Chlorine in PDB 7nx6: Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs

Protein crystallography data

The structure of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs, PDB code: 7nx6 was solved by D.Zhou, J.Ren, D.Stuart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 105.85 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.391, 120.146, 211.706, 90, 90, 90
R / Rfree (%) 20.7 / 24.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs (pdb code 7nx6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs, PDB code: 7nx6:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 7nx6

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Chlorine binding site 1 out of 7 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl301

b:63.6
occ:1.00
 O H:GLY100 2.9 69.0 1.0
O H:HOH420 3.0 48.5 1.0
OH H:TYR32 3.3 51.5 1.0
O H:HOH419 3.4 50.7 1.0
NZ H:LYS98 3.6 47.8 1.0
C H:GLY100 3.9 66.3 1.0
CZ H:TYR32 4.1 45.9 1.0
CE1 H:TYR32 4.1 51.1 1.0
CE H:LYS102 4.2 58.0 1.0
CA H:GLY100 4.3 56.5 1.0
CE H:LYS98 4.5 38.5 1.0
OD2 H:ASP109 4.5 49.5 1.0
CG H:LYS102 4.6 60.2 1.0
O H:HOH406 4.9 47.6 1.0

Chlorine binding site 2 out of 7 in 7nx6

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Chlorine binding site 2 out of 7 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl302

b:56.0
occ:1.00
 OG H:SER30 2.8 62.3 1.0
N H:SER30 3.5 43.9 1.0
N H:PHE29 3.7 46.3 1.0
CB H:SER30 3.7 40.5 1.0
CG2 H:THR28 3.8 47.5 1.0
C H:THR28 4.1 43.7 1.0
CA H:THR28 4.1 50.5 1.0
CA H:SER30 4.2 53.5 1.0
C H:PHE29 4.5 45.3 1.0
CA H:PHE29 4.5 42.0 1.0
CB H:THR28 4.6 54.0 1.0
OD1 H:ASN77 4.7 64.9 1.0
O H:THR28 4.8 50.8 1.0
CB H:PHE29 4.8 41.5 1.0
C H:SER30 5.0 52.0 1.0

Chlorine binding site 3 out of 7 in 7nx6

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Chlorine binding site 3 out of 7 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl707

b:78.2
occ:1.00
 OG1 E:THR500 3.0 75.8 1.0
CB E:GLN498 3.3 54.1 1.0
CD E:PRO499 3.3 60.0 1.0
N E:THR500 3.6 61.7 1.0
N E:PRO499 3.7 60.7 1.0
C E:GLN498 3.9 55.8 1.0
CG E:PRO499 3.9 57.1 1.0
CB E:THR500 4.0 62.1 1.0
CA E:GLN498 4.0 47.0 1.0
CG2 E:THR500 4.2 65.9 1.0
O E:VAL445 4.2 71.7 1.0
CG E:GLN498 4.2 71.9 1.0
CA E:THR500 4.3 56.8 1.0
CD E:GLN498 4.5 88.5 1.0
C E:PRO499 4.5 61.2 1.0
O E:GLN498 4.5 61.2 1.0
CA E:PRO499 4.6 62.2 1.0
NE2 E:GLN498 4.9 79.2 1.0
CB E:PRO499 4.9 57.8 1.0
OE1 E:GLN498 4.9 71.3 1.0
C E:THR500 4.9 63.1 1.0
C E:VAL445 5.0 65.8 1.0

Chlorine binding site 4 out of 7 in 7nx6

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Chlorine binding site 4 out of 7 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl708

b:57.5
occ:1.00
 O E:HOH801 3.1 29.3 1.0
NZ E:LYS417 3.3 47.0 1.0
NH2 E:ARG403 3.3 39.0 1.0
O E:HOH832 3.5 46.7 1.0
CE1 B:TYR92 3.6 39.6 1.0
CD1 B:TYR92 3.8 43.4 1.0
CE E:LYS417 3.9 36.2 1.0
OH E:TYR453 3.9 46.5 1.0
O2 E:SO4706 3.9 58.7 1.0
CB A:SER101 4.1 44.5 1.0
CD E:LYS417 4.1 35.8 1.0
O B:HOH409 4.2 46.0 1.0
CZ E:ARG403 4.4 37.1 1.0
CE2 B:TYR33 4.4 46.0 1.0
OE2 E:GLU406 4.5 39.5 1.0
CZ B:TYR92 4.5 48.0 1.0
OG A:SER101 4.5 47.3 1.0
CZ E:TYR453 4.6 40.8 1.0
NE E:ARG403 4.8 37.4 1.0
CG B:TYR92 4.8 41.3 1.0
CE2 E:TYR453 4.8 31.2 1.0
OH B:TYR33 4.8 55.2 1.0
CD A:PRO102 4.9 45.4 1.0

Chlorine binding site 5 out of 7 in 7nx6

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Chlorine binding site 5 out of 7 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:51.1
occ:1.00
 N A:VAL156 3.3 47.4 1.0
OH A:TYR151 3.3 42.9 1.0
CA A:PRO155 3.4 43.3 1.0
CG A:GLU154 3.6 46.1 1.0
CB A:ALA174 3.7 46.9 1.0
C A:PRO155 3.8 47.8 1.0
CB A:GLU154 3.8 45.8 1.0
CE2 A:TYR151 3.9 47.5 1.0
CB A:PRO155 4.0 48.5 1.0
CD2 A:LEU184 4.0 47.5 1.0
CD A:GLU154 4.0 54.8 1.0
CZ A:TYR151 4.1 43.8 1.0
CA A:GLU154 4.2 40.0 1.0
OE2 A:GLU154 4.2 66.5 1.0
O A:VAL156 4.2 50.8 1.0
CG2 A:VAL156 4.4 40.1 1.0
CA A:VAL156 4.4 51.8 1.0
N A:PRO155 4.6 42.2 1.0
OE1 A:GLU154 4.7 72.6 1.0
CB A:VAL156 4.8 47.3 1.0
C A:VAL156 4.8 51.0 1.0
CG1 A:VAL156 4.9 48.2 1.0
N A:ALA174 4.9 49.1 1.0
CA A:ALA174 4.9 42.1 1.0
C A:GLU154 4.9 42.6 1.0
O A:PRO155 5.0 53.0 1.0

Chlorine binding site 6 out of 7 in 7nx6

Go back to Chlorine Binding Sites List in 7nx6
Chlorine binding site 6 out of 7 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:77.5
occ:1.00
 N A:ALA87 2.8 56.6 1.0
CA A:GLY86 3.5 44.9 1.0
CB A:ALA87 3.5 45.6 1.0
C A:GLY86 3.6 50.5 1.0
CA A:ALA87 3.7 51.1 1.0
CB A:PRO14 4.7 52.5 1.0
O A:GLY86 4.7 53.9 1.0
N A:GLY86 4.9 48.3 1.0
C A:ALA87 5.0 48.5 1.0

Chlorine binding site 7 out of 7 in 7nx6

Go back to Chlorine Binding Sites List in 7nx6
Chlorine binding site 7 out of 7 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl308

b:83.6
occ:1.00
 O E:HOH844 2.8 60.8 1.0
OG B:SER32 3.4 54.5 1.0
N B:SER32 3.4 42.5 1.0
N B:SER31 3.4 51.2 1.0
CB B:PRO30 3.6 46.8 1.0
O E:HOH848 3.8 61.1 1.0
CB B:SER32 3.8 50.8 1.0
O E:HOH865 3.9 49.3 1.0
OE1 E:GLN498 3.9 71.3 1.0
C B:PRO30 4.0 53.0 1.0
CA B:PRO30 4.1 52.2 1.0
CA B:SER31 4.2 47.7 1.0
O E:GLY496 4.2 54.4 1.0
CA B:SER32 4.2 42.7 1.0
C B:SER31 4.2 43.2 1.0
CB B:SER31 4.3 45.4 1.0
CD E:GLN498 4.4 88.5 1.0
OH E:TYR449 4.4 71.8 1.0
O B:HOH457 4.7 56.4 1.0
O E:TYR495 4.8 56.4 1.0
NE2 E:GLN498 4.8 79.2 1.0
CA E:GLY496 4.9 58.7 1.0
CG B:PRO30 5.0 52.5 1.0
O B:PRO30 5.0 52.2 1.0
C E:GLY496 5.0 53.2 1.0

Reference:

W.Dejnirattisai, D.Zhou, P.Supasa, C.Liu, A.J.Mentzer, H.M.Ginn, Y.Zhao, H.M.Duyvesteyn, A.Tuekprakhon, R.Nutalai, B.Wang, G.C.Paesen, C.Lopez-Camacho, J.Slon-Campos, T.S.Walter, D.Skelly, F.G.Naveca, V.Nascimento, F.Nascimento, P.C.Resende, A.Pauvolid-Correa, M.M.Siqueira, C.Dold, R.Levin, T.Dong, A.J.Pollard, J.C.Knight, D.Crook, T.Lambe, E.Clutterbuck, S.Bibi, A.Flaxman, M.Bittaye, S.Belij-Rammerstorfer, S.Gilbert, M.W.Carroll, P.Klenerman, E.Barnes, S.J.Dunachie, N.G.Paterson, M.A.Williams, D.R.Hall, R.J.Hulswit, T.A.Bowden, E.E.Fry, J.Mongkolsapaya, J.Ren, D.I.Stuart, G.R.Screaton. Antibody Evasion By the P.1 Strain of Sars-Cov-2 Cell(Cambridge,Mass.) 2021.
ISSN: ISSN 0092-8674
DOI: 10.1016/J.CELL.2021.03.055
Page generated: Tue Jul 30 01:08:15 2024

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