Atomistry » Magnesium » PDB 6dp5-6dw4 » 6dw4
Atomistry »
  Magnesium »
    PDB 6dp5-6dw4 »
      6dw4 »

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

Go back to Magnesium Binding Sites List in 6dw4
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

Go back to Magnesium Binding Sites List in 6dw4
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

Go back to Magnesium Binding Sites List in 6dw4
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

Go back to Magnesium Binding Sites List in 6dw4
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

Go back to Magnesium Binding Sites List in 6dw4
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

Go back to Magnesium Binding Sites List in 6dw4
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

Go back to Magnesium Binding Sites List in 6dw4
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

Go back to Magnesium Binding Sites List in 6dw4
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy