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Potassium in PDB 7q0g: Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs

Protein crystallography data

The structure of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs, PDB code: 7q0g was solved by D.Zhou, J.Ren, D.I.Stuart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 107.81 / 1.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.292, 106.538, 215.611, 90, 90, 90
R / Rfree (%) 19.2 / 22.4

Other elements in 7q0g:

The structure of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs also contains other interesting chemical elements:

Chlorine (Cl) 14 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Potassium atom in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs (pdb code 7q0g). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 14 binding sites of Potassium where determined in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs, PDB code: 7q0g:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 14 in 7q0g

Go back to Potassium Binding Sites List in 7q0g
Potassium binding site 1 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K709

b:78.6
occ:1.00
 O E:PHE347 3.2 37.1 1.0
O E:HOH823 3.3 42.0 1.0
CE1 E:TYR451 4.1 42.5 1.0
O E:ASN450 4.3 42.5 1.0
CZ E:TYR451 4.4 40.9 1.0
C E:PHE347 4.4 42.9 1.0
CD1 E:TYR451 4.5 44.7 1.0
O E:HOH839 4.6 32.9 1.0
N E:SER349 4.6 34.9 1.0
OH E:TYR451 4.7 34.9 1.0
CB E:ASN450 4.7 62.6 1.0
CA E:ALA348 4.8 36.8 1.0
OG E:SER349 4.8 32.3 1.0
C E:ASN450 4.9 40.1 1.0
C E:ALA348 4.9 37.9 1.0
CE2 E:TYR451 4.9 47.8 1.0
O E:HOH835 5.0 43.0 1.0

Potassium binding site 2 out of 14 in 7q0g

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Potassium binding site 2 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K407

b:61.6
occ:1.00
 O H:HOH564 2.5 35.5 1.0
O H:GLY44 3.1 33.3 1.0
N H:ALA40 3.2 44.2 1.0
CB H:ALA40 3.8 40.4 1.0
C H:GLY44 4.0 37.0 1.0
CB H:LYS43 4.0 45.0 1.0
CA H:GLN39 4.0 38.0 1.0
CA H:ALA40 4.1 38.1 1.0
C H:GLN39 4.1 35.0 1.0
O H:HOH562 4.1 45.1 1.0
O H:ARG38 4.3 29.1 1.0
N H:GLY44 4.3 42.0 1.0
CB H:GLU46 4.4 28.5 1.0
OE1 H:GLU46 4.6 42.1 1.0
N H:GLN39 4.7 32.7 1.0
N H:GLU46 4.7 28.8 1.0
CA H:GLY44 4.7 39.3 1.0
C H:ARG38 4.8 35.8 1.0
C H:LYS43 4.8 40.1 1.0
O H:ALA40 4.8 48.4 1.0
N H:LEU45 4.9 30.3 1.0
C H:LEU45 4.9 30.4 1.0
CG H:LYS43 4.9 52.8 1.0

Potassium binding site 3 out of 14 in 7q0g

Go back to Potassium Binding Sites List in 7q0g
Potassium binding site 3 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K408

b:69.5
occ:1.00
 O E:LYS458 2.7 32.4 1.0
O H:SER30 2.8 28.5 1.0
O H:SER53 3.5 31.9 1.0
O H:HOH575 3.6 42.8 1.0
C E:LYS458 3.7 37.4 1.0
C H:SER30 3.8 38.5 1.0
NH2 H:ARG71 3.8 34.9 1.0
CA E:LYS458 4.2 39.5 1.0
CB E:LYS458 4.3 44.3 1.0
CB H:SER30 4.3 36.7 1.0
CA H:SER30 4.6 37.5 1.0
CZ H:ARG71 4.6 35.7 1.0
C H:SER53 4.6 36.6 1.0
CA H:GLY54 4.7 33.7 1.0
N H:SER31 4.8 40.2 1.0
OG H:SER30 4.9 57.7 1.0
CG E:LYS458 4.9 53.8 1.0
CA H:SER31 4.9 36.7 1.0
N E:SER459 4.9 36.6 1.0
C H:GLY54 4.9 31.1 1.0
NE H:ARG71 5.0 32.6 1.0

Potassium binding site 4 out of 14 in 7q0g

Go back to Potassium Binding Sites List in 7q0g
Potassium binding site 4 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K409

b:79.3
occ:1.00
 O H:HOH534 2.5 32.6 1.0
N H:LEU4 3.5 42.5 1.0
O H:LEU4 3.8 43.4 1.0
CA H:GLN3 3.9 46.3 1.0
C H:GLN3 4.3 41.6 1.0
O H:TRP107 4.3 35.1 1.0
CB H:GLN3 4.4 53.3 1.0
C H:LEU4 4.4 42.2 1.0
O H:VAL2 4.5 47.6 1.0
CA H:LEU4 4.5 38.5 1.0
CD1 H:ILE106 4.6 46.4 1.0
CB H:LEU4 4.8 37.1 1.0
CG H:GLN3 4.8 72.7 1.0
CA H:GLY108 4.9 38.4 1.0
CG1 H:ILE106 4.9 46.9 1.0
N H:GLN3 5.0 45.1 1.0

Potassium binding site 5 out of 14 in 7q0g

Go back to Potassium Binding Sites List in 7q0g
Potassium binding site 5 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K410

b:79.8
occ:1.00
 O H:HOH568 2.9 31.2 1.0
N H:MET112 3.6 35.3 1.0
OG1 H:THR111 4.0 33.8 1.0
CA H:THR111 4.1 39.0 1.0
CB H:MET112 4.3 38.3 1.0
C H:THR111 4.4 34.5 1.0
CG H:PRO153 4.5 30.1 1.0
CA H:MET112 4.5 37.4 1.0
CD H:PRO153 4.6 34.6 1.0
CB H:THR111 4.7 43.5 1.0
O H:GLY110 4.7 36.1 1.0
O H:MET112 4.9 31.5 1.0

Potassium binding site 6 out of 14 in 7q0g

Go back to Potassium Binding Sites List in 7q0g
Potassium binding site 6 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K411

b:60.4
occ:1.00
 O H:HOH544 2.6 33.7 1.0
OG L:SER176 2.7 25.8 1.0
O L:HOH416 2.9 24.4 1.0
O L:HOH425 3.2 24.8 1.0
O L:HOH462 3.2 31.5 1.0
N H:SER183 3.4 33.8 1.0
CB L:SER176 3.7 32.2 1.0
CB H:PHE170 3.8 37.2 1.0
CB H:SER183 3.9 37.6 1.0
CA H:LEU182 4.0 30.9 1.0
CB L:SER162 4.0 33.9 1.0
O H:HOH513 4.0 28.8 1.0
C H:LEU182 4.0 33.3 1.0
CG H:PHE170 4.2 35.6 1.0
OG1 L:THR178 4.2 27.7 1.0
CA H:SER183 4.2 36.1 1.0
OG H:SER183 4.4 32.0 1.0
CD1 H:PHE170 4.4 36.5 1.0
OG L:SER162 4.6 33.5 1.0
O H:SER183 4.7 27.1 1.0
O H:PRO171 4.7 37.5 1.0
CB H:LEU182 4.7 37.8 1.0
C H:SER183 5.0 37.7 1.0
CD2 H:PHE170 5.0 34.1 1.0

Potassium binding site 7 out of 14 in 7q0g

Go back to Potassium Binding Sites List in 7q0g
Potassium binding site 7 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K304

b:73.1
occ:1.00
 O L:HOH454 2.7 37.8 1.0
NZ L:LYS45 3.0 77.6 1.0
OE1 L:GLN37 3.4 44.3 1.0
CE L:LYS45 4.1 83.4 1.0
CD L:GLN37 4.3 38.2 1.0
CD2 L:LEU47 4.4 40.6 1.0
NE2 L:GLN37 4.4 34.9 1.0
CD L:PRO59 4.5 55.1 1.0
CD L:LYS45 4.6 73.5 1.0
NZ L:LYS39 4.7 58.9 1.0
CE2 L:PHE62 4.7 49.4 1.0
CE L:LYS39 4.8 56.5 1.0
CG L:PRO59 5.0 58.9 1.0

Potassium binding site 8 out of 14 in 7q0g

Go back to Potassium Binding Sites List in 7q0g
Potassium binding site 8 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K305

b:81.2
occ:1.00
 O L:HOH459 2.6 58.1 1.0
OE2 L:GLU161 3.1 46.9 1.0
CD L:GLU161 3.8 46.8 1.0
OE1 L:GLU161 3.9 41.3 1.0
N L:VAL146 4.0 37.8 1.0
O L:ALA144 4.2 37.2 1.0
O L:VAL146 4.2 35.1 1.0
CA L:LYS145 4.3 41.1 1.0
O L:HOH410 4.5 33.6 1.0
C L:LYS145 4.7 37.1 1.0
CA L:VAL146 4.9 45.2 1.0
C L:VAL146 4.9 36.5 1.0

Potassium binding site 9 out of 14 in 7q0g

Go back to Potassium Binding Sites List in 7q0g
Potassium binding site 9 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K306

b:70.3
occ:1.00
 O1 L:GOL301 2.9 42.7 1.0
OG1 L:THR172 3.0 30.8 1.0
C L:TYR173 3.1 35.6 1.0
OG L:SER174 3.1 29.1 1.0
C1 L:GOL301 3.2 63.9 1.0
N L:SER174 3.3 30.5 1.0
O L:THR172 3.3 31.1 1.0
O L:TYR173 3.3 25.1 1.0
CE1 H:HIS168 3.3 44.4 1.0
OD1 L:ASN138 3.4 43.6 1.0
CA L:TYR173 3.5 33.7 1.0
C L:THR172 3.5 36.2 1.0
N L:TYR173 3.6 36.2 1.0
CB L:SER174 3.7 29.2 1.0
NE2 H:HIS168 3.8 42.4 1.0
OG1 L:THR164 4.0 32.5 1.0
CB L:THR172 4.0 41.5 1.0
CA L:SER174 4.0 39.0 1.0
CA L:ASN138 4.1 42.4 1.0
ND1 H:HIS168 4.1 39.8 1.0
CG L:ASN138 4.3 36.8 1.0
N L:ASN138 4.3 37.9 1.0
CA L:THR172 4.3 40.9 1.0
CB L:ASP167 4.4 55.4 1.0
C2 L:GOL301 4.5 55.1 1.0
O2 L:GOL301 4.7 48.2 1.0
OD1 L:ASP170 4.7 52.3 1.0
CD2 H:HIS168 4.7 37.9 1.0
CB L:ASN138 4.8 46.4 1.0
CG H:HIS168 4.9 39.4 1.0
CB L:TYR173 5.0 38.3 1.0

Potassium binding site 10 out of 14 in 7q0g

Go back to Potassium Binding Sites List in 7q0g
Potassium binding site 10 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-49 and Fi-3A Fabs within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K307

b:90.9
occ:1.00
 O L:HOH412 2.9 45.7 1.0
OG L:SER67 3.2 51.4 1.0
CB L:SER67 4.1 49.1 1.0
N L:GLY68 4.1 46.4 1.0
CD1 E:TYR501 4.3 67.7 1.0
CA L:GLY68 4.3 49.9 1.0
C L:SER67 4.4 54.5 1.0
O E:THR500 4.5 58.5 1.0
OD1 L:ASP28 4.5 50.2 1.0
CA E:TYR501 4.5 52.0 1.0
OD2 L:ASP28 4.6 52.1 1.0
CA L:SER30 4.7 47.5 1.0
CE1 E:TYR501 4.8 73.0 1.0
CA L:SER67 4.8 45.1 1.0
O L:SER67 4.8 43.0 1.0
N E:GLY502 4.9 49.3 1.0
CG L:ASP28 5.0 46.5 1.0
OG L:SER30 5.0 47.9 1.0

Reference:

C.Liu, D.Zhou, R.Nutalai, H.M.Duyvesteyn, A.Tuekprakhon, H.M.Ginn, W.Dejnirattisai, P.Supasa, A.J.Mentzer, B.Wang, J.B.Case, Y.Zhao, D.T.Skelly, R.E.Chen, S.A.Johnson, T.G.Ritter, C.Mason, T.Malik, N.Temperton, N.G.Paterson, M.A.Williams, D.R.Hall, D.K.Clare, A.Howe, P.J.Goulder, E.E.Fry, M.S.Diamond, J.Mongkolsapaya, J.Ren, D.I.Stuart, G.R.Screaton. The Antibody Response to Sars-Cov-2 Beta Underscores the Antigenic Distance to Other Variants Cell Host Microbe 2021.
ISSN: ESSN 1934-6069
DOI: 10.1016/J.CHOM.2021.11.013
Page generated: Mon Aug 12 20:26:20 2024

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