Bromine in PDB 7xby: The Crystal Structure of Sars-Cov-2 Omicron Ba.1 Variant Rbd in Complex with Equine ACE2

Protein crystallography data

The structure of The Crystal Structure of Sars-Cov-2 Omicron Ba.1 Variant Rbd in Complex with Equine ACE2, PDB code: 7xby was solved by Z.P.Xu, K.F.Liu, P.Han, J.X.Qi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.90 / 2.85
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.975, 113.975, 152.738, 90, 90, 120
R / Rfree (%) 22.8 / 26.3

Other elements in 7xby:

The structure of The Crystal Structure of Sars-Cov-2 Omicron Ba.1 Variant Rbd in Complex with Equine ACE2 also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the The Crystal Structure of Sars-Cov-2 Omicron Ba.1 Variant Rbd in Complex with Equine ACE2 (pdb code 7xby). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the The Crystal Structure of Sars-Cov-2 Omicron Ba.1 Variant Rbd in Complex with Equine ACE2, PDB code: 7xby:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in 7xby

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Bromine binding site 1 out of 6 in the The Crystal Structure of Sars-Cov-2 Omicron Ba.1 Variant Rbd in Complex with Equine ACE2


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of The Crystal Structure of Sars-Cov-2 Omicron Ba.1 Variant Rbd in Complex with Equine ACE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br902

b:44.5
occ:1.00
 CG2 A:ILE223 3.8 42.1 1.0
CG A:MET462 3.9 46.4 1.0
NZ A:LYS458 4.0 45.0 1.0
CB A:TRP461 4.1 47.4 1.0
CD1 A:ILE223 4.1 46.6 1.0
NZ A:LYS465 4.1 58.0 1.0
CE3 A:TRP461 4.3 46.5 1.0
CG A:LYS458 4.5 44.0 1.0
O A:LYS458 4.6 50.4 1.0
CG1 A:ILE223 4.7 47.0 1.0
N A:MET462 4.7 49.0 1.0
CE A:LYS465 4.7 59.6 1.0
C A:TRP461 4.9 52.4 1.0
CB A:ILE223 4.9 46.9 1.0
SD A:MET462 4.9 50.7 1.0
CG A:TRP461 4.9 45.6 1.0
OE2 A:GLU227 4.9 44.1 1.0
CD2 A:TRP461 4.9 47.4 1.0

Bromine binding site 2 out of 6 in 7xby

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Bromine binding site 2 out of 6 in the The Crystal Structure of Sars-Cov-2 Omicron Ba.1 Variant Rbd in Complex with Equine ACE2


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of The Crystal Structure of Sars-Cov-2 Omicron Ba.1 Variant Rbd in Complex with Equine ACE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br903

b:39.2
occ:1.00
 CG A:PRO346 3.2 48.7 1.0
CD A:PRO346 3.4 50.9 1.0
N A:PRO346 3.5 49.8 1.0
N A:CYS361 3.7 52.8 1.0
C A:HIS345 3.9 59.1 1.0
CB A:PRO346 4.0 39.4 1.0
CA A:PRO346 4.0 44.0 1.0
N A:HIS345 4.1 70.0 1.0
C A:CYS344 4.1 65.1 1.0
CA A:HIS345 4.2 63.2 1.0
O A:CYS344 4.2 59.6 1.0
CA A:MET360 4.3 48.5 1.0
CB A:CYS361 4.5 54.4 1.0
CA A:CYS361 4.5 53.8 1.0
C A:MET360 4.5 51.8 1.0
CB A:CYS344 4.5 65.6 1.0
O A:CYS361 4.5 53.5 1.0
CB A:MET360 4.6 45.9 1.0
O A:HIS345 4.7 57.5 1.0
C A:CYS361 4.7 52.0 1.0
CA A:CYS344 4.7 67.2 1.0
CG A:MET360 4.7 46.3 1.0

Bromine binding site 3 out of 6 in 7xby

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Bromine binding site 3 out of 6 in the The Crystal Structure of Sars-Cov-2 Omicron Ba.1 Variant Rbd in Complex with Equine ACE2


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of The Crystal Structure of Sars-Cov-2 Omicron Ba.1 Variant Rbd in Complex with Equine ACE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br904

b:60.0
occ:1.00
 CD1 A:LEU539 3.9 37.3 1.0
CB A:CYS530 4.0 40.5 1.0
O A:HIS535 4.1 51.1 1.0
CG A:GLN531 4.3 43.5 1.0
ND1 A:HIS535 4.4 43.3 1.0
N A:GLN531 4.6 39.0 1.0
C A:CYS530 4.6 43.1 1.0
CB A:LEU539 4.6 36.4 1.0
O A:GLY537 4.6 49.7 1.0
CA A:LEU539 4.7 37.8 1.0
O A:GLU527 4.7 42.9 1.0
CG A:GLU527 4.7 42.8 1.0
CG A:LEU539 4.9 38.0 1.0
O A:CYS530 4.9 45.6 1.0
ND2 A:ASN586 4.9 52.6 1.0
CA A:GLN531 5.0 42.3 1.0
CA A:CYS530 5.0 43.1 1.0

Bromine binding site 4 out of 6 in 7xby

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Bromine binding site 4 out of 6 in the The Crystal Structure of Sars-Cov-2 Omicron Ba.1 Variant Rbd in Complex with Equine ACE2


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of The Crystal Structure of Sars-Cov-2 Omicron Ba.1 Variant Rbd in Complex with Equine ACE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br905

b:65.3
occ:1.00
 NE A:ARG169 3.2 57.6 1.0
NH2 A:ARG169 3.4 57.5 1.0
NE1 A:TRP477 3.6 47.2 1.0
CZ A:ARG169 3.7 55.3 1.0
CH2 A:TRP478 3.8 45.4 1.0
CB A:ASP499 3.9 54.8 1.0
CZ2 A:TRP477 3.9 43.6 1.0
CE A:LYS481 3.9 39.1 1.0
CZ2 A:TRP478 3.9 48.0 1.0
CE2 A:TRP477 4.1 46.2 1.0
CD A:ARG169 4.3 54.5 1.0
O A:ASP499 4.4 49.4 1.0
CZ2 A:TRP165 4.4 43.0 1.0
CD A:LYS481 4.6 37.8 1.0
C A:ASP499 4.6 50.7 1.0
CG A:ASP499 4.7 56.2 1.0
CZ3 A:TRP478 4.8 43.5 1.0
CA A:ASP499 4.8 53.9 1.0
CD1 A:TRP477 4.9 47.1 1.0
OD2 A:ASP499 4.9 54.5 1.0
CE2 A:TRP478 5.0 46.4 1.0

Bromine binding site 5 out of 6 in 7xby

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Bromine binding site 5 out of 6 in the The Crystal Structure of Sars-Cov-2 Omicron Ba.1 Variant Rbd in Complex with Equine ACE2


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of The Crystal Structure of Sars-Cov-2 Omicron Ba.1 Variant Rbd in Complex with Equine ACE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br906

b:92.7
occ:1.00
 N A:LEU143 3.4 76.5 1.0
CD2 A:LEU142 3.5 66.6 1.0
N A:GLY147 3.6 80.2 1.0
CD A:PRO146 3.6 84.7 1.0
CA A:GLY147 3.8 78.4 1.0
CA A:LEU142 3.9 71.0 1.0
CB A:LEU142 4.1 62.6 1.0
C A:LEU142 4.2 69.1 1.0
CB A:LEU143 4.2 76.4 1.0
CG A:PRO146 4.3 87.4 1.0
N A:PRO146 4.3 81.2 1.0
CA A:LEU143 4.3 73.8 1.0
O A:LEU143 4.4 74.4 1.0
CG A:LEU142 4.4 64.7 1.0
C A:PRO146 4.6 75.7 1.0
O A:GLU145 4.7 77.8 1.0
C A:LEU143 4.7 72.0 1.0
C A:GLU145 4.8 78.6 1.0
CG A:LEU143 4.9 77.1 1.0
O A:CYS141 5.0 80.3 1.0
CA A:PRO146 5.0 76.4 1.0

Bromine binding site 6 out of 6 in 7xby

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Bromine binding site 6 out of 6 in the The Crystal Structure of Sars-Cov-2 Omicron Ba.1 Variant Rbd in Complex with Equine ACE2


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of The Crystal Structure of Sars-Cov-2 Omicron Ba.1 Variant Rbd in Complex with Equine ACE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br602

b:71.9
occ:1.00
 O B:TYR369 3.0 88.2 1.0
C B:TYR369 3.9 94.1 1.0
CB B:ASN370 4.7 91.8 1.0
N B:ASN370 4.7 90.4 1.0
CA B:TYR369 4.8 101.6 1.0
ND2 B:ASN370 4.8 94.9 1.0
CA B:ASN370 5.0 87.0 1.0

Reference:

Z.Xu, X.Kang, P.Han, P.Du, L.Li, A.Zheng, C.Deng, J.Qi, X.Zhao, Q.Wang, K.Liu, G.F.Gao. Binding and Structural Basis of Equine ACE2 to Rbds From Sars-Cov, Sars-Cov-2 and Related Coronaviruses. Nat Commun V. 13 3547 2022.
ISSN: ESSN 2041-1723
PubMed: 35729237
DOI: 10.1038/S41467-022-31276-6
Page generated: Thu Jul 11 04:42:29 2024

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