Chlorine in PDB 8cwj: Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd)

Protein crystallography data

The structure of Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd), PDB code: 8cwj 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) 48.69 / 2.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.433, 144.097, 168.842, 90, 117.51, 90
R / Rfree (%) 19.6 / 23

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd) (pdb code 8cwj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd), PDB code: 8cwj:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 8cwj

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Chlorine binding site 1 out of 10 in the Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl604

b:97.8
occ:1.00
 NH1 G:ARG417 3.5 54.0 1.0
OH G:TYR453 3.6 43.5 1.0
OG1 I:THR415 3.8 69.1 1.0
NH2 G:ARG417 3.8 54.3 1.0
CZ G:ARG417 4.1 55.1 1.0
CD2 G:LEU455 4.2 50.9 1.0
CD1 G:LEU455 4.3 50.2 1.0
NE2 G:GLN493 4.7 84.4 1.0
CZ G:TYR453 4.7 44.3 1.0
CG G:LEU455 5.0 49.8 1.0
CE1 G:TYR453 5.0 42.2 1.0

Chlorine binding site 2 out of 10 in 8cwj

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Chlorine binding site 2 out of 10 in the Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl605

b:93.6
occ:1.00
 OD1 G:ASN460 3.6 43.6 1.0
O G:HOH754 3.7 55.0 1.0
O G:GLY416 4.0 47.9 1.0
CE1 G:TYR421 4.2 42.8 1.0
OH G:TYR421 4.2 57.9 1.0
CZ G:TYR421 4.2 48.8 1.0
CG G:ASN460 4.4 39.0 1.0
ND2 G:ASN460 4.5 37.2 1.0
C G:GLY416 4.5 45.4 1.0
CA G:GLY420 4.6 39.8 1.0
N G:GLY416 4.8 44.9 1.0
CD1 G:TYR421 4.8 41.7 1.0
CE2 G:TYR421 4.9 39.7 1.0
CG2 G:THR415 4.9 51.2 1.0
CA G:GLY416 5.0 41.7 1.0

Chlorine binding site 3 out of 10 in 8cwj

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Chlorine binding site 3 out of 10 in the Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl606

b:115.8
occ:1.00
 OE2 G:GLU465 3.3 43.4 1.0
O G:ASN460 3.3 45.9 1.0
NH1 G:ARG457 3.6 40.3 1.0
OE1 G:GLU465 3.7 44.5 1.0
CD G:GLU465 3.9 43.1 1.0
OG G:SER459 3.9 47.7 1.0
NH2 G:ARG457 4.0 43.0 1.0
CE G:LYS462 4.2 77.9 1.0
CZ G:ARG457 4.3 40.7 1.0
CA G:LEU461 4.3 40.8 1.0
N G:LYS462 4.3 42.4 1.0
C G:ASN460 4.3 42.5 1.0
O G:HOH719 4.4 57.2 1.0
CD G:LYS462 4.4 66.7 1.0
CG G:LYS462 4.5 56.8 1.0
NZ G:LYS462 4.5 83.7 1.0
C G:LEU461 4.6 46.1 1.0
N G:LEU461 4.7 38.9 1.0
O G:HOH753 4.9 63.8 1.0

Chlorine binding site 4 out of 10 in 8cwj

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Chlorine binding site 4 out of 10 in the Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl606

b:91.8
occ:1.00
 NH1 I:ARG355 3.5 43.0 1.0
CD2 I:PHE464 3.6 52.4 1.0
CE2 I:PHE464 3.9 56.3 1.0
CG I:PHE464 4.1 50.9 1.0
NH2 I:ARG355 4.2 43.3 1.0
CZ I:ARG355 4.3 45.2 1.0
CE2 I:TYR396 4.3 49.4 1.0
CD2 I:TYR396 4.4 49.8 1.0
CB I:PHE464 4.6 38.7 1.0
CZ I:PHE464 4.7 55.1 1.0
CZ I:TYR396 4.8 53.7 1.0
CD1 I:PHE464 4.9 49.9 1.0
CG I:TYR396 4.9 50.3 1.0

Chlorine binding site 5 out of 10 in 8cwj

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Chlorine binding site 5 out of 10 in the Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl607

b:96.0
occ:1.00
 O I:HOH729 3.7 50.1 1.0
O I:HOH733 3.8 44.7 1.0
NZ I:LYS424 3.9 55.4 1.0
CG2 I:THR415 4.0 58.4 1.0
O I:GLN414 4.3 54.8 1.0
OH G:TYR489 4.5 80.7 1.0
O I:HOH712 4.5 49.1 1.0
O I:GLY413 4.8 50.8 1.0
CE2 G:TYR489 4.8 72.8 1.0
C I:GLY413 4.8 49.5 1.0
O I:HOH740 4.9 54.0 1.0
CZ G:TYR489 4.9 75.5 1.0
C I:GLN414 5.0 51.9 1.0
CA I:GLY413 5.0 45.0 1.0

Chlorine binding site 6 out of 10 in 8cwj

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Chlorine binding site 6 out of 10 in the Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl608

b:88.6
occ:1.00
 O I:HOH721 3.0 52.2 1.0
OD1 I:ASN460 3.2 48.2 1.0
O I:GLY416 4.0 53.5 1.0
CE1 I:TYR421 4.0 39.8 1.0
CG I:ASN460 4.1 45.1 1.0
ND2 I:ASN460 4.2 44.0 1.0
CZ I:TYR421 4.2 45.1 1.0
OH I:TYR421 4.2 52.0 1.0
CA I:GLY420 4.3 44.8 1.0
CD1 I:TYR421 4.6 35.9 1.0
C I:GLY416 4.6 49.9 1.0
N I:GLY416 4.9 50.1 1.0
CE2 I:TYR421 4.9 37.2 1.0
N I:GLY420 5.0 47.4 1.0

Chlorine binding site 7 out of 10 in 8cwj

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Chlorine binding site 7 out of 10 in the Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl609

b:87.0
occ:1.00
 N I:GLY502 3.7 41.8 1.0
CA I:ASN501 4.1 39.7 1.0
CB I:TYR505 4.1 37.8 1.0
CG I:TYR505 4.1 44.1 1.0
CD1 I:TYR505 4.2 46.6 1.0
NH1 G:ARG408 4.3 76.7 1.0
O H:SER56 4.3 44.9 1.0
CB I:ASN501 4.3 41.4 1.0
CB H:SER56 4.3 49.5 1.0
CG I:ASN501 4.4 44.4 1.0
C I:ASN501 4.4 41.2 1.0
OD1 I:ASN501 4.4 46.0 1.0
CA I:GLY502 4.6 38.8 1.0
O H:ASP55 4.6 54.9 1.0
CD2 I:TYR505 4.8 42.9 1.0
O I:HOH704 4.9 46.1 1.0
CE1 I:TYR505 4.9 47.4 1.0
C H:SER56 4.9 47.2 1.0

Chlorine binding site 8 out of 10 in 8cwj

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Chlorine binding site 8 out of 10 in the Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl303

b:97.5
occ:1.00
 O J:HOH436 3.3 61.9 1.0
O J:HOH442 3.4 68.5 1.0
OG1 J:THR58 3.5 46.4 1.0
N J:THR58 3.6 34.5 1.0
O J:THR58 4.0 46.1 1.0
CA J:SER57 4.2 42.4 1.0
C J:SER57 4.4 43.1 1.0
CA J:THR58 4.4 37.0 1.0
CB J:THR58 4.5 45.6 1.0
CB J:SER57 4.6 42.5 1.0
C J:THR58 4.6 43.0 1.0
O J:HOH414 4.8 56.3 1.0
OG J:SER57 4.9 44.1 1.0
O J:HOH443 4.9 69.3 1.0
CG2 J:THR58 4.9 44.3 1.0

Chlorine binding site 9 out of 10 in 8cwj

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Chlorine binding site 9 out of 10 in the Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl302

b:105.8
occ:1.00
 N K:THR20 3.2 50.6 1.0
O K:THR20 3.6 60.8 1.0
CA K:VAL19 3.9 53.3 1.0
CA K:THR20 4.0 56.3 1.0
C K:VAL19 4.0 46.7 1.0
O K:ARG18 4.1 57.2 1.0
CB K:THR20 4.1 58.3 1.0
C K:THR20 4.2 58.4 1.0
CG1 K:VAL19 4.6 56.3 1.0
CB K:VAL19 4.8 52.8 1.0
N K:VAL19 4.9 59.0 1.0
C K:ARG18 4.9 59.3 1.0
OG1 K:THR20 4.9 63.3 1.0

Chlorine binding site 10 out of 10 in 8cwj

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Chlorine binding site 10 out of 10 in the Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Fab Arms of Antibodies 4C12-B12 and CR3022 Bound to Pangolin Receptor Binding Domain (Prbd) within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cl302

b:101.2
occ:1.00
 NH1 U:ARG72 3.5 50.5 1.0
O U:HOH419 3.8 49.5 1.0
ND2 U:ASN74 4.2 66.8 1.0
CB U:ARG72 4.4 47.2 1.0
CZ U:ARG72 4.8 51.9 1.0
CB U:ALA56 4.8 47.5 1.0
CD U:ARG72 4.8 48.3 1.0
O U:ARG72 4.8 45.6 1.0
CG U:ARG72 4.9 47.5 1.0
OD1 U:ASN74 4.9 72.5 1.0
CG U:ASN74 5.0 64.8 1.0

Reference:

D.B.Langley, D.Christ. Neutralization of Cov-2 Omicron Lineages By Affinity-Matured Class 5 Antibodies To Be Published.
Page generated: Tue Jul 30 08:18:22 2024

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