Zinc in PDB 8bjz: Crystal Structure of Antibody Fab with Sialac-Amidine-Lys

The structure of Crystal Structure of Antibody Fab with Sialac-Amidine-Lys, PDB code: 8bjz was solved by L.Moynie, J.H.Naismith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.24 / 1.89
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.91, 130.68, 76.91, 90, 123.66, 90
R / Rfree (%)	18.6 / 22.3

The binding sites of Zinc atom in the Crystal Structure of Antibody Fab with Sialac-Amidine-Lys (pdb code 8bjz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Antibody Fab with Sialac-Amidine-Lys, PDB code: 8bjz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Antibody Fab with Sialac-Amidine-Lys


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 Antibody Fab with Sialac-Amidine-Lys within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:57.9 occ:1.00 NE2 H:HIS173 2.2 37.3 1.0 O L:HOH430 2.2 39.5 1.0 O H:HOH470 2.4 39.8 1.0 OD1 L:ASN143 2.4 32.2 1.0 O L:HOH484 2.8 45.1 1.0 CE1 H:HIS173 3.1 29.6 1.0 CG L:ASN143 3.2 28.4 1.0 CD2 H:HIS173 3.2 29.5 1.0 ND2 L:ASN143 3.3 38.6 1.0 O L:HOH467 3.8 25.6 1.0 OD2 L:ASP172 4.1 45.5 1.0 ND1 H:HIS173 4.2 31.2 1.0 OD1 L:ASN142 4.3 34.8 1.0 CG H:HIS173 4.3 31.9 1.0 OD2 L:ASP175 4.5 38.8 1.0 OG L:SER179 4.6 25.9 1.0 ND2 L:ASN142 4.6 32.6 1.0 CB L:ASN143 4.6 25.2 1.0 CG L:ASN142 4.7 33.3 1.0 OG1 L:THR177 5.0 28.8 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Antibody Fab with Sialac-Amidine-Lys


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 Antibody Fab with Sialac-Amidine-Lys within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn302 b:42.8 occ:1.00 ND1 L:HIS35 2.0 34.3 1.0 O L:HOH472 2.0 43.6 1.0 O L:HOH486 2.3 25.2 1.0 O L:HOH483 2.8 46.1 1.0 CE1 L:HIS35 2.9 33.7 1.0 O L:HOH480 2.9 43.2 1.0 CG L:HIS35 3.1 29.9 1.0 CB L:HIS35 3.5 23.3 1.0 CA L:HIS35 4.0 27.0 1.0 NE2 L:HIS35 4.0 32.8 1.0 CD2 L:HIS35 4.2 32.8 1.0 OD1 L:ASN33 4.6 32.6 1.0 C L:HIS35 4.9 25.0 1.0 ND2 L:ASN33 5.0 39.0 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Antibody Fab with Sialac-Amidine-Lys


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 Antibody Fab with Sialac-Amidine-Lys within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn303 b:83.0 occ:1.00 O L:HOH478 2.2 47.6 1.0 NE2 L:HIS194 2.2 37.5 1.0 CE1 L:HIS194 3.1 35.3 1.0 O L:HOH485 3.2 46.7 1.0 CD2 L:HIS194 3.3 31.8 1.0 OD1 L:ASP190 4.2 45.6 1.0 ND1 L:HIS194 4.2 33.5 1.0 O L:ASP190 4.3 29.6 1.0 CB L:ASP190 4.3 28.6 1.0 CG L:ASP190 4.4 45.8 1.0 CG L:HIS194 4.4 28.9 1.0 CA L:ASP190 4.6 29.4 1.0 CD L:LYS193 4.6 41.6 1.0 CB L:LYS193 4.7 32.5 1.0 C L:ASP190 4.8 31.0 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Antibody Fab with Sialac-Amidine-Lys


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Antibody Fab with Sialac-Amidine-Lys within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:56.5 occ:1.00 OD1 B:ASN143 2.1 31.7 1.0 NE2 A:HIS173 2.1 32.5 1.0 O B:HOH453 2.1 44.9 1.0 O B:HOH419 2.3 45.0 1.0 CG B:ASN143 2.8 33.8 1.0 ND2 B:ASN143 3.0 35.7 1.0 CE1 A:HIS173 3.0 37.0 1.0 CD2 A:HIS173 3.2 28.0 1.0 O B:HOH408 3.4 33.2 1.0 O B:HOH440 3.5 31.9 1.0 ND1 A:HIS173 4.2 36.8 1.0 OG B:SER179 4.2 26.9 1.0 OD2 B:ASP175 4.2 41.8 1.0 ND2 B:ASN142 4.2 32.5 1.0 OD1 B:ASN142 4.2 33.7 1.0 CB B:ASN143 4.3 33.7 1.0 CG A:HIS173 4.3 33.1 1.0 OD2 B:ASP172 4.4 45.4 1.0 OG1 B:THR177 4.5 29.2 1.0 CG B:ASN142 4.5 36.7 1.0 CA B:ASN143 4.7 27.5 1.0 N B:ASN143 4.9 30.7 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Antibody Fab with Sialac-Amidine-Lys


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Antibody Fab with Sialac-Amidine-Lys within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:37.0 occ:1.00 ND1 B:HIS35 2.0 30.9 1.0 CE1 B:HIS35 3.0 31.2 1.0 CG B:HIS35 3.0 29.8 1.0 CB B:HIS35 3.4 26.4 1.0 CA B:HIS35 4.0 21.9 1.0 NE2 B:HIS35 4.1 36.6 1.0 CD2 B:HIS35 4.1 32.3 1.0 C B:HIS35 4.9 24.6 1.0 OD1 B:ASN33 4.9 27.2 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Antibody Fab with Sialac-Amidine-Lys


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Antibody Fab with Sialac-Amidine-Lys within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:82.5 occ:1.00 OD1 B:ASP190 2.3 56.4 1.0 NE2 B:HIS194 2.4 47.9 1.0 NZ B:LYS193 2.6 59.0 1.0 CG B:ASP190 3.2 43.5 1.0 CE1 B:HIS194 3.3 48.4 1.0 OD2 B:ASP190 3.4 48.0 1.0 CD2 B:HIS194 3.5 45.1 1.0 CE B:LYS193 3.7 56.1 1.0 ND1 B:HIS194 4.5 45.1 1.0 CB B:ASP190 4.6 34.9 1.0 CG B:HIS194 4.6 47.6 1.0 CD B:LYS193 4.8 52.7 1.0 O B:ASP190 4.8 40.1 1.0 CA B:ASP190 5.0 34.1 1.0

L.Moynie, J.H.Naismith, Q.Sattentau, L.Deimel, A.Khan, B.Davis, A.Baldwin, C.Buchanan. Crystal Structure of Antibody Fab with Sialac-Amidine-Lys To Be Published.