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Sodium in PDB 6h7l: Activated Turkey BETA1 Adrenoceptor with Bound Partial Agonist Dobutamine and Nanobody NB6B9

Protein crystallography data

The structure of Activated Turkey BETA1 Adrenoceptor with Bound Partial Agonist Dobutamine and Nanobody NB6B9, PDB code: 6h7l was solved by T.Warne, P.C.Edwards, A.S.Dore, A.G.W.Leslie, C.G.Tate, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.08 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.513, 119.699, 129.156, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 27.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Activated Turkey BETA1 Adrenoceptor with Bound Partial Agonist Dobutamine and Nanobody NB6B9 (pdb code 6h7l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Activated Turkey BETA1 Adrenoceptor with Bound Partial Agonist Dobutamine and Nanobody NB6B9, PDB code: 6h7l:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6h7l

Go back to Sodium Binding Sites List in 6h7l
Sodium binding site 1 out of 2 in the Activated Turkey BETA1 Adrenoceptor with Bound Partial Agonist Dobutamine and Nanobody NB6B9


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Activated Turkey BETA1 Adrenoceptor with Bound Partial Agonist Dobutamine and Nanobody NB6B9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:42.8
occ:1.00
O A:CYS198 2.4 51.8 1.0
O A:ASP195 2.5 86.1 1.0
O A:CYS192 2.6 64.3 1.0
C A:CYS198 3.6 56.4 1.0
O A:TYR193 3.6 66.4 1.0
C A:ASP195 3.6 76.6 1.0
C A:CYS192 3.8 67.5 1.0
OG A:SER111 3.9 73.9 1.0
C A:TYR193 3.9 71.7 1.0
CA A:TYR193 4.0 71.1 1.0
CA A:PRO196 4.1 67.1 1.0
N A:PRO196 4.3 69.0 1.0
N A:TYR193 4.4 67.8 1.0
CA A:CYS198 4.4 58.5 1.0
N A:CYS198 4.5 56.9 1.0
C A:PRO196 4.5 62.7 1.0
CB A:CYS198 4.6 62.5 1.0
N A:CYS199 4.6 57.4 1.0
N A:ASP195 4.7 80.4 1.0
O A:PRO196 4.7 59.9 1.0
CB A:SER111 4.7 73.3 1.0
CA A:ASP195 4.7 76.0 1.0
SG A:CYS114 4.7 43.8 1.0
CA A:CYS199 4.8 54.6 1.0
N A:GLN194 4.8 79.1 1.0
SG A:CYS192 4.8 74.4 1.0
CA A:SER111 4.9 71.8 1.0

Sodium binding site 2 out of 2 in 6h7l

Go back to Sodium Binding Sites List in 6h7l
Sodium binding site 2 out of 2 in the Activated Turkey BETA1 Adrenoceptor with Bound Partial Agonist Dobutamine and Nanobody NB6B9


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Activated Turkey BETA1 Adrenoceptor with Bound Partial Agonist Dobutamine and Nanobody NB6B9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:39.3
occ:1.00
O B:CYS198 2.4 55.5 1.0
O B:ASP195 2.5 67.4 1.0
O B:CYS192 2.6 73.3 1.0
C B:ASP195 3.6 65.8 1.0
C B:CYS198 3.6 58.0 1.0
O B:TYR193 3.6 63.6 1.0
C B:CYS192 3.8 71.7 1.0
OG B:SER111 3.9 57.5 1.0
C B:TYR193 3.9 68.2 1.0
CA B:TYR193 4.0 68.2 1.0
CA B:PRO196 4.1 64.4 1.0
N B:PRO196 4.3 65.8 1.0
N B:TYR193 4.4 67.5 1.0
CA B:CYS198 4.5 58.3 1.0
C B:PRO196 4.5 64.9 1.0
N B:CYS198 4.5 56.9 1.0
CB B:CYS198 4.6 60.8 1.0
N B:CYS199 4.6 56.6 1.0
O B:PRO196 4.6 69.6 1.0
N B:ASP195 4.7 63.7 1.0
CA B:ASP195 4.7 61.1 1.0
CB B:SER111 4.8 56.0 1.0
SG B:CYS114 4.8 47.8 1.0
CA B:CYS199 4.8 55.0 1.0
N B:GLN194 4.8 72.9 1.0
SG B:CYS192 4.9 71.1 1.0
CA B:SER111 5.0 55.8 1.0

Reference:

T.Warne, P.C.Edwards, A.S.Dore, A.G.W.Leslie, C.G.Tate. Molecular Basis For High-Affinity Agonist Binding in Gpcrs. Science V. 364 775 2019.
ISSN: ESSN 1095-9203
PubMed: 31072904
DOI: 10.1126/SCIENCE.AAU5595
Page generated: Tue Dec 15 12:19:13 2020

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