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Sodium in PDB 4qkx: Structure of BETA2 Adrenoceptor Bound to A Covalent Agonist and An Engineered Nanobody

Enzymatic activity of Structure of BETA2 Adrenoceptor Bound to A Covalent Agonist and An Engineered Nanobody

All present enzymatic activity of Structure of BETA2 Adrenoceptor Bound to A Covalent Agonist and An Engineered Nanobody:
3.2.1.17;

Protein crystallography data

The structure of Structure of BETA2 Adrenoceptor Bound to A Covalent Agonist and An Engineered Nanobody, PDB code: 4qkx was solved by D.Weichert, A.C.Kruse, A.Manglik, C.Hiller, C.Zhang, H.Huebner, B.K.Kobilka, P.Gmeiner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.26 / 3.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.558, 67.211, 301.269, 90.00, 90.00, 90.00
R / Rfree (%) 23.6 / 28

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of BETA2 Adrenoceptor Bound to A Covalent Agonist and An Engineered Nanobody (pdb code 4qkx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of BETA2 Adrenoceptor Bound to A Covalent Agonist and An Engineered Nanobody, PDB code: 4qkx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4qkx

Go back to Sodium Binding Sites List in 4qkx
Sodium binding site 1 out of 2 in the Structure of BETA2 Adrenoceptor Bound to A Covalent Agonist and An Engineered Nanobody


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of BETA2 Adrenoceptor Bound to A Covalent Agonist and An Engineered Nanobody within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1401

b:84.0
occ:0.00
OD1 A:ASN1103 2.7 0.8 1.0
O A:CYS1184 2.7 88.1 1.0
O A:CYS1190 2.7 68.3 1.0
O A:GLU1187 2.9 0.7 1.0
CG A:ASN1103 3.4 0.7 1.0
C A:CYS1184 3.9 88.6 1.0
C A:CYS1190 4.0 75.1 1.0
CB A:ASN1103 4.1 0.1 1.0
CA A:TYR1185 4.1 99.3 1.0
SG A:CYS1106 4.1 99.1 1.0
C A:GLU1187 4.1 0.9 1.0
CA A:ASN1103 4.1 98.6 1.0
ND2 A:ASN1103 4.2 0.7 1.0
O A:TYR1185 4.3 0.8 1.0
C A:TYR1185 4.3 0.8 1.0
CB A:CYS1106 4.4 78.1 1.0
N A:TYR1185 4.4 93.0 1.0
CA A:CYS1191 4.6 78.3 1.0
N A:CYS1191 4.8 75.4 1.0
N A:GLU1187 4.8 0.5 1.0
SG A:CYS1184 4.8 0.5 1.0
CA A:CYS1190 5.0 78.5 1.0
O A:ASN1103 5.0 98.5 1.0
N A:ASN1103 5.0 0.4 1.0

Sodium binding site 2 out of 2 in 4qkx

Go back to Sodium Binding Sites List in 4qkx
Sodium binding site 2 out of 2 in the Structure of BETA2 Adrenoceptor Bound to A Covalent Agonist and An Engineered Nanobody


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of BETA2 Adrenoceptor Bound to A Covalent Agonist and An Engineered Nanobody within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1402

b:82.5
occ:0.00
OD1 A:ASN861 2.4 0.9 1.0
CG A:ASN861 3.5 0.2 1.0
ND2 A:ASN861 4.1 0.3 1.0
CB A:ASN861 4.8 0.7 1.0

Reference:

D.Weichert, A.C.Kruse, A.Manglik, C.Hiller, C.Zhang, H.Hubner, B.K.Kobilka, P.Gmeiner. Covalent Agonists For Studying G Protein-Coupled Receptor Activation. Proc.Natl.Acad.Sci.Usa V. 111 10744 2014.
ISSN: ISSN 0027-8424
PubMed: 25006259
DOI: 10.1073/PNAS.1410415111
Page generated: Tue Dec 15 07:05:54 2020

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