28.3 1.0

Magnesium binding site 2 out of 9 in 6dwk

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Magnesium binding site 2 out of 9 in the SAMHD1 Bound to Fludarabine-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 Fludarabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg705

b:20.1
occ:1.00
 O A:HOH823 2.0 21.5 1.0
O2G B:DTP703 2.0 23.8 1.0
O1B A:GTP706 2.0 25.0 1.0
O1B B:DTP703 2.1 22.4 1.0
O1G A:GTP706 2.2 28.7 1.0
O1A A:GTP706 2.2 21.9 1.0
PB A:GTP706 3.1 28.5 1.0
PB B:DTP703 3.3 22.6 1.0
PG A:GTP706 3.3 30.2 1.0
PG B:DTP703 3.3 23.6 1.0
PA A:GTP706 3.3 22.3 1.0
O3B A:GTP706 3.5 27.9 1.0
O3B B:DTP703 3.5 23.3 1.0
O3A A:GTP706 3.6 24.7 1.0
NZ A:LYS116 3.9 35.5 1.0
O3' A:GTP706 4.0 18.1 1.0
O2B B:DTP703 4.0 22.0 1.0
NZ B:LYS523 4.1 40.3 1.0
O2G A:GTP706 4.1 29.7 1.0
O1G B:DTP703 4.2 22.7 1.0
C5' A:GTP706 4.2 20.9 1.0
O3G A:GTP706 4.2 28.6 1.0
O5' A:GTP706 4.2 23.1 1.0
O3A B:DTP703 4.4 22.1 1.0
O3G B:DTP703 4.4 25.3 1.0
O B:HOH806 4.4 38.3 1.0
O2B A:GTP706 4.5 29.1 1.0
O A:HOH834 4.5 23.1 1.0
C3' A:GTP706 4.6 19.8 1.0
O2A A:GTP706 4.6 23.1 1.0
C4' A:GTP706 4.9 19.8 1.0

Magnesium binding site 3 out of 9 in 6dwk

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Magnesium binding site 3 out of 9 in the SAMHD1 Bound to Fludarabine-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 Fludarabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg714

b:61.0
occ:1.00
 O1B A:HFD701 1.8 88.8 1.0
NZ A:LYS312 3.2 40.7 1.0
PB A:HFD701 3.2 85.0 1.0
OD1 A:ASP309 3.4 35.3 1.0
O1G A:HFD701 3.4 95.5 1.0
OD2 A:ASP309 3.7 42.5 1.0
CG A:LYS312 3.7 33.4 1.0
OD2 A:ASP311 3.8 37.3 1.0
O3B A:HFD701 3.9 98.9 1.0
NH2 A:ARG206 3.9 43.0 1.0
O2B A:HFD701 3.9 68.5 1.0
NH1 A:ARG206 4.0 41.7 1.0
CG A:ASP309 4.0 38.4 1.0
CB A:ASP311 4.2 31.9 1.0
PG A:HFD701 4.3 91.3 1.0
CE A:LYS312 4.3 38.7 1.0
CZ A:ARG206 4.3 42.7 1.0
N A:LYS312 4.4 29.0 1.0
O3A A:HFD701 4.4 96.0 1.0
CG A:ASP311 4.5 33.4 1.0
CD A:LYS312 4.6 35.9 1.0
CE2 A:TYR315 4.8 27.4 1.0
O2G A:HFD701 4.8 91.5 1.0
CB A:LYS312 4.9 30.6 1.0
CA A:LYS312 4.9 29.0 1.0
C A:ASP311 5.0 29.5 1.0

Magnesium binding site 4 out of 9 in 6dwk

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Magnesium binding site 4 out of 9 in the SAMHD1 Bound to Fludarabine-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 Fludarabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg710

b:67.0
occ:1.00
 O3G B:HFD701 3.0 45.5 1.0
O1B B:HFD701 3.3 65.4 1.0
OD1 B:ASP311 3.4 41.2 1.0
NH2 B:ARG206 3.5 37.4 1.0
NZ B:LYS312 3.7 33.2 1.0
PG B:HFD701 3.8 71.1 1.0
OD1 B:ASP309 3.8 36.0 1.0
O3B B:HFD701 3.9 64.9 1.0
PB B:HFD701 3.9 73.8 1.0
NH1 B:ARG206 4.0 35.1 1.0
O3A B:HFD701 4.0 77.9 1.0
CG B:LYS312 4.0 28.6 1.0
CB B:ASP311 4.1 30.8 1.0
CG B:ASP311 4.1 36.1 1.0
CZ B:ARG206 4.1 36.1 1.0
OD2 B:ASP309 4.3 41.0 1.0
N B:LYS312 4.4 23.8 1.0
CE2 B:TYR315 4.5 25.3 1.0
O1G B:HFD701 4.5 66.0 1.0
CG B:ASP309 4.5 34.2 1.0
CE B:LYS312 4.7 31.6 1.0
C B:ASP311 4.9 25.0 1.0
PA B:HFD701 4.9 82.7 1.0
O1A B:HFD701 4.9 67.6 1.0
CA B:LYS312 5.0 24.4 1.0

Magnesium binding site 5 out of 9 in 6dwk

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Magnesium binding site 5 out of 9 in the SAMHD1 Bound to Fludarabine-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 Fludarabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg703

b:30.3
occ:1.00
 O1G D:DTP702 2.0 28.3 1.0
O2B D:DTP702 2.0 28.5 1.0
O2G B:GTP702 2.0 31.6 1.0
O D:HOH844 2.1 25.2 1.0
O3A B:GTP702 2.2 38.6 1.0
O2B B:GTP702 2.5 32.0 1.0
PB B:GTP702 3.1 33.1 1.0
PB D:DTP702 3.2 28.4 1.0
PG B:GTP702 3.3 32.7 1.0
PG D:DTP702 3.3 28.2 1.0
PA B:GTP702 3.4 31.8 1.0
O5' B:GTP702 3.5 33.6 1.0
O3B B:GTP702 3.5 32.6 1.0
O3B D:DTP702 3.6 27.8 1.0
O3' B:GTP702 3.9 20.9 1.0
NZ C:LYS116 3.9 38.4 1.0
O1B D:DTP702 4.0 27.1 1.0
NZ D:LYS523 4.0 52.8 1.0
O2G D:DTP702 4.1 28.6 1.0
O3G B:GTP702 4.2 35.4 1.0
O1A B:GTP702 4.2 34.9 1.0
O1G B:GTP702 4.2 32.6 1.0
O1B B:GTP702 4.3 34.1 1.0
O B:HOH859 4.4 27.7 1.0
C5' B:GTP702 4.4 26.6 1.0
O3A D:DTP702 4.4 26.6 1.0
O3G D:DTP702 4.5 31.1 1.0
C3' B:GTP702 4.6 22.5 1.0
O2A B:GTP702 4.6 37.7 1.0
C4' B:GTP702 4.9 23.6 1.0
O D:HOH832 4.9 37.0 1.0
CE C:LYS116 5.0 36.8 1.0

Magnesium binding site 6 out of 9 in 6dwk

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Magnesium binding site 6 out of 9 in the SAMHD1 Bound to Fludarabine-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 Fludarabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg709

b:69.4
occ:1.00
 O3A C:HFD704 1.6 0.3 1.0
PB C:HFD704 2.4 0.5 1.0
OH C:TYR315 2.7 28.9 1.0
O2B C:HFD704 2.8 0.0 1.0
O1B C:HFD704 2.9 0.1 1.0
NE C:ARG366 3.0 37.0 1.0
PA C:HFD704 3.0 96.8 1.0
CE C:LYS312 3.4 41.0 1.0
NZ C:LYS312 3.4 45.1 1.0
O5' C:HFD704 3.5 86.6 1.0
CZ C:TYR315 3.7 26.8 1.0
NH2 C:ARG366 3.7 39.6 1.0
CE2 C:TYR315 3.7 26.2 1.0
O1A C:HFD704 3.8 96.2 1.0
CD C:ARG366 3.8 35.5 1.0
CZ C:ARG366 3.8 39.8 1.0
O3B C:HFD704 3.9 0.6 1.0
CG C:LYS312 3.9 34.4 1.0
O2A C:HFD704 4.1 99.3 1.0
CD C:LYS312 4.2 37.2 1.0
CG C:ARG366 4.8 32.8 1.0
C5' C:HFD704 4.9 68.7 1.0
CE1 C:TYR315 5.0 26.9 1.0

Magnesium binding site 7 out of 9 in 6dwk

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Magnesium binding site 7 out of 9 in the SAMHD1 Bound to Fludarabine-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 Fludarabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:29.2
occ:1.00
 O2G C:DTP702 2.0 31.0 1.0
O1G A:GTP702 2.0 30.6 1.0
O2B C:DTP702 2.1 29.3 1.0
O A:HOH852 2.2 24.4 1.0
O3A A:GTP702 2.3 36.8 1.0
O1B A:GTP702 2.4 34.8 1.0
PB A:GTP702 3.1 35.2 1.0
PB C:DTP702 3.3 28.7 1.0
PG A:GTP702 3.3 33.1 1.0
PG C:DTP702 3.3 31.4 1.0
PA A:GTP702 3.5 32.8 1.0
O3B A:GTP702 3.5 32.8 1.0
O5' A:GTP702 3.6 34.7 1.0
O3B C:DTP702 3.6 29.2 1.0
NZ D:LYS116 3.8 37.9 1.0
O3' A:GTP702 3.9 24.5 1.0
NZ C:LYS523 4.1 50.8 1.0
O1G C:DTP702 4.1 30.6 1.0
O3G A:GTP702 4.1 32.2 1.0
O1B C:DTP702 4.1 27.9 1.0
O2G A:GTP702 4.3 33.9 1.0
O2A A:GTP702 4.3 41.5 1.0
O A:HOH843 4.4 22.6 1.0
O2B A:GTP702 4.4 36.0 1.0
O1A A:GTP702 4.4 37.6 1.0
O3A C:DTP702 4.4 26.0 1.0
O3G C:DTP702 4.5 33.2 1.0
C5' A:GTP702 4.6 28.1 1.0
C3' A:GTP702 4.7 24.6 1.0
C4' A:GTP702 5.0 25.5 1.0
CE D:LYS116 5.0 36.7 1.0

Magnesium binding site 8 out of 9 in 6dwk

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Magnesium binding site 8 out of 9 in the SAMHD1 Bound to Fludarabine-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 Fludarabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg710

b:78.6
occ:1.00
 O1A D:HFD703 2.6 82.3 1.0
O2G D:HFD703 2.7 74.1 1.0
CE1 D:HIS215 3.8 54.3 1.0
PA D:HFD703 3.8 80.9 1.0
O3A D:HFD703 3.9 81.1 1.0
ND1 D:HIS215 4.1 48.4 1.0
PG D:HFD703 4.2 80.1 1.0
O3G D:HFD703 4.8 71.5 1.0
NE2 D:HIS215 4.8 46.6 1.0
O5' D:HFD703 4.8 69.3 1.0
O1G D:HFD703 4.8 84.7 1.0
NE2 D:HIS233 4.8 42.2 1.0
O2A D:HFD703 4.9 75.4 1.0

Magnesium binding site 9 out of 9 in 6dwk

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Magnesium binding site 9 out of 9 in the SAMHD1 Bound to Fludarabine-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 9 of SAMHD1 Bound to Fludarabine-Tp in the Catalytic Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg711

b:51.4
occ:1.00
 O1G D:HFD703 1.9 84.7 1.0
O D:HOH819 2.4 36.2 1.0
O D:HOH865 2.9 43.0 1.0
NE2 D:HIS210 3.3 23.0 1.0
PG D:HFD703 3.3 80.1 1.0
NH1 D:ARG164 3.5 21.3 1.0
NE2 D:HIS215 3.6 46.6 1.0
CE1 D:HIS233 3.8 43.0 1.0
OD1 D:ASN207 3.8 24.1 1.0
O3G D:HFD703 3.8 71.5 1.0
NE2 D:HIS233 3.9 42.2 1.0
CE1 D:HIS210 3.9 25.3 1.0
CE1 D:HIS215 4.0 54.3 1.0
O2G D:HFD703 4.0 74.1 1.0
NH2 D:ARG206 4.1 38.1 1.0
O5' D:HFD703 4.2 69.3 1.0
OD2 D:ASP311 4.2 33.9 1.0
O3B D:HFD703 4.2 80.5 1.0
CZ D:ARG164 4.3 21.7 1.0
O4' D:HFD703 4.3 47.3 1.0
NH2 D:ARG164 4.4 21.5 1.0
C4' D:HFD703 4.4 47.8 1.0
CD2 D:HIS210 4.5 23.6 1.0
ND1 D:HIS233 4.5 41.3 1.0
CD2 D:HIS233 4.7 41.8 1.0
CD2 D:HIS215 4.8 42.9 1.0
C5' D:HFD703 4.8 56.0 1.0
OD1 D:ASP311 4.9 34.4 1.0
CG D:ASN207 4.9 24.4 1.0
CG D:ASP311 4.9 30.1 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 23:42:57 2024

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