Chlorine in PDB 8df5: Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab

Enzymatic activity of Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab

All present enzymatic activity of Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab:
3.4.17.23;

Protein crystallography data

The structure of Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab, PDB code: 8df5 was solved by M.Mccallum, Seattle Structural Genomics Center For Infectious Disease(Ssgcid), G.Snell, D.Veesler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.27 / 2.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 78.531, 126.773, 145.663, 91.78, 103.66, 96.02
R / Rfree (%) 17.7 / 21.7

Other elements in 8df5:

The structure of Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Chlorine atom in the Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab (pdb code 8df5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 22 binding sites of Chlorine where determined in the Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab, PDB code: 8df5:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 22 in 8df5

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Chlorine binding site 1 out of 22 in the Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:86.7
occ:1.00
 ND2 A:ASN169 3.7 84.5 1.0
NE2 A:GLN206 4.0 81.3 1.0
CD A:GLN206 4.1 80.7 1.0
OE1 A:GLN206 4.1 83.5 1.0
CD1 A:LEU173 4.3 75.2 1.0
O A:ALA172 4.5 81.0 1.0
CB A:LEU173 4.5 76.0 1.0
C A:ALA172 4.7 79.9 1.0
CB A:ALA172 4.7 84.0 1.0
CA A:LEU173 4.8 80.5 1.0
CG A:ASN169 4.8 83.1 1.0
CG A:GLN206 4.8 77.3 1.0
N A:LEU173 4.9 82.0 1.0
CG A:LEU173 5.0 73.6 1.0

Chlorine binding site 2 out of 22 in 8df5

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Chlorine binding site 2 out of 22 in the Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:90.9
occ:1.00
 N A:THR74 3.3 65.0 1.0
OG1 A:THR74 3.5 62.3 1.0
O A:THR72 3.7 63.1 1.0
CA A:ASP73 3.8 60.4 1.0
O A:HOH465 3.8 61.5 1.0
CB A:THR74 4.0 59.5 1.0
C A:ASP73 4.0 61.9 1.0
OD1 A:ASP73 4.1 72.2 1.0
CA A:THR74 4.2 65.2 1.0
C A:THR72 4.4 56.5 1.0
N A:ASP73 4.5 57.9 1.0
O A:HOH466 4.8 63.8 1.0
CB A:ASP73 4.8 58.0 1.0
CG A:ASP73 4.8 68.9 1.0
O A:HOH406 4.8 56.9 1.0

Chlorine binding site 3 out of 22 in 8df5

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Chlorine binding site 3 out of 22 in the Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:65.6
occ:1.00
 N B:PHE98 3.3 44.2 1.0
N A:TRP47 3.3 47.9 1.0
CA B:THR97 3.7 43.2 1.0
CD1 B:PHE98 3.8 45.2 1.0
CA A:GLU46 3.9 50.0 1.0
C B:THR97 4.0 44.7 1.0
CB A:TRP47 4.1 44.2 1.0
O A:LEU45 4.1 50.0 1.0
CB B:PHE98 4.1 42.5 1.0
C A:GLU46 4.1 48.3 1.0
O B:HOH407 4.2 56.4 1.0
CA B:PHE98 4.3 41.9 1.0
CA A:TRP47 4.3 45.4 1.0
CB B:THR97 4.3 44.0 1.0
O B:LEU96 4.4 49.9 1.0
CG B:PHE98 4.4 42.3 1.0
CG A:GLU46 4.6 51.0 1.0
O B:PHE98 4.6 41.1 1.0
N B:THR97 4.7 46.3 1.0
CG2 B:THR97 4.8 47.7 1.0
CE1 B:PHE98 4.8 48.3 1.0
N A:GLU46 4.8 51.5 1.0
C A:LEU45 4.8 50.2 1.0
CB A:GLU46 4.8 49.3 1.0
O A:TRP47 4.9 46.9 1.0
C B:PHE98 4.9 43.5 1.0
C B:LEU96 5.0 47.3 1.0

Chlorine binding site 4 out of 22 in 8df5

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Chlorine binding site 4 out of 22 in the Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl302

b:76.4
occ:1.00
 O C:HOH436 2.5 53.3 1.0
NH1 C:ARG102 2.7 65.3 1.0
OD1 C:ASN59 3.6 71.3 1.0
CZ C:ARG102 3.9 64.7 1.0
CH2 C:TRP47 4.2 52.3 1.0
CD C:ARG102 4.3 53.3 1.0
CZ2 C:TRP47 4.3 50.2 1.0
CG C:ASN59 4.4 73.5 1.0
O D:SER95 4.4 52.7 1.0
NE C:ARG102 4.5 62.9 1.0
C D:SER95 4.6 51.8 1.0
CB C:ASN59 4.7 62.0 1.0
CB D:LEU96 4.8 52.8 1.0
CB C:ARG102 4.8 49.4 1.0
CD1 D:LEU96 4.9 54.3 1.0
CA D:SER95 4.9 50.2 1.0
NH2 C:ARG102 4.9 65.4 1.0

Chlorine binding site 5 out of 22 in 8df5

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Chlorine binding site 5 out of 22 in the Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl303

b:77.5
occ:1.00
 N C:SER109 3.1 47.8 1.0
NE S:ARG346 3.5 75.2 1.0
CB C:SER109 3.6 50.6 1.0
NH2 S:ARG346 3.7 73.0 1.0
CB C:GLU108 3.8 47.7 1.0
OG C:SER109 3.9 64.3 1.0
CA C:SER109 3.9 49.3 1.0
CZ S:ARG346 3.9 78.2 1.0
CA C:GLU108 4.0 49.6 1.0
C C:GLU108 4.0 47.6 1.0
OG1 S:THR345 4.1 57.2 1.0
CD S:ARG346 4.4 74.2 1.0
CG C:GLU108 4.4 49.1 1.0
O C:HOH402 4.5 53.2 1.0
O C:SER109 4.5 53.4 1.0
CB S:ARG346 4.5 55.4 1.0
C C:SER109 4.7 51.9 1.0
CG S:ARG346 4.7 64.5 1.0
NH2 C:ARG102 4.9 65.4 1.0
OE1 C:GLU108 4.9 60.3 1.0

Chlorine binding site 6 out of 22 in 8df5

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Chlorine binding site 6 out of 22 in the Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl303

b:64.7
occ:1.00
 NE2 D:GLN38 3.2 49.1 1.0
O D:HOH428 3.4 55.9 1.0
NH1 D:ARG46 3.8 73.2 1.0
CD D:GLN38 4.0 47.8 1.0
OE1 D:GLN38 4.2 54.0 1.0
CD1 D:ILE59 4.2 55.8 1.0
CD D:ARG46 4.4 59.1 1.0
CD2 D:LEU48 4.5 52.9 1.0
CE2 D:PHE63 4.6 62.1 1.0
CZ D:ARG46 4.8 74.5 1.0
CD D:PRO60 4.8 65.1 1.0
NZ D:LYS40 4.8 70.2 1.0
CZ D:PHE63 4.9 59.8 1.0
NE D:ARG46 5.0 69.8 1.0

Chlorine binding site 7 out of 22 in 8df5

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Chlorine binding site 7 out of 22 in the Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl304

b:67.0
occ:1.00
 N D:PHE98 3.3 47.7 1.0
N C:TRP47 3.5 45.9 1.0
CA D:THR97 3.5 48.9 1.0
C D:THR97 3.9 49.7 1.0
CA C:GLU46 4.0 48.3 1.0
O D:HOH430 4.0 53.4 1.0
CB D:THR97 4.1 45.4 1.0
CD2 D:PHE98 4.1 47.4 1.0
O C:LEU45 4.2 55.7 1.0
CB C:TRP47 4.2 48.8 1.0
CB D:PHE98 4.2 46.1 1.0
C C:GLU46 4.3 48.2 1.0
O D:LEU96 4.3 48.1 1.0
CA D:PHE98 4.3 45.7 1.0
CG2 D:THR97 4.3 48.7 1.0
O D:HOH419 4.4 56.5 1.0
CA C:TRP47 4.5 47.5 1.0
O D:PHE98 4.6 44.7 1.0
N D:THR97 4.6 48.9 1.0
CG D:PHE98 4.7 48.6 1.0
CG C:GLU46 4.7 46.5 1.0
CB C:GLU46 4.8 48.4 1.0
O D:HOH478 4.9 52.2 1.0
N C:GLU46 4.9 47.2 1.0
C D:LEU96 4.9 48.6 1.0
C C:LEU45 4.9 49.1 1.0
C D:PHE98 5.0 43.4 1.0

Chlorine binding site 8 out of 22 in 8df5

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Chlorine binding site 8 out of 22 in the Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1112

b:96.9
occ:1.00
 NH2 E:ARG169 3.0 95.5 1.0
CH2 E:TRP478 3.4 103.3 1.0
NE1 E:TRP477 3.6 93.9 1.0
CZ2 E:TRP478 3.6 104.0 1.0
NE E:ARG169 3.7 100.7 1.0
NZ E:LYS481 3.7 87.7 1.0
CB E:ASP499 3.8 100.4 1.0
CZ E:ARG169 3.8 99.7 1.0
CE E:LYS481 3.8 95.5 1.0
CZ2 E:TRP477 4.2 84.3 1.0
O E:ASP499 4.2 93.1 1.0
CE2 E:TRP477 4.2 93.8 1.0
CZ2 E:TRP165 4.3 110.1 1.0
CZ3 E:TRP478 4.4 100.9 1.0
C E:ASP499 4.5 90.6 1.0
CA E:ASP499 4.6 97.3 1.0
CG E:ASP499 4.7 99.0 1.0
CD1 E:TRP477 4.7 95.4 1.0
OG E:SER502 4.7 98.8 1.0
CE2 E:TRP478 4.7 105.2 1.0
NE1 E:TRP165 4.8 98.5 1.0
CE2 E:TRP165 4.9 106.8 1.0
OD2 E:ASP499 4.9 98.4 1.0
CD E:ARG169 5.0 100.7 1.0

Chlorine binding site 9 out of 22 in 8df5

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Chlorine binding site 9 out of 22 in the Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1113

b:88.6
occ:1.00
 NH2 E:ARG518 2.6 82.8 1.0
CZ E:ARG518 3.7 81.0 1.0
OG1 E:THR519 3.9 68.4 1.0
NH1 E:ARG518 4.0 79.7 1.0
CE1 E:PHE274 4.5 80.5 1.0
CG1 E:ILE446 4.5 77.8 1.0
CG2 E:THR449 4.6 85.5 1.0
CA E:ILE446 4.6 86.4 1.0
NE E:ARG518 4.8 78.3 1.0
CG2 E:THR445 4.8 86.8 1.0
CB E:ILE446 5.0 81.6 1.0

Chlorine binding site 10 out of 22 in 8df5

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Chlorine binding site 10 out of 22 in the Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Sars-Cov-2 Beta Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1114

b:80.8
occ:1.00
 NH1 E:ARG393 3.3 71.4 1.0
CA E:GLY352 3.8 55.2 1.0
OD1 E:ASP350 3.8 64.7 1.0
CD E:ARG393 3.9 64.4 1.0
CE2 E:PHE40 3.9 53.7 1.0
N E:GLY352 4.0 56.1 1.0
CE1 E:PHE390 4.0 58.6 1.0
OD2 E:ASP350 4.1 62.0 1.0
CD2 E:PHE40 4.2 55.2 1.0
CG E:ASP350 4.2 59.0 1.0
CD1 E:PHE390 4.3 58.5 1.0
CZ E:ARG393 4.4 60.1 1.0
O E:ASP350 4.4 63.7 1.0
O E:HOH1204 4.6 56.6 1.0
C E:LEU351 4.6 56.4 1.0
NE E:ARG393 4.6 54.0 1.0
O E:HOH1203 4.6 55.4 1.0
O E:LEU351 4.8 51.1 1.0
CZ E:PHE40 4.9 51.5 1.0
CB E:ARG393 4.9 54.3 1.0
CZ E:PHE390 4.9 56.5 1.0

Reference:

T.N.Starr, A.J.Greaney, W.W.Hannon, A.N.Loes, K.Hauser, J.R.Dillen, E.Ferri, A.G.Farrell, B.Dadonaite, M.Mccallum, K.A.Matreyek, D.Corti, D.Veesler, G.Snell, J.D.Bloom. Shifting Mutational Constraints in the Sars-Cov-2 Receptor-Binding Domain During Viral Evolution. Science V. 377 420 2022.
ISSN: ESSN 1095-9203
PubMed: 35762884
DOI: 10.1126/SCIENCE.ABO7896
Page generated: Tue Apr 4 22:44:58 2023

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