Zinc in PDB 8ef0: Crystal Structure of A Nhp Anti-Zikv Neutralizing Antibody RHMZ104-D

The structure of Crystal Structure of A Nhp Anti-Zikv Neutralizing Antibody RHMZ104-D, PDB code: 8ef0 was solved by R.S.Sankhala, M.G.Joyce, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.95 / 2.55
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.728, 71.728, 159.991, 90, 90, 120
R / Rfree (%)	18.5 / 24

The binding sites of Zinc atom in the Crystal Structure of A Nhp Anti-Zikv Neutralizing Antibody RHMZ104-D (pdb code 8ef0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of A Nhp Anti-Zikv Neutralizing Antibody RHMZ104-D, PDB code: 8ef0:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of A Nhp Anti-Zikv Neutralizing Antibody RHMZ104-D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Nhp Anti-Zikv Neutralizing Antibody RHMZ104-D within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:67.3 occ:1.00 NE2 H:HIS164 2.1 49.8 1.0 O L:HOH404 2.2 22.6 1.0 O L:HOH450 2.2 21.7 1.0 OD2 L:ASP138 2.4 65.6 1.0 CE1 H:HIS164 2.8 50.3 1.0 O H:HOH420 3.1 17.8 1.0 CD2 H:HIS164 3.3 41.9 1.0 CG L:ASP138 3.3 57.4 1.0 OD1 L:ASP138 3.6 63.1 1.0 ND1 H:HIS164 4.0 52.5 1.0 OG L:SER137 4.2 40.9 1.0 CG H:HIS164 4.3 44.3 1.0 O L:HOH453 4.6 36.9 1.0 CB L:SER137 4.6 24.9 1.0 CB L:ASP138 4.7 42.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of A Nhp Anti-Zikv Neutralizing Antibody RHMZ104-D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Nhp Anti-Zikv Neutralizing Antibody RHMZ104-D within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn301 b:37.9 occ:1.00 ND1 L:HIS197 2.1 36.5 1.0 O L:HOH451 2.2 27.1 1.0 O L:HOH458 2.6 28.1 1.0 CE1 L:HIS197 3.0 25.7 1.0 CG L:HIS197 3.2 29.4 1.0 O L:HIS197 3.4 33.1 1.0 CB L:HIS197 3.6 23.3 1.0 C L:HIS197 4.1 29.3 1.0 CA L:ALA112 4.1 42.1 1.0 NE2 L:HIS197 4.1 28.1 1.0 CD2 L:HIS197 4.3 31.1 1.0 CD L:PRO113 4.3 28.9 1.0 CB L:ALA112 4.4 22.1 1.0 CA L:HIS197 4.5 23.1 1.0 O L:ALA111 4.5 36.5 1.0 CB L:SER200 4.6 34.2 1.0 N L:ALA112 4.7 35.2 1.0 OE1 L:GLU198 4.7 78.4 1.0 CB L:GLU198 4.8 35.7 1.0 C L:ALA111 4.8 35.8 1.0 OG L:SER200 5.0 34.4 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of A Nhp Anti-Zikv Neutralizing Antibody RHMZ104-D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Nhp Anti-Zikv Neutralizing Antibody RHMZ104-D within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn302 b:105.2 occ:1.00 NE2 L:HIS188 1.9 105.3 1.0 CE1 L:HIS188 2.8 92.9 1.0 O L:HOH456 2.9 36.4 1.0 CD2 L:HIS188 2.9 91.4 1.0 ND1 L:HIS188 3.9 90.9 1.0 CG L:HIS188 4.0 83.9 1.0 CB L:ALA150 4.4 42.9 1.0 O L:ALA150 4.7 58.5 1.0

R.S.Sankhala, V.Dussupt, G.Donofrio, G.D.Gromowski, R.A.De La Barrera, R.A.Larocca, L.Mendez-Rivera, A.Lee, M.Choe, W.Zaky, G.Mantus, J.L.Jensen, W.H.Chen, N.Gohain, H.Bai, M.K.Mccracken, R.D.Mason, D.Leggat, B.M.Slike, U.Tran, N.Jian, P.Abbink, R.Peterson, E.A.Mendes, R.Freitas De Oliveira Franca, G.A.Calvet, A.M.Bispo De Filippis, A.Mcdermott, M.Roederer, M.Hernandez, A.Albertus, E.Davidson, B.J.Doranz, M.Rolland, M.L.Robb, R.M.Lynch, D.H.Barouch, R.G.Jarman, S.J.Thomas, K.Modjarrad, N.L.Michael, S.J.Krebs, M.G.Joyce. Zika-Specific Neutralizing Antibodies Targeting Inter-Dimer Envelope Epitopes. Cell Rep V. 42 12942 2023.
ISSN: ESSN 2211-1247
PubMed: 37561630
DOI: 10.1016/J.CELREP.2023.112942