Zinc in PDB 1yej: Catalytic Antibody Complex

The structure of Catalytic Antibody Complex, PDB code: 1yej was solved by B.Gigant, M.Knossow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.00 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.271, 78.271, 158.674, 90.00, 90.00, 120.00
R / Rfree (%)	21.2 / 24.6

The binding sites of Zinc atom in the Catalytic Antibody Complex (pdb code 1yej). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Catalytic Antibody Complex, PDB code: 1yej:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Catalytic Antibody Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Antibody Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn601 b:30.1 occ:1.00 NZ L:LYS30 4.5 41.0 1.0 O L:HOH682 4.6 50.4 1.0

Zinc binding site 2 out of 7 in the Catalytic Antibody Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Antibody Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn603 b:23.6 occ:1.00 O L:HOH647 1.9 42.8 1.0 OD1 H:ASP100C 2.1 24.8 1.0 NE2 L:HIS49 2.3 16.8 1.0 CE L:LYS53 2.8 37.0 1.0 CG H:ASP100C 2.9 27.4 1.0 NZ L:LYS53 3.0 42.9 1.0 OD2 H:ASP100C 3.0 27.0 1.0 CD2 L:HIS49 3.2 15.6 1.0 CE1 L:HIS49 3.3 16.1 1.0 CD L:LYS53 4.0 35.8 1.0 ND1 L:HIS49 4.3 16.3 1.0 CG L:HIS49 4.4 16.9 1.0 CB H:ASP100C 4.4 25.2 1.0 CB L:LYS53 4.4 23.1 1.0 N H:TYR100D 4.4 20.4 1.0 O H:TYR100D 4.6 24.4 1.0 CG L:LYS53 4.7 26.7 1.0 CA H:ASP100C 4.9 24.3 1.0 CD1 L:LEU50 4.9 19.3 1.0

Zinc binding site 3 out of 7 in the Catalytic Antibody Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Catalytic Antibody Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn604 b:25.2 occ:1.00 ND1 L:HIS93 2.2 18.6 1.0 O7 L:PNF551 2.2 56.3 1.0 O L:HOH691 2.8 40.7 1.0 CE1 L:HIS93 2.8 18.3 1.0 ZN L:ZN602 3.0 44.9 1.0 C17 L:PNF551 3.1 55.1 1.0 CG L:HIS93 3.4 17.7 1.0 O L:HOH696 3.5 47.6 1.0 O8 L:PNF551 3.6 59.5 1.0 CB L:HIS93 3.9 13.8 1.0 OE1 L:GLN27 4.0 50.5 1.0 NE2 L:HIS93 4.0 21.5 1.0 C16 L:PNF551 4.1 53.4 1.0 CA L:HIS93 4.3 14.3 1.0 CD2 L:HIS93 4.3 18.6 1.0 C15 L:PNF551 4.5 52.4 1.0 O L:THR92 4.6 15.3 1.0

Zinc binding site 4 out of 7 in the Catalytic Antibody Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Catalytic Antibody Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn605 b:24.2 occ:1.00 O L:HOH642 1.7 18.2 1.0 OD2 L:ASP151 1.9 23.2 1.0 O L:HOH657 2.1 26.2 1.0 ND1 L:HIS189 2.3 26.8 1.0 CG L:ASP151 2.9 17.6 1.0 CG L:HIS189 3.2 28.2 1.0 CE1 L:HIS189 3.2 26.6 1.0 CB L:ASP151 3.3 16.0 1.0 ZN L:ZN606 3.3 27.0 1.0 O L:HOH615 3.5 37.3 1.0 CB L:HIS189 3.5 25.7 1.0 O L:HOH658 3.6 28.9 1.0 CA L:HIS189 3.7 24.6 1.0 OD1 L:ASP151 4.0 20.6 1.0 NE2 L:HIS189 4.2 28.8 1.0 CD2 L:HIS189 4.3 30.2 1.0 CG2 L:ILE150 4.4 21.1 1.0 O L:ARG188 4.4 28.8 1.0 O L:HOH698 4.5 40.9 1.0 N L:HIS189 4.6 25.3 1.0 O L:HOH697 4.6 35.2 1.0 CA L:ASP151 4.7 17.3 1.0 N L:ASN190 4.7 26.5 1.0 C L:HIS189 4.8 23.2 1.0 C L:ARG188 4.8 28.4 1.0 O L:HOH629 4.8 21.9 1.0 O L:ILE150 4.9 19.9 1.0 ZN L:ZN607 5.0 29.4 1.0 N L:ASP151 5.0 19.5 1.0

Zinc binding site 5 out of 7 in the Catalytic Antibody Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Catalytic Antibody Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn602 b:44.9 occ:1.00 O L:HOH696 1.7 47.6 1.0 O L:HOH691 1.8 40.7 1.0 ZN L:ZN604 3.0 25.2 1.0 O7 L:PNF551 4.6 56.3 1.0 O L:HOH678 4.6 31.3 1.0 C17 L:PNF551 4.9 55.1 1.0 ND1 L:HIS93 4.9 18.6 1.0

Zinc binding site 6 out of 7 in the Catalytic Antibody Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Catalytic Antibody Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn606 b:27.0 occ:1.00 O L:HOH697 1.6 35.2 1.0 O L:HOH658 1.7 28.9 1.0 O L:HOH642 1.7 18.2 1.0 O L:HOH615 3.2 37.3 1.0 ZN L:ZN605 3.3 24.2 1.0 ZN L:ZN607 3.4 29.4 1.0 O L:HOH629 3.5 21.9 1.0 O L:HOH657 3.6 26.2 1.0 O L:HOH660 3.9 28.1 1.0 O L:HOH698 3.9 40.9 1.0 CB L:ASP151 4.4 16.0 1.0 OG L:SER153 4.6 33.0 1.0 OD2 L:ASP151 4.6 23.2 1.0 ND1 L:HIS189 4.9 26.8 1.0 O L:ASP151 5.0 19.9 1.0

Zinc binding site 7 out of 7 in the Catalytic Antibody Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Catalytic Antibody Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn607 b:29.4 occ:1.00 O L:HOH698 1.6 40.9 1.0 O L:HOH658 1.9 28.9 1.0 O L:HOH660 1.9 28.1 1.0 ZN L:ZN606 3.4 27.0 1.0 O L:HOH657 3.7 26.2 1.0 O L:HOH629 3.7 21.9 1.0 O L:HOH642 4.3 18.2 1.0 O L:HOH697 4.4 35.2 1.0 ZN L:ZN605 5.0 24.2 1.0

B.Gigant, J.B.Charbonnier, Z.Eshhar, B.S.Green, M.Knossow. Crossreactivity, Efficiency and Catalytic Specificity of An Esterase-Like Antibody. J.Mol.Biol. V. 284 741 1998.
ISSN: ISSN 0022-2836
PubMed: 9826512
DOI: 10.1006/JMBI.1998.2198