Magnesium in PDB 6dw7: SAMHD1 Without Catalytic Nucleotides

Protein crystallography data

The structure of SAMHD1 Without Catalytic Nucleotides, PDB code: 6dw7 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 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.546, 146.372, 98.929, 90.00, 113.67, 90.00
R / Rfree (%) 21.2 / 25

Other elements in 6dw7:

The structure of SAMHD1 Without Catalytic Nucleotides also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the SAMHD1 Without Catalytic Nucleotides (pdb code 6dw7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the SAMHD1 Without Catalytic Nucleotides, PDB code: 6dw7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6dw7

Go back to Magnesium Binding Sites List in 6dw7
Magnesium binding site 1 out of 4 in the SAMHD1 Without Catalytic Nucleotides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of SAMHD1 Without Catalytic Nucleotides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:47.0
occ:1.00
O1G A:GTP703 1.9 52.8 1.0
O1B B:DTP703 2.0 34.8 1.0
O1A A:GTP703 2.0 38.0 1.0
O3G B:DTP703 2.1 35.7 1.0
O1B A:GTP703 2.6 36.1 1.0
CD A:LYS116 3.2 36.7 1.0
PG A:GTP703 3.3 45.2 1.0
PB B:DTP703 3.3 34.7 1.0
O3' A:GTP703 3.4 29.0 1.0
PG B:DTP703 3.5 36.4 1.0
PA A:GTP703 3.5 39.0 1.0
PB A:GTP703 3.6 40.6 1.0
O3B A:GTP703 3.7 44.2 1.0
O3B B:DTP703 3.7 38.4 1.0
O3A A:GTP703 4.0 42.1 1.0
O2G A:GTP703 4.1 40.8 1.0
CG A:LYS116 4.1 42.9 1.0
NZ B:LYS523 4.2 58.5 1.0
C3' A:GTP703 4.2 36.1 1.0
O1G B:DTP703 4.2 35.5 1.0
O3A B:DTP703 4.3 36.4 1.0
O3G A:GTP703 4.3 44.6 1.0
CE A:LYS116 4.3 33.6 1.0
C5' A:GTP703 4.4 39.6 1.0
O2B B:DTP703 4.4 36.3 1.0
O2A A:GTP703 4.5 34.0 1.0
O5' A:GTP703 4.5 40.9 1.0
CE B:LYS523 4.6 60.0 1.0
O2G B:DTP703 4.6 32.8 1.0
O B:HOH811 4.7 31.1 1.0
C4' A:GTP703 4.8 35.2 1.0

Magnesium binding site 2 out of 4 in 6dw7

Go back to Magnesium Binding Sites List in 6dw7
Magnesium binding site 2 out of 4 in the SAMHD1 Without Catalytic Nucleotides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of SAMHD1 Without Catalytic Nucleotides within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:48.3
occ:1.00
O2G B:GTP702 1.7 57.6 1.0
O2A B:GTP702 2.1 43.6 1.0
O2B B:GTP702 2.1 30.3 1.0
O1G A:DTP701 2.1 34.7 1.0
O1B A:DTP701 2.1 38.6 1.0
PG B:GTP702 3.0 49.0 1.0
PB B:GTP702 3.2 37.4 1.0
PG A:DTP701 3.3 42.8 1.0
PB A:DTP701 3.3 35.2 1.0
O B:HOH813 3.4 52.1 1.0
O3B B:GTP702 3.4 41.6 1.0
PA B:GTP702 3.4 36.7 1.0
O3B A:DTP701 3.6 37.5 1.0
O3A B:GTP702 3.8 39.0 1.0
O3G A:DTP701 3.8 41.3 1.0
O3G B:GTP702 3.9 48.2 1.0
O1G B:GTP702 4.0 46.9 1.0
NZ A:LYS523 4.1 57.7 1.0
CE B:LYS116 4.1 52.0 1.0
O2B A:DTP701 4.1 34.1 1.0
O3' B:GTP702 4.2 39.0 1.0
C5' B:GTP702 4.4 36.3 1.0
O5' B:GTP702 4.4 35.5 1.0
CE A:LYS523 4.5 60.0 1.0
O1A B:GTP702 4.5 41.8 1.0
O3A A:DTP701 4.5 36.7 1.0
NZ B:LYS116 4.5 52.1 1.0
O2G A:DTP701 4.6 44.1 1.0
O1B B:GTP702 4.6 34.4 1.0
CD B:LYS116 4.9 49.7 1.0
C3' B:GTP702 4.9 37.4 1.0

Magnesium binding site 3 out of 4 in 6dw7

Go back to Magnesium Binding Sites List in 6dw7
Magnesium binding site 3 out of 4 in the SAMHD1 Without Catalytic Nucleotides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of SAMHD1 Without Catalytic Nucleotides within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:36.0
occ:1.00
O1G D:GTP701 1.8 65.6 1.0
O3G C:DTP701 2.0 37.9 1.0
O2B C:DTP701 2.0 32.7 1.0
O3A D:GTP701 2.3 44.8 1.0
O1B D:GTP701 2.8 40.4 1.0
PG D:GTP701 3.2 52.0 1.0
PB D:GTP701 3.2 42.0 1.0
PB C:DTP701 3.3 37.4 1.0
PG C:DTP701 3.3 40.2 1.0
O1A D:GTP701 3.4 44.4 1.0
PA D:GTP701 3.5 44.3 1.0
O3' D:GTP701 3.6 39.7 1.0
O3B D:GTP701 3.6 42.4 1.0
NZ D:LYS116 3.6 58.1 1.0
O3B C:DTP701 3.7 37.7 1.0
C5' D:GTP701 4.0 37.9 1.0
O2G D:GTP701 4.0 44.3 1.0
O1G C:DTP701 4.1 36.2 1.0
NZ C:LYS523 4.1 45.3 1.0
O3G D:GTP701 4.2 54.2 1.0
O5' D:GTP701 4.2 45.3 1.0
O3A C:DTP701 4.2 33.6 1.0
C3' D:GTP701 4.3 43.8 1.0
O1B C:DTP701 4.3 37.0 1.0
O2G C:DTP701 4.5 37.5 1.0
O2B D:GTP701 4.6 36.7 1.0
CE C:LYS523 4.6 49.2 1.0
C4' D:GTP701 4.6 41.9 1.0
O2A D:GTP701 4.7 54.0 1.0
CE D:LYS116 4.8 54.7 1.0

Magnesium binding site 4 out of 4 in 6dw7

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Magnesium binding site 4 out of 4 in the SAMHD1 Without Catalytic Nucleotides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of SAMHD1 Without Catalytic Nucleotides within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg703

b:43.4
occ:1.00
O2G C:GTP704 1.7 56.9 1.0
O2A C:GTP704 2.0 42.6 1.0
O2B D:DTP702 2.1 51.5 1.0
O1G D:DTP702 2.1 41.9 1.0
O2B C:GTP704 2.6 47.5 1.0
PG C:GTP704 3.1 51.3 1.0
NZ C:LYS116 3.3 56.7 1.0
PB D:DTP702 3.4 42.5 1.0
PG D:DTP702 3.4 45.0 1.0
PA C:GTP704 3.5 46.2 1.0
PB C:GTP704 3.6 47.8 1.0
O3B C:GTP704 3.6 44.5 1.0
O3B D:DTP702 3.8 46.3 1.0
O1G C:GTP704 3.8 43.9 1.0
NZ D:LYS523 3.8 67.3 1.0
O3' C:GTP704 3.9 34.4 1.0
O3A C:GTP704 4.0 44.3 1.0
O3G D:DTP702 4.0 40.8 1.0
O3G C:GTP704 4.1 56.2 1.0
O3A D:DTP702 4.4 44.2 1.0
O1A C:GTP704 4.4 48.2 1.0
O1B D:DTP702 4.5 40.3 1.0
C5' C:GTP704 4.5 47.0 1.0
C3' C:GTP704 4.5 38.9 1.0
O5' C:GTP704 4.6 48.0 1.0
CE C:LYS116 4.6 54.0 1.0
CE D:LYS523 4.6 68.7 1.0
O2G D:DTP702 4.7 45.1 1.0
CG C:LYS116 4.8 52.1 1.0
CD C:LYS116 4.9 45.5 1.0
O1B C:GTP704 5.0 41.4 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 22:37:27 2020

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