Bromine in PDB 7ben: Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs

The structure of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs, PDB code: 7ben was solved by D.Zhou, Y.Zhao, J.Ren, D.Stuart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.38 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.188, 149.794, 229.099, 90, 90, 90
R / Rfree (%)	24 / 28.2

The structure of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs also contains other interesting chemical elements:

Iodine

(I)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Bromine atom in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs (pdb code 7ben). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 14 binding sites of Bromine where determined in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs, PDB code: 7ben:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ H:Br301 b:141.3 occ:1.00 OG1 H:THR58 3.5 66.5 1.0 N H:THR58 3.9 60.2 1.0 O H:GLY56 3.9 63.9 1.0 CA H:ASN57 4.1 61.2 1.0 C H:ASN57 4.5 56.0 1.0 CB H:THR58 4.6 62.9 1.0 OD1 H:ASN57 4.6 78.4 1.0 ND2 A:ASN108 4.6 66.0 1.0 C H:GLY56 4.8 60.8 1.0 CG2 H:THR58 4.8 56.6 1.0 CA H:THR58 4.8 62.4 1.0 O A:ALA106 4.9 79.0 1.0 N H:ASN57 4.9 54.2 1.0 CB H:ASN57 5.0 64.1 1.0

Bromine binding site 2 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ H:Br302 b:78.8 occ:1.00 N L:PHE99 3.3 55.4 1.0 NH2 H:ARG44 3.4 70.0 1.0 N H:TRP47 3.4 52.9 1.0 NH1 H:ARG44 3.7 64.4 1.0 CA L:THR98 3.9 55.7 1.0 CB L:PHE99 4.0 42.6 1.0 O H:LEU45 4.0 59.1 1.0 CA H:GLU46 4.0 57.3 1.0 CZ H:ARG44 4.0 85.5 1.0 CD1 L:PHE99 4.1 48.7 1.0 CB H:TRP47 4.1 50.5 1.0 C L:THR98 4.1 48.8 1.0 CA L:PHE99 4.2 46.0 1.0 C H:GLU46 4.2 59.9 1.0 CB L:THR98 4.3 53.0 1.0 CA H:TRP47 4.3 49.0 1.0 O L:PHE99 4.4 59.7 1.0 CG L:PHE99 4.5 52.5 1.0 CG2 L:THR98 4.5 43.8 1.0 O L:HOH424 4.7 54.4 1.0 C L:PHE99 4.7 58.5 1.0 O H:TRP47 4.8 54.6 1.0 C H:LEU45 4.8 64.2 1.0 O L:TYR97 4.8 67.9 1.0 CB H:GLU46 4.9 59.4 1.0 N H:GLU46 4.9 63.0 1.0

Bromine binding site 3 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ A:Br301 b:132.0 occ:1.00 NE2 A:GLN53 2.7 77.3 1.0 O A:HOH416 3.0 58.2 1.0 OH A:TYR111 3.7 59.6 1.0 CD A:GLN53 4.0 72.6 1.0 CD2 A:TYR110 4.0 46.8 1.0 CB A:SER52 4.1 53.4 1.0 CZ A:TYR111 4.3 58.7 1.0 CG A:TYR110 4.3 54.5 1.0 CE2 A:TYR110 4.4 50.5 1.0 CE2 A:TYR111 4.6 65.1 1.0 CB A:TYR110 4.6 51.0 1.0 OE1 A:GLN53 4.6 77.9 1.0 ND2 A:ASN57 4.8 75.1 1.0 CA A:SER52 4.8 59.0 1.0 CG A:PRO33 4.8 54.8 1.0 CD1 A:TYR110 4.9 51.4 1.0 N A:GLN53 5.0 66.3 1.0

Bromine binding site 4 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ A:Br302 b:238.6 occ:1.00 NZ A:LYS58 3.7 85.5 1.0 CE A:LYS58 3.8 76.2 1.0 CD1 A:ILE51 4.0 57.2 1.0 N A:ARG72 4.0 58.8 1.0 CB A:SER71 4.0 54.4 1.0 O A:GLY55 4.0 85.0 1.0 CA A:SER71 4.0 58.4 1.0 CA A:GLY55 4.2 65.5 1.0 O A:ARG72 4.3 71.3 1.0 C A:GLY55 4.5 79.8 1.0 C A:SER71 4.6 62.7 1.0 CG A:ARG72 4.8 64.3 1.0 O A:ILE70 4.9 63.4 1.0

Bromine binding site 5 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ B:Br304 b:94.0 occ:1.00 NH1 B:ARG211 3.4 83.0 1.0 C B:HIS189 3.8 83.4 1.0 O B:HIS189 3.9 79.2 1.0 CB B:LYS190 4.1 74.9 1.0 N B:LYS190 4.1 76.0 1.0 O B:LYS188 4.1 95.5 1.0 CA B:HIS189 4.1 89.7 1.0 N B:HIS189 4.2 82.0 1.0 C B:LYS188 4.2 79.5 1.0 CA B:LYS190 4.4 80.5 1.0 O B:GLU187 4.5 84.4 1.0 CZ B:ARG211 4.5 84.1 1.0 NE B:ARG211 4.8 75.8 1.0

Bromine binding site 6 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ B:Br305 b:256.2 occ:1.00 OG B:SER30 3.4 90.8 1.0 N B:SER30 3.5 75.1 1.0 CA B:SER30 3.9 68.4 1.0 C B:GLY28 3.9 78.0 1.0 CA B:GLY28 4.0 83.6 1.0 N B:ILE29 4.1 64.1 1.0 O E:THR345 4.2 95.8 1.0 CB B:SER30 4.3 63.2 1.0 O B:GLY28 4.3 73.4 1.0 CA B:GLY68 4.4 82.3 1.0 C B:ILE29 4.5 71.6 1.0 OG1 E:THR345 4.6 127.9 1.0 O E:LEU441 4.6 62.2 1.0 CA B:ILE29 4.7 60.1 1.0 CD2 E:LEU441 5.0 83.5 1.0

Bromine binding site 7 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ D:Br301 b:78.7 occ:1.00 O D:HOH414 3.0 40.8 1.0 N D:TRP47 3.4 62.6 1.0 N F:PHE99 3.4 59.3 1.0 NH2 D:ARG44 3.5 67.3 1.0 NH1 D:ARG44 3.7 70.7 1.0 CA F:THR98 3.9 45.7 1.0 CA D:GLU46 3.9 53.8 1.0 O D:LEU45 4.0 57.9 1.0 CB D:TRP47 4.0 53.8 1.0 CZ D:ARG44 4.1 66.3 1.0 C D:GLU46 4.2 67.3 1.0 C F:THR98 4.2 51.5 1.0 CB F:PHE99 4.2 44.0 1.0 CD1 F:PHE99 4.3 50.5 1.0 CA D:TRP47 4.3 57.0 1.0 CB F:THR98 4.3 50.0 1.0 CA F:PHE99 4.3 50.9 1.0 CG2 F:THR98 4.5 46.5 1.0 O F:PHE99 4.5 53.2 1.0 O D:TRP47 4.7 68.7 1.0 CB D:GLU46 4.8 60.3 1.0 CG F:PHE99 4.8 45.5 1.0 O F:TYR97 4.8 75.2 1.0 C D:LEU45 4.8 58.1 1.0 C F:PHE99 4.9 60.9 1.0 N D:GLU46 4.9 52.5 1.0

Bromine binding site 8 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ G:Br303 b:136.5 occ:1.00 NE2 G:GLN53 2.7 67.5 1.0 O G:HOH401 3.2 53.7 1.0 OH G:TYR111 3.8 71.7 1.0 CD G:GLN53 3.8 68.2 1.0 CB G:SER52 4.0 63.3 1.0 OE1 G:GLN53 4.2 71.3 1.0 CD2 G:TYR110 4.3 45.6 1.0 ND2 G:ASN57 4.3 74.2 1.0 CZ G:TYR111 4.4 58.1 1.0 CE2 G:TYR111 4.6 55.4 1.0 CE2 G:TYR110 4.7 54.8 1.0 CG G:TYR110 4.7 58.9 1.0 CA G:SER52 4.8 60.5 1.0 N G:GLN53 4.9 60.3 1.0

Bromine binding site 9 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ G:Br304 b:112.0 occ:1.00 N G:ARG72 3.3 47.2 1.0 O G:ARG72 3.4 69.4 1.0 CB G:SER71 3.6 52.4 1.0 CA G:SER71 3.8 46.6 1.0 C G:SER71 4.1 49.7 1.0 CD1 G:ILE51 4.1 58.9 1.0 C G:ARG72 4.3 60.5 1.0 CA G:ARG72 4.3 53.3 1.0 CG G:ARG72 4.4 52.1 1.0 NZ G:LYS58 4.6 79.9 1.0 CA G:GLY55 4.6 57.8 1.0 CE G:LYS58 4.7 78.8 1.0 OG G:SER71 4.8 62.5 1.0 O G:GLY55 4.8 75.5 1.0 CB G:ARG72 4.9 58.7 1.0

Bromine binding site 10 out of 14 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in A Ternary Complex with Covox-253 and Covox-75 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ G:Br305 b:141.5 occ:1.00 O G:HOH433 2.7 55.0 1.0 O G:HOH402 3.3 67.0 1.0 NZ G:LYS223 3.4 80.5 1.0 CE G:LYS223 3.9 73.6 1.0 CG1 G:VAL221 4.0 47.7 1.0 O G:VAL135 4.0 58.3 1.0 N G:VAL135 4.2 43.7 1.0 CB G:VAL135 4.8 55.7 1.0 C G:VAL135 4.8 39.1 1.0 CA G:VAL135 4.9 48.6 1.0

W.Dejnirattisai, D.Zhou, H.M.Ginn, H.M.Duyvesteyn, P.Supasa, J.B.Case, Y.Zhao, T.S.Walter, A.J.Mentzer, C.Liu, B.Wang, G.C.Paesen, J.Slon-Campos, C.Lopez-Camacho, N.M.Kafai, A.L.Bailey, R.E.Chen, B.Ying, C.Thompson, J.Bolton, A.Fyfe, S.Gupta, T.K.Tan, J.Gilbert-Jaramillo, W.James, M.Knight, M.W.Carroll, D.Skelly, C.Dold, Y.Peng, R.Levin, T.Dong, A.J.Pollard, J.C.Knight, P.Klenerman, N.Temperton, D.R.Hall, M.A.Williams, N.G.Paterson, F.K.Bertram, C.A.Seibert, D.K.Clare, A.Howe, J.Raedecke, Y.Song, A.R.Townsend, K.Y.A.Huang, E.E.Fry, J.Mongkolsapaya, M.S.Diamond, J.Ren, D.I.Stuart, G.R.Screaton. The Antigenic Anatomy of Sars-Cov-2 Receptor Binding Domain Cell(Cambridge,Mass.) 2021.
ISSN: ISSN 0092-8674
DOI: 10.1016/J.CELL.2021.02.032