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Sodium 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:

Magnesium (Mg) 4 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 3 in 6dw7

Go back to Sodium Binding Sites List in 6dw7
Sodium binding site 1 out of 3 in the SAMHD1 Without Catalytic Nucleotides


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of SAMHD1 Without Catalytic Nucleotides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na705

b:74.3
occ:1.00
O A:HOH810 2.7 46.0 1.0
OD2 A:ASP311 2.9 72.1 1.0
NZ A:LYS312 3.5 64.5 1.0
OD1 A:ASP309 3.9 70.4 1.0
N A:GLY704 3.9 75.0 1.0
CG A:ASP311 3.9 65.2 1.0
CG A:LYS312 3.9 54.3 1.0
NH1 A:ARG206 4.0 73.2 1.0
CB A:ASP311 4.2 53.8 1.0
NH2 A:ARG206 4.3 82.5 1.0
OD2 A:ASP309 4.3 72.9 1.0
CE2 A:TYR315 4.4 36.1 1.0
CE A:LYS312 4.5 60.2 1.0
CG A:ASP309 4.5 64.5 1.0
CZ A:ARG206 4.5 76.2 1.0
N A:LYS312 4.6 48.5 1.0
OH A:TYR315 4.8 43.9 1.0
CD A:LYS312 4.9 59.0 1.0

Sodium binding site 2 out of 3 in 6dw7

Go back to Sodium Binding Sites List in 6dw7
Sodium binding site 2 out of 3 in the SAMHD1 Without Catalytic Nucleotides


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of SAMHD1 Without Catalytic Nucleotides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na706

b:74.9
occ:1.00
O A:THR114 2.5 94.9 1.0
O A:HOH814 2.6 49.3 1.0
N A:LYS116 3.6 55.9 1.0
C A:THR114 3.7 0.8 1.0
CG A:LYS116 3.8 42.9 1.0
CG2 A:VAL133 3.8 45.1 1.0
CA A:PRO130 3.8 48.0 1.0
CG A:PRO130 3.8 42.6 1.0
C A:MET115 3.9 67.6 1.0
CB A:PRO130 3.9 43.3 1.0
CB A:LYS116 4.0 39.3 1.0
CA A:MET115 4.2 77.3 1.0
N A:PRO130 4.3 49.2 1.0
CA A:LYS116 4.3 46.3 1.0
O A:LEU128 4.4 51.4 1.0
CD A:PRO130 4.4 47.1 1.0
N A:MET115 4.4 88.3 1.0
CE A:LYS116 4.4 33.6 1.0
CB A:VAL133 4.4 45.1 1.0
O A:MET115 4.5 71.6 1.0
CD A:LYS116 4.6 36.7 1.0
NZ A:LYS116 4.6 36.1 1.0
CG1 A:VAL133 4.8 44.8 1.0
N A:THR114 4.8 0.1 1.0
CA A:THR114 4.9 0.9 1.0
C A:HIS129 4.9 50.0 1.0

Sodium binding site 3 out of 3 in 6dw7

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of SAMHD1 Without Catalytic Nucleotides within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na706

b:68.5
occ:1.00
O C:GLN510 2.4 97.8 1.0
O C:LYS512 2.8 71.2 1.0
N C:MET509 3.1 64.9 1.0
O C:PHE545 3.3 57.6 1.0
C C:MET509 3.3 74.4 1.0
N C:TYR507 3.3 51.9 1.0
C C:GLN510 3.4 80.7 1.0
N C:GLN510 3.5 80.9 1.0
O C:MET509 3.5 71.5 1.0
C C:TYR507 3.6 56.0 1.0
N C:GLY508 3.6 58.3 1.0
CA C:MET509 3.6 71.5 1.0
CA C:TYR507 3.6 53.6 1.0
CB C:TYR507 3.6 47.4 1.0
C C:LYS512 3.9 69.1 1.0
CB C:ASP506 3.9 65.2 1.0
N C:LYS512 4.0 63.7 1.0
CB C:MET509 4.0 83.0 1.0
CB C:PHE545 4.0 59.2 1.0
CA C:GLN510 4.1 81.9 1.0
O C:TYR507 4.2 62.5 1.0
C C:PHE545 4.2 56.8 1.0
C C:GLY508 4.3 64.5 1.0
C C:GLU511 4.3 75.2 1.0
C C:ASP506 4.3 60.5 1.0
N C:GLU511 4.3 76.5 1.0
CA C:GLY508 4.5 63.2 1.0
CA C:LYS512 4.5 67.1 1.0
CD C:PRO514 4.6 60.2 1.0
CG C:ASP506 4.6 78.4 1.0
CA C:ASP506 4.6 63.9 1.0
CA C:GLU511 4.6 77.9 1.0
OD1 C:ASP506 4.7 77.3 1.0
CA C:PHE545 4.8 58.5 1.0
O C:GLU511 4.8 77.2 1.0
CG C:TYR507 4.9 49.5 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: Tue Oct 8 08:11:11 2024

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