Chlorine in PDB 7msq: Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd)

Protein crystallography data

The structure of Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd), PDB code: 7msq was solved by D.B.Langley, D.Christ, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.00 / 2.29
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 109.764, 115.494, 240.758, 90, 90, 90
R / Rfree (%) 19.4 / 24.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd) (pdb code 7msq). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd), PDB code: 7msq:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 7msq

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Chlorine binding site 1 out of 7 in the Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:84.9
occ:1.00
 NH1 A:ARG457 3.5 53.0 1.0
CZ A:ARG457 3.5 52.5 1.0
CB A:LYS458 3.8 77.8 1.0
NH2 A:ARG457 3.8 53.1 1.0
CG A:ARG457 3.9 58.0 1.0
OG A:SER459 3.9 61.6 1.0
N A:LYS458 3.9 70.3 1.0
NE A:ARG457 4.0 54.4 1.0
N A:SER459 4.0 67.0 1.0
CE A:LYS458 4.3 81.6 1.0
CA A:LYS458 4.3 74.8 1.0
O A:SER459 4.4 57.3 1.0
CD A:ARG457 4.5 55.5 1.0
C A:LYS458 4.6 71.8 1.0
CG A:LYS458 4.6 80.7 1.0
CB A:SER459 4.8 63.0 1.0
CA A:SER459 4.8 63.4 1.0
C A:ARG457 5.0 64.9 1.0

Chlorine binding site 2 out of 7 in 7msq

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Chlorine binding site 2 out of 7 in the Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:77.5
occ:1.00
 CB B:PRO463 3.8 39.3 1.0
O B:HOH706 3.9 51.0 1.0
CB B:PRO426 4.2 38.1 1.0
CG B:PRO426 4.4 36.0 1.0
CD2 B:PHE464 4.5 37.9 1.0
CG B:PRO463 4.5 40.0 1.0
O B:PRO463 4.6 37.1 1.0
CE2 B:PHE464 4.9 37.7 1.0

Chlorine binding site 3 out of 7 in 7msq

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Chlorine binding site 3 out of 7 in the Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:63.5
occ:1.00
 O D:TYR59 3.3 53.5 1.0
CB E:TYR94 3.7 40.4 1.0
CH2 D:TRP47 3.9 41.1 1.0
CZ3 D:TRP47 3.9 42.0 1.0
N E:PRO95 4.0 42.3 1.0
CA E:PRO95 4.0 41.1 1.0
CD D:PRO61 4.1 59.3 1.0
CB E:PRO95 4.1 41.6 1.0
C D:TYR59 4.2 48.6 1.0
C E:TYR94 4.3 43.1 1.0
CD E:PRO95 4.3 43.0 1.0
CG E:TYR94 4.4 38.4 1.0
CG D:PRO61 4.5 58.4 1.0
N D:TYR59 4.5 46.6 1.0
CA E:TYR94 4.5 42.1 1.0
CD1 E:TYR94 4.6 37.6 1.0
CB D:ASN58 4.6 43.5 1.0
CG E:PRO95 4.8 43.5 1.0
N D:ASN60 4.9 50.1 1.0
CA D:ASN60 4.9 50.5 1.0
C D:ASN58 5.0 46.8 1.0

Chlorine binding site 4 out of 7 in 7msq

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Chlorine binding site 4 out of 7 in the Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl302

b:89.4
occ:1.00
 O D:GLY120 3.8 46.4 1.0
O D:GLN119 4.4 39.0 1.0
C D:GLY120 4.5 45.4 1.0
O E:GLY41 4.7 46.9 1.0
CG1 D:VAL92 4.9 35.6 1.0

Chlorine binding site 5 out of 7 in 7msq

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Chlorine binding site 5 out of 7 in the Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl301

b:59.9
occ:1.00
 ND2 E:ASN137 3.3 42.2 1.0
OG E:SER114 3.5 39.3 1.0
CB E:SER114 3.6 40.1 1.0
CB E:ASN137 4.0 40.5 1.0
CG2 D:THR197 4.1 47.4 1.0
CG2 D:THR149 4.1 63.5 1.0
CG E:ASN137 4.2 40.2 1.0
CE1 E:PHE116 4.2 37.9 1.0
CZ E:PHE116 4.2 38.7 1.0
CB D:THR197 4.6 46.2 1.0
ND2 E:ASN138 4.6 41.8 1.0
OG1 D:THR197 4.7 46.8 1.0
CB D:THR149 4.8 62.6 1.0
O E:ASN137 4.9 39.2 1.0
O E:HOH409 5.0 22.1 1.0

Chlorine binding site 6 out of 7 in 7msq

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Chlorine binding site 6 out of 7 in the Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl302

b:64.1
occ:1.00
 O D:HOH424 3.1 48.6 1.0
N E:ALA50 3.3 42.5 1.0
CD1 E:LEU91 3.3 44.6 1.0
CA E:ALA50 3.8 45.6 1.0
CB E:LEU91 3.9 38.8 1.0
N E:LEU33 4.0 41.2 1.0
CA E:TYR32 4.1 43.6 1.0
CG E:LEU91 4.2 43.1 1.0
C E:TYR32 4.3 42.4 1.0
CB E:ALA50 4.4 44.1 1.0
O E:LEU33 4.4 40.0 1.0
C E:TYR49 4.4 40.7 1.0
CB E:TYR49 4.4 41.2 1.0
O E:SER31 4.5 42.5 1.0
CD1 E:TYR32 4.5 46.0 1.0
C E:LEU33 4.6 41.3 1.0
CA E:TYR49 4.7 39.5 1.0
CB E:TYR32 4.7 45.5 1.0
CA E:LEU33 4.9 42.8 1.0

Chlorine binding site 7 out of 7 in 7msq

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Chlorine binding site 7 out of 7 in the Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl301

b:63.3
occ:1.00
 O H:TYR59 3.5 52.5 1.0
CB L:TYR94 3.7 43.5 1.0
CA L:PRO95 4.0 45.5 1.0
N L:PRO95 4.0 47.8 1.0
CD H:PRO61 4.1 60.7 1.0
CB L:PRO95 4.1 48.1 1.0
CZ3 H:TRP47 4.2 41.3 1.0
CH2 H:TRP47 4.3 40.4 1.0
C L:TYR94 4.3 46.7 1.0
C H:TYR59 4.4 50.3 1.0
CD L:PRO95 4.4 48.0 1.0
CG L:TYR94 4.5 40.9 1.0
CA L:TYR94 4.5 45.1 1.0
O H:HOH424 4.6 46.2 1.0
CD1 L:TYR94 4.6 40.6 1.0
CB H:ASN58 4.7 48.1 1.0
N H:TYR59 4.8 46.9 1.0
CG L:PRO95 4.8 46.8 1.0
O L:TYR94 4.9 48.9 1.0
CG H:PRO61 4.9 65.2 1.0
N H:PRO61 4.9 57.8 1.0

Reference:

D.L.Burnett, K.J.L.Jackson, D.B.Langley, A.Aggrawal, A.O.Stella, M.D.Johansen, H.Balachandran, H.Lenthall, R.Rouet, G.Walker, B.M.Saunders, M.Singh, H.Li, J.Y.Henry, J.Jackson, A.G.Stewart, F.Witthauer, M.A.Spence, N.G.Hansbro, C.Jackson, P.Schofield, C.Milthorpe, M.Martinello, S.R.Schulz, E.Roth, A.Kelleher, S.Emery, W.J.Britton, W.D.Rawlinson, R.Karl, S.Schafer, T.H.Winkler, R.Brink, R.A.Bull, P.M.Hansbro, H.M.Jack, S.Turville, D.Christ, C.C.Goodnow. Immunizations with Diverse Sarbecovirus Receptor-Binding Domains Elicit Sars-Cov-2 Neutralizing Antibodies Against A Conserved Site of Vulnerability. Immunity V. 54 2908 2021.
ISSN: ISSN 1074-7613
PubMed: 34788600
DOI: 10.1016/J.IMMUNI.2021.10.019
Page generated: Tue Apr 4 20:50:32 2023

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