Chlorine in PDB 7u0n: Crystal Structure of Chimeric Omicron Rbd (Strain Ba.1) Complexed with Human ACE2

Enzymatic activity of Crystal Structure of Chimeric Omicron Rbd (Strain Ba.1) Complexed with Human ACE2

All present enzymatic activity of Crystal Structure of Chimeric Omicron Rbd (Strain Ba.1) Complexed with Human ACE2:
3.4.17.23;

Protein crystallography data

The structure of Crystal Structure of Chimeric Omicron Rbd (Strain Ba.1) Complexed with Human ACE2, PDB code: 7u0n was solved by Q.Geng, K.Shi, G.Ye, W.Zhang, H.Aihara, F.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.11 / 2.61
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.13, 120.179, 113.325, 90, 92.44, 90
R / Rfree (%) 18.8 / 23.5

Other elements in 7u0n:

The structure of Crystal Structure of Chimeric Omicron Rbd (Strain Ba.1) Complexed with Human ACE2 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Magnesium (Mg) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Chimeric Omicron Rbd (Strain Ba.1) Complexed with Human ACE2 (pdb code 7u0n). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Chimeric Omicron Rbd (Strain Ba.1) Complexed with Human ACE2, PDB code: 7u0n:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 7u0n

Go back to Chlorine Binding Sites List in 7u0n
Chlorine binding site 1 out of 5 in the Crystal Structure of Chimeric Omicron Rbd (Strain Ba.1) Complexed with Human ACE2


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 Chimeric Omicron Rbd (Strain Ba.1) Complexed with Human ACE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl703

b:63.7
occ:1.00
 NE A:ARG169 3.1 58.4 1.0
NH2 A:ARG169 3.3 79.4 1.0
CZ A:ARG169 3.6 60.8 1.0
CB A:ASP499 3.7 66.3 1.0
CZ2 A:TRP478 3.7 66.7 1.0
NE1 A:TRP477 3.7 59.8 1.0
CH2 A:TRP478 3.8 59.3 1.0
CZ2 A:TRP477 4.0 67.7 1.0
CE2 A:TRP477 4.2 60.4 1.0
CD A:ARG169 4.2 71.3 1.0
CE A:LYS481 4.3 63.4 1.0
O A:ASP499 4.3 65.0 1.0
C A:ASP499 4.5 63.2 1.0
NZ A:LYS481 4.5 70.8 1.0
CZ2 A:TRP165 4.5 63.3 1.0
CG A:ASP499 4.6 73.6 1.0
CA A:ASP499 4.6 68.5 1.0
CE2 A:TRP478 4.7 61.6 1.0
OD2 A:ASP499 4.8 70.8 1.0
CZ3 A:TRP478 4.8 66.6 1.0
CD1 A:TRP271 4.9 65.2 1.0
NH1 A:ARG169 4.9 56.0 1.0
CD1 A:TRP477 4.9 70.8 1.0
OG A:SER502 5.0 79.9 1.0
NE1 A:TRP165 5.0 60.7 1.0

Chlorine binding site 2 out of 5 in 7u0n

Go back to Chlorine Binding Sites List in 7u0n
Chlorine binding site 2 out of 5 in the Crystal Structure of Chimeric Omicron Rbd (Strain Ba.1) Complexed with Human ACE2


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 Chimeric Omicron Rbd (Strain Ba.1) Complexed with Human ACE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl707

b:109.5
occ:1.00
 O A:TRP606 3.7 95.9 1.0
NE1 A:TRP606 4.1 71.4 1.0
CE2 A:TRP606 4.3 66.6 1.0
CD1 A:TRP606 4.4 75.8 1.0
N A:TRP606 4.5 77.5 1.0
CD2 A:TRP606 4.7 71.0 1.0
CZ2 A:TRP606 4.7 74.4 1.0
CG A:TRP606 4.7 64.7 1.0
C A:TRP606 4.8 82.6 1.0

Chlorine binding site 3 out of 5 in 7u0n

Go back to Chlorine Binding Sites List in 7u0n
Chlorine binding site 3 out of 5 in the Crystal Structure of Chimeric Omicron Rbd (Strain Ba.1) Complexed with Human ACE2


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 Chimeric Omicron Rbd (Strain Ba.1) Complexed with Human ACE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl703

b:101.3
occ:1.00
 NH2 B:ARG169 3.1 79.3 1.0
NE B:ARG169 3.3 82.5 1.0
CB B:ASP499 3.5 79.2 1.0
NE1 B:TRP477 3.6 83.0 1.0
CZ B:ARG169 3.7 79.4 1.0
CZ2 B:TRP477 3.8 89.1 1.0
CZ2 B:TRP478 4.0 90.4 1.0
CE2 B:TRP477 4.0 75.1 1.0
O B:ASP499 4.1 97.2 1.0
CH2 B:TRP478 4.1 75.0 1.0
C B:ASP499 4.2 97.2 1.0
CE B:LYS481 4.3 79.2 1.0
CA B:ASP499 4.4 92.9 1.0
CD B:ARG169 4.5 94.4 1.0
CG B:ASP499 4.6 94.7 1.0
NZ B:LYS481 4.6 88.4 1.0
N B:PRO500 4.7 94.6 1.0
OD2 B:ASP499 4.8 79.0 1.0
CZ2 B:TRP165 4.8 68.4 1.0
CD1 B:TRP477 4.8 93.2 1.0
OG B:SER502 4.8 102.7 1.0
CE2 B:TRP478 4.9 85.9 1.0
NH1 B:ARG169 5.0 77.6 1.0

Chlorine binding site 4 out of 5 in 7u0n

Go back to Chlorine Binding Sites List in 7u0n
Chlorine binding site 4 out of 5 in the Crystal Structure of Chimeric Omicron Rbd (Strain Ba.1) Complexed with Human ACE2


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 Chimeric Omicron Rbd (Strain Ba.1) Complexed with Human ACE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl708

b:88.5
occ:1.00
 ND2 B:ASN290 3.1 67.3 1.0
CE2 B:TYR279 4.0 62.4 1.0
CG B:ASN290 4.0 61.1 1.0
CD2 B:TYR279 4.2 57.3 1.0
OD1 B:ASN290 4.3 79.3 1.0
CA B:SER280 4.5 56.6 1.0
CB B:SER280 4.7 61.6 1.0

Chlorine binding site 5 out of 5 in 7u0n

Go back to Chlorine Binding Sites List in 7u0n
Chlorine binding site 5 out of 5 in the Crystal Structure of Chimeric Omicron Rbd (Strain Ba.1) Complexed with Human ACE2


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 Chimeric Omicron Rbd (Strain Ba.1) Complexed with Human ACE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl602

b:76.2
occ:1.00
 N F:VAL503 2.9 86.1 1.0
CA F:GLY502 3.4 84.2 1.0
CB B:THR324 3.4 78.1 1.0
C F:GLY502 3.6 83.5 1.0
CG1 F:VAL503 3.7 91.7 1.0
CG2 B:THR324 3.8 81.0 1.0
CB F:VAL503 3.9 65.0 1.0
CA F:VAL503 4.0 61.0 1.0
N B:GLN325 4.0 69.4 1.0
OG1 B:THR324 4.2 78.4 1.0
CA B:THR324 4.2 69.0 1.0
N B:GLY326 4.3 70.7 1.0
O B:GLY354 4.4 84.0 1.0
C B:THR324 4.6 67.6 1.0
N F:GLY502 4.7 80.9 1.0
CB B:GLN325 4.8 86.9 1.0
O F:GLY502 4.8 86.8 1.0
CA B:GLN325 4.9 67.6 1.0
O F:TYR501 4.9 93.9 1.0

Reference:

Q.Geng, K.Shi, G.Ye, W.Zhang, H.Aihara, F.Li. Structural Basis For Human Receptor Recognition By Sars-Cov-2 Omicron Variant Ba.1. J.Virol. V. 96 24922 2022.
ISSN: ESSN 1098-5514
PubMed: 35343765
DOI: 10.1128/JVI.00249-22
Page generated: Tue Jul 30 04:54:40 2024

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