Zinc in PDB 6b6z: Crystal Structure of the Apo Antibody Fragment (Fab) Raised Against C- Terminal Domain of Ebola Nucleoprotein (Ebov, Tafv, Bdbv Strains)

The structure of Crystal Structure of the Apo Antibody Fragment (Fab) Raised Against C- Terminal Domain of Ebola Nucleoprotein (Ebov, Tafv, Bdbv Strains), PDB code: 6b6z was solved by M.J.Radwanska, U.Derewenda, A.A.Kossiakoff, Z.S.Derewenda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 2.11
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	74.621, 74.621, 323.695, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 25.8

The binding sites of Zinc atom in the Crystal Structure of the Apo Antibody Fragment (Fab) Raised Against C- Terminal Domain of Ebola Nucleoprotein (Ebov, Tafv, Bdbv Strains) (pdb code 6b6z). 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 the Apo Antibody Fragment (Fab) Raised Against C- Terminal Domain of Ebola Nucleoprotein (Ebov, Tafv, Bdbv Strains), PDB code: 6b6z:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Apo Antibody Fragment (Fab) Raised Against C- Terminal Domain of Ebola Nucleoprotein (Ebov, Tafv, Bdbv Strains)


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 the Apo Antibody Fragment (Fab) Raised Against C- Terminal Domain of Ebola Nucleoprotein (Ebov, Tafv, Bdbv Strains) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:0.9 occ:1.00 NE2 B:HIS178 2.1 40.1 1.0 OD1 A:ASN139 2.1 43.4 1.0 O B:HOH333 2.4 27.6 1.0 OD1 A:ASN138 2.5 53.9 1.0 HD21 A:ASN139 2.9 64.1 1.0 HD21 A:ASN138 2.9 54.4 1.0 CD2 B:HIS178 3.0 28.3 1.0 CG A:ASN139 3.0 33.9 1.0 HD2 B:HIS178 3.1 34.0 1.0 CE1 B:HIS178 3.1 31.9 1.0 ND2 A:ASN139 3.3 53.5 1.0 CG A:ASN138 3.3 43.0 1.0 HE1 B:HIS178 3.4 38.3 1.0 ND2 A:ASN138 3.4 45.3 1.0 O A:HOH402 3.5 39.2 1.0 HG A:SER175 3.6 27.6 1.0 HG1 B:THR197 3.9 49.0 1.0 HA2 B:GLY176 3.9 53.3 1.0 HD22 A:ASN139 4.1 64.1 1.0 CG B:HIS178 4.2 36.3 1.0 ND1 B:HIS178 4.2 31.6 1.0 HD22 A:ASN138 4.3 54.4 1.0 OG A:SER175 4.3 23.0 1.0 OG1 B:THR197 4.3 40.8 1.0 CB A:ASN139 4.4 29.4 1.0 H A:ASN139 4.4 23.4 1.0 O B:GLY176 4.4 23.1 1.0 HB2 A:ASN139 4.6 35.2 1.0 N A:ASN139 4.7 19.5 1.0 HG21 B:THR197 4.7 38.0 1.0 HG23 B:THR197 4.7 38.0 1.0 CB A:ASN138 4.7 25.3 1.0 CA B:GLY176 4.7 44.4 1.0 OD2 A:ASP168 4.8 62.1 1.0 O A:HOH482 4.8 28.9 1.0 C B:GLY176 4.8 24.1 1.0 HA A:ASN138 4.9 27.8 1.0 HA A:ASN139 5.0 28.6 1.0 HD1 B:HIS178 5.0 38.0 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Apo Antibody Fragment (Fab) Raised Against C- Terminal Domain of Ebola Nucleoprotein (Ebov, Tafv, Bdbv Strains)


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 the Apo Antibody Fragment (Fab) Raised Against C- Terminal Domain of Ebola Nucleoprotein (Ebov, Tafv, Bdbv Strains) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:29.8 occ:1.00 OD1 C:ASN138 2.0 25.4 1.0 NE2 D:HIS178 2.1 16.7 1.0 O C:HOH525 2.2 33.5 1.0 O D:HOH321 2.3 17.2 0.9 O C:HOH512 2.5 20.7 1.0 CD2 D:HIS178 2.8 20.5 1.0 HD2 D:HIS178 2.9 24.6 1.0 HD21 C:ASN138 3.0 34.4 1.0 CG C:ASN138 3.0 19.0 1.0 HG C:SER175 3.1 23.4 1.0 CE1 D:HIS178 3.2 26.2 1.0 ND2 C:ASN138 3.4 28.7 1.0 HE1 D:HIS178 3.5 31.4 1.0 HB2 C:ASN139 3.7 34.1 1.0 OG C:SER175 3.8 19.5 1.0 HG1 D:THR197 3.8 30.7 1.0 O C:HOH421 3.9 32.8 1.0 HA2 D:GLY176 4.0 29.3 1.0 H C:ASN139 4.1 23.8 1.0 CG D:HIS178 4.1 19.2 1.0 O D:GLY176 4.2 23.8 1.0 ND1 D:HIS178 4.2 21.7 1.0 HD22 C:ASN138 4.2 34.4 1.0 OG1 D:THR197 4.3 25.6 1.0 N C:ASN139 4.4 19.9 1.0 CB C:ASN138 4.4 19.2 1.0 O D:HOH418 4.4 46.6 1.0 HA C:ASN138 4.5 23.8 1.0 CB C:ASN139 4.6 28.5 1.0 O C:HOH510 4.6 18.6 0.8 HA C:ASN139 4.6 27.4 1.0 HB2 C:ASN138 4.7 23.0 1.0 HG21 D:THR197 4.8 27.9 1.0 C D:GLY176 4.8 23.4 1.0 CA D:GLY176 4.8 24.4 1.0 HG23 D:THR197 4.8 27.9 1.0 CA C:ASN139 4.8 22.8 1.0 CA C:ASN138 4.9 19.8 1.0 C C:ASN138 5.0 18.6 1.0 CB C:SER175 5.0 22.5 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Apo Antibody Fragment (Fab) Raised Against C- Terminal Domain of Ebola Nucleoprotein (Ebov, Tafv, Bdbv Strains)


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 the Apo Antibody Fragment (Fab) Raised Against C- Terminal Domain of Ebola Nucleoprotein (Ebov, Tafv, Bdbv Strains) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:91.1 occ:1.00 O C:HOH505 2.1 70.8 1.0 NE2 C:HIS190 2.1 52.3 1.0 OD1 C:ASP186 2.2 70.2 1.0 CE1 C:HIS190 2.9 38.0 1.0 HE1 C:HIS190 3.0 45.5 1.0 CG C:ASP186 3.1 67.0 1.0 CD2 C:HIS190 3.2 36.2 1.0 OD2 C:ASP186 3.3 68.2 1.0 HD2 C:HIS190 3.4 43.5 1.0 ND1 C:HIS190 4.1 33.4 1.0 CG C:HIS190 4.3 32.1 1.0 HB2 C:LYS189 4.4 62.6 1.0 CB C:ASP186 4.4 56.2 1.0 HA C:ASP186 4.5 55.5 1.0 O C:ASP186 4.5 35.1 1.0 HD2 C:LYS189 4.6 63.9 1.0 HB2 C:ASP186 4.6 67.5 1.0 HB3 A:SER68 4.7 82.7 1.0 HD1 C:HIS190 4.9 40.1 1.0 CA C:ASP186 4.9 46.3 1.0 O A:HOH445 4.9 43.8 1.0 HB3 C:LYS189 5.0 62.6 1.0 HG11 C:VAL151 5.0 30.8 1.0

M.J.Radwanska, U.Derewenda, A.A.Kossiakoff, Z.S.Derewenda. Crystal Structure of the Apo Antibody Fragment (Fab) Raised Against C-Terminal Domain of Ebola Nucleoprotein (Ebov, Tafv, Bdbv Strains) To Be Published.