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Sodium in PDB 6q9s: Hdmx (14-111; C17S) Complexed with Compound 14 at 2.4A: Structural States of HDM2 and Hdmx: X-Ray Elucidation of Adaptations and Binding Interactions For Different Chemical Compound Classes

Protein crystallography data

The structure of Hdmx (14-111; C17S) Complexed with Compound 14 at 2.4A: Structural States of HDM2 and Hdmx: X-Ray Elucidation of Adaptations and Binding Interactions For Different Chemical Compound Classes, PDB code: 6q9s was solved by J.Kallen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.95 / 2.40
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.581, 93.581, 198.467, 90.00, 90.00, 120.00
R / Rfree (%) 24.9 / 26.8

Other elements in 6q9s:

The structure of Hdmx (14-111; C17S) Complexed with Compound 14 at 2.4A: Structural States of HDM2 and Hdmx: X-Ray Elucidation of Adaptations and Binding Interactions For Different Chemical Compound Classes also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Hdmx (14-111; C17S) Complexed with Compound 14 at 2.4A: Structural States of HDM2 and Hdmx: X-Ray Elucidation of Adaptations and Binding Interactions For Different Chemical Compound Classes (pdb code 6q9s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Hdmx (14-111; C17S) Complexed with Compound 14 at 2.4A: Structural States of HDM2 and Hdmx: X-Ray Elucidation of Adaptations and Binding Interactions For Different Chemical Compound Classes, PDB code: 6q9s:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6q9s

Go back to Sodium Binding Sites List in 6q9s
Sodium binding site 1 out of 3 in the Hdmx (14-111; C17S) Complexed with Compound 14 at 2.4A: Structural States of HDM2 and Hdmx: X-Ray Elucidation of Adaptations and Binding Interactions For Different Chemical Compound Classes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hdmx (14-111; C17S) Complexed with Compound 14 at 2.4A: Structural States of HDM2 and Hdmx: X-Ray Elucidation of Adaptations and Binding Interactions For Different Chemical Compound Classes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:73.7
occ:1.00
OAP A:O4B202 2.9 57.4 1.0
OAN A:O4B202 3.0 55.1 1.0
OAM A:O4B202 3.1 55.6 1.0
OAQ A:O4B202 3.2 55.5 1.0
OAR A:O4B202 3.4 56.2 1.0
C90 A:HRN201 3.7 46.5 1.0
CAJ A:O4B202 3.8 57.0 1.0
OAO A:O4B202 3.8 54.9 1.0
CAD A:O4B202 3.9 54.4 1.0
CAG A:O4B202 3.9 53.6 1.0
CAF A:O4B202 3.9 55.9 1.0
CAI A:O4B202 3.9 57.0 1.0
CAL A:O4B202 4.0 54.9 1.0
CAB A:O4B202 4.0 54.8 1.0
CAE A:O4B202 4.0 54.9 1.0
CAC A:O4B202 4.1 54.8 1.0
CAA A:O4B202 4.1 55.4 1.0
CAH A:O4B202 4.1 53.9 1.0
CAK A:O4B202 4.1 55.0 1.0

Sodium binding site 2 out of 3 in 6q9s

Go back to Sodium Binding Sites List in 6q9s
Sodium binding site 2 out of 3 in the Hdmx (14-111; C17S) Complexed with Compound 14 at 2.4A: Structural States of HDM2 and Hdmx: X-Ray Elucidation of Adaptations and Binding Interactions For Different Chemical Compound Classes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hdmx (14-111; C17S) Complexed with Compound 14 at 2.4A: Structural States of HDM2 and Hdmx: X-Ray Elucidation of Adaptations and Binding Interactions For Different Chemical Compound Classes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na207

b:68.3
occ:1.00
O A:LYS64 2.7 48.4 1.0
OAM A:O4B208 2.9 50.5 1.0
OAP A:O4B208 3.0 46.6 1.0
OAR A:O4B208 3.1 51.4 1.0
OAQ A:O4B208 3.1 48.6 1.0
OAN A:O4B208 3.1 43.8 1.0
O A:GLN65 3.2 47.5 1.0
OAO A:O4B208 3.6 47.8 1.0
CAG A:O4B208 3.7 46.5 1.0
CAB A:O4B208 3.8 46.1 1.0
CAE A:O4B208 3.8 43.8 1.0
CAD A:O4B208 3.8 47.6 1.0
CAH A:O4B208 3.9 46.3 1.0
CAA A:O4B208 3.9 47.2 1.0
C A:LYS64 3.9 48.5 1.0
CD2 A:LEU66 3.9 43.0 1.0
CAJ A:O4B208 3.9 48.4 1.0
C A:GLN65 3.9 47.6 1.0
CAC A:O4B208 3.9 48.7 1.0
CAF A:O4B208 3.9 45.1 1.0
C90 B:HRN201 4.0 50.0 1.0
CAI A:O4B208 4.0 47.9 1.0
CAL A:O4B208 4.0 50.1 1.0
CAK A:O4B208 4.1 48.5 1.0
CB A:GLN65 4.4 47.8 1.0
CA A:GLN65 4.5 47.7 1.0
N A:GLN65 4.7 47.8 1.0
N A:LEU66 4.8 47.3 1.0
CA A:LYS64 5.0 48.8 1.0
CA A:LEU66 5.0 46.9 1.0

Sodium binding site 3 out of 3 in 6q9s

Go back to Sodium Binding Sites List in 6q9s
Sodium binding site 3 out of 3 in the Hdmx (14-111; C17S) Complexed with Compound 14 at 2.4A: Structural States of HDM2 and Hdmx: X-Ray Elucidation of Adaptations and Binding Interactions For Different Chemical Compound Classes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Hdmx (14-111; C17S) Complexed with Compound 14 at 2.4A: Structural States of HDM2 and Hdmx: X-Ray Elucidation of Adaptations and Binding Interactions For Different Chemical Compound Classes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na211

b:89.9
occ:1.00
OAN C:O4B206 3.1 84.0 1.0
OAP C:O4B206 3.2 85.5 1.0
OAM C:O4B206 3.2 82.1 1.0
OAQ C:O4B206 3.3 83.0 1.0
OAO C:O4B206 3.5 81.9 1.0
C90 C:HRN201 3.8 55.2 1.0
CAG C:O4B206 3.9 82.2 1.0
CAD C:O4B206 4.0 81.7 1.0
CAL C:O4B206 4.0 83.1 1.0
CAB C:O4B206 4.0 82.9 1.0
CAE C:O4B206 4.1 84.4 1.0
CAA C:O4B206 4.1 82.3 1.0
CAJ C:O4B206 4.1 84.7 1.0
CAF C:O4B206 4.1 85.1 1.0
OAR C:O4B206 4.1 83.9 1.0
CAI C:O4B206 4.1 85.2 1.0
CAH C:O4B206 4.2 82.5 1.0
CAK C:O4B206 4.2 83.3 1.0
CAC C:O4B206 4.2 81.8 1.0

Reference:

J.Kallen, A.Izaac, S.Chau, E.Wirth, J.Schoepfer, R.Mah, A.Schlapbach, S.Stutz, A.Vaupel, V.Guagnano, K.Masuya, T.M.Stachyra, B.Salem, P.Chene, F.Gessier, P.Holzer, P.Furet. Structural States of HDM2 and Hdmx: X-Ray Elucidation of Adaptations and Binding Interactions For Different Chemical Compound Classes. Chemmedchem V. 14 1305 2019.
ISSN: ESSN 1860-7187
PubMed: 31066983
DOI: 10.1002/CMDC.201900201
Page generated: Tue Dec 15 12:48:05 2020

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