Chlorine in PDB 7kkj: Structure of Anti-Sars-Cov-2 Spike Nanobody MNB6

The structure of Structure of Anti-Sars-Cov-2 Spike Nanobody MNB6, PDB code: 7kkj was solved by M.S.Schoof, B.F.Faust, R.A.Saunders, S.Sangwan, V.Rezelj, N.Hoppe, M.Boone, C.B.Billesboelle, C.Puchades, C.M.Azumaya, H.T.Kratochvil, M.Zimanyi, I.Desphande, J.Liang, S.Dickinson, H.C.Nguyen, C.M.Chio, G.E.Merz, M.C.Thompson, D.Diwanji, K.Schaefer, A.A.Anand, N.Dobzinski, B.S.Zha, C.R.Simoneau, K.Leon, K.M.White, U.S.Chio, M.Gupta, M.Jin, F.Li, Y.Liu, K.Zhang, D.Bulkley, M.Sun, A.M.Smith, A.N.Rizo, F.Moss, A.F.Brilot, S.Pourmal, R.Trenker, T.Pospiech, S.Gupta, B.Barsi-Rhyne, V.Belyy, A.W.Barile-Hill, S.Nock, Y.Liu, N.J.Krogan, C.Y.Ralston, D.L.Swaney, A.Garcia-Sastre, M.Ott, M.Vignuzzi, P.Walter, A.Manglik, Qcrg Structuralbiology Consortium, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.11 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.569, 71.253, 46.430, 90.00, 114.93, 90.00
R / Rfree (%)	21.2 / 24.8

The binding sites of Chlorine atom in the Structure of Anti-Sars-Cov-2 Spike Nanobody MNB6 (pdb code 7kkj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Structure of Anti-Sars-Cov-2 Spike Nanobody MNB6, PDB code: 7kkj:

Chlorine binding site 1 out of 1 in the Structure of Anti-Sars-Cov-2 Spike Nanobody MNB6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Anti-Sars-Cov-2 Spike Nanobody MNB6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:37.9 occ:1.00 H A:ARG54 2.5 37.7 1.0 H A:ARG53 2.7 37.4 1.0 O C:HOH343 2.8 38.0 1.0 HB A:THR52 3.0 37.1 1.0 HB3 A:ARG53 3.0 41.9 1.0 O C:HOH309 3.1 25.8 1.0 HA C:THR52 3.2 39.1 1.0 N A:ARG53 3.3 31.2 1.0 HG22 C:THR52 3.3 44.6 1.0 N A:ARG54 3.4 31.4 1.0 HB3 A:ARG54 3.5 35.8 1.0 HH C:TYR59 3.6 32.1 1.0 HB2 A:ARG54 3.7 35.8 1.0 CB A:ARG53 3.7 34.9 1.0 HA A:THR52 3.8 33.7 1.0 HB1 C:ALA33 3.8 35.4 1.0 HB2 A:ARG53 3.8 41.9 1.0 CB A:THR52 3.9 31.0 1.0 CA A:ARG53 3.9 33.7 1.0 CB A:ARG54 4.0 29.8 1.0 HB C:THR52 4.0 45.7 1.0 HE2 C:TYR59 4.0 32.8 1.0 CA C:THR52 4.1 32.6 1.0 HB2 A:ALA33 4.1 36.2 1.0 H C:ARG53 4.1 48.8 1.0 CA A:THR52 4.1 28.1 1.0 C A:ARG53 4.2 35.7 1.0 HB2 C:ALA33 4.2 35.4 1.0 CG2 C:THR52 4.2 37.1 1.0 C A:THR52 4.2 31.2 1.0 OH C:TYR59 4.3 26.8 1.0 CA A:ARG54 4.3 32.5 1.0 CB C:THR52 4.3 38.1 1.0 CB C:ALA33 4.4 29.5 1.0 HE A:ARG54 4.4 36.1 1.0 HG22 A:THR52 4.5 37.1 1.0 HG21 C:THR52 4.6 44.6 1.0 O C:ILE51 4.6 28.0 1.0 CE2 C:TYR59 4.6 27.3 1.0 CG2 A:THR52 4.7 30.9 1.0 HB3 C:ALA33 4.8 35.4 1.0 OG1 A:THR52 4.8 29.6 1.0 N C:ARG53 4.8 40.7 1.0 HG21 A:THR52 4.8 37.1 1.0 CZ C:TYR59 4.8 26.2 1.0 HA A:ARG53 4.8 40.4 1.0 HG23 C:THR52 4.9 44.6 1.0 N C:THR52 4.9 32.6 1.0 HE A:ARG53 4.9 68.4 1.0 HG1 A:THR52 4.9 35.5 1.0 CB A:ALA33 5.0 30.2 1.0 C C:THR52 5.0 37.9 1.0

M.Schoof, B.Faust, R.A.Saunders, S.Sangwan, V.Rezelj, N.Hoppe, M.Boone, C.B.Billesbolle, C.Puchades, C.M.Azumaya, H.T.Kratochvil, M.Zimanyi, I.Deshpande, J.Liang, S.Dickinson, H.C.Nguyen, C.M.Chio, G.E.Merz, M.C.Thompson, D.Diwanji, K.Schaefer, A.A.Anand, N.Dobzinski, B.S.Zha, C.R.Simoneau, K.Leon, K.M.White, U.S.Chio, M.Gupta, M.Jin, F.Li, Y.Liu, K.Zhang, D.Bulkley, M.Sun, A.M.Smith, A.N.Rizo, F.Moss, A.F.Brilot, S.Pourmal, R.Trenker, T.Pospiech, S.Gupta, B.Barsi-Rhyne, V.Belyy, A.W.Barile-Hill, S.Nock, Y.Liu, N.J.Krogan, C.Y.Ralston, D.L.Swaney, A.Garcia-Sastre, M.Ott, M.Vignuzzi, P.Walter, A.Manglik. An Ultrapotent Synthetic Nanobody Neutralizes Sars-Cov-2 By Stabilizing Inactive Spike. Science 2020.
ISSN: ESSN 1095-9203
PubMed: 33154106
DOI: 10.1126/SCIENCE.ABE3255