Zinc in PDB 1yei: Catalytic Antibody D2.3 Complex

The structure of Catalytic Antibody D2.3 Complex, PDB code: 1yei 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 / 1.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.345, 78.345, 159.278, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 24.1

The binding sites of Zinc atom in the Catalytic Antibody D2.3 Complex (pdb code 1yei). 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 D2.3 Complex, PDB code: 1yei:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Catalytic Antibody D2.3 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 D2.3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn603 b:25.4 occ:1.00 O L:HOH684 1.8 21.4 1.0 O L:HOH686 1.8 48.5 1.0 OD2 L:ASP151 2.0 19.1 1.0 ND1 L:HIS189 2.5 24.3 1.0 CG L:ASP151 3.0 15.4 1.0 ZN L:ZN605 3.3 28.4 1.0 CG L:HIS189 3.3 25.4 1.0 CB L:ASP151 3.4 17.7 1.0 ZN L:ZN606 3.4 27.8 1.0 CB L:HIS189 3.5 22.4 1.0 CE1 L:HIS189 3.5 23.4 1.0 CA L:HIS189 3.6 23.4 1.0 O L:HOH685 3.9 22.6 1.0 O L:HOH650 3.9 35.9 1.0 O L:HOH658 4.0 32.6 1.0 OD1 L:ASP151 4.1 18.3 1.0 O L:ARG188 4.2 29.6 1.0 O L:HOH683 4.3 24.8 1.0 CG2 L:ILE150 4.4 21.6 1.0 CD2 L:HIS189 4.5 25.9 1.0 N L:HIS189 4.5 24.2 1.0 NE2 L:HIS189 4.6 26.6 1.0 N L:ASN190 4.6 26.5 1.0 C L:HIS189 4.7 24.4 1.0 C L:ARG188 4.7 29.4 1.0 CA L:ASP151 4.8 19.6 1.0 O L:ILE150 4.9 19.5 1.0 ZN L:ZN604 4.9 27.8 1.0

Zinc binding site 2 out of 7 in the Catalytic Antibody D2.3 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 D2.3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn607 b:38.2 occ:1.00 O L:HOH666 1.7 26.6 1.0 O L:HOH619 2.1 32.0 1.0 ZN L:ZN602 3.4 23.7 1.0 O L:HOH669 3.6 49.5 1.0 O L:HOH682 4.3 30.2 1.0 O L:HOH654 4.3 38.8 1.0 O L:HOH639 4.4 43.3 1.0 ND1 L:HIS93 4.9 22.5 1.0

Zinc binding site 3 out of 7 in the Catalytic Antibody D2.3 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 D2.3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn601 b:22.7 occ:1.00 O H:HOH292 1.7 45.9 1.0 O L:HOH629 1.8 38.3 1.0 OD1 H:ASP100C 2.1 25.0 1.0 NE2 L:HIS49 2.3 19.8 1.0 CG H:ASP100C 2.9 26.2 1.0 OD2 H:ASP100C 3.0 26.4 1.0 CD2 L:HIS49 3.2 17.8 1.0 CE1 L:HIS49 3.3 18.1 1.0 CB H:ASP100C 4.3 22.4 1.0 N H:TYR100D 4.3 20.1 1.0 ND1 L:HIS49 4.3 19.4 1.0 CG L:HIS49 4.4 15.9 1.0 CB L:LYS53 4.4 22.1 1.0 O H:TYR100D 4.5 24.7 1.0 CG L:LYS53 4.6 27.0 1.0 CA H:ASP100C 4.8 21.1 1.0 CD1 L:LEU50 5.0 14.6 1.0 CD1 H:TYR100D 5.0 13.9 1.0

Zinc binding site 4 out of 7 in the Catalytic Antibody D2.3 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 D2.3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn602 b:23.7 occ:1.00 O L:HOH682 1.7 30.2 1.0 O L:HOH619 1.8 32.0 1.0 ND1 L:HIS93 2.4 22.5 1.0 CG L:HIS93 3.3 20.3 1.0 ZN L:ZN607 3.4 38.2 1.0 CE1 L:HIS93 3.4 21.8 1.0 CB L:HIS93 3.5 15.0 1.0 O L:HOH639 3.5 43.3 1.0 O L:HOH666 3.6 26.6 1.0 CA L:HIS93 4.0 16.8 1.0 CD2 L:HIS93 4.4 22.4 1.0 NE2 L:HIS93 4.5 24.3 1.0 O L:HOH625 4.6 25.3 1.0 O L:THR92 4.7 17.9 1.0 N L:PHE94 4.9 17.6 1.0 C L:HIS93 4.9 18.3 1.0 N L:HIS93 5.0 16.0 1.0

Zinc binding site 5 out of 7 in the Catalytic Antibody D2.3 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 D2.3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn604 b:27.8 occ:1.00 O L:HOH683 1.7 24.8 1.0 O L:HOH608 1.9 28.8 1.0 O L:HOH685 2.0 22.6 1.0 ZN L:ZN606 3.2 27.8 1.0 ZN L:ZN605 3.4 28.4 1.0 O L:HOH658 3.9 32.6 1.0 O L:HOH686 4.1 48.5 1.0 O L:HOH684 4.3 21.4 1.0 O L:HOH680 4.6 53.5 1.0 ZN L:ZN603 4.9 25.4 1.0

Zinc binding site 6 out of 7 in the Catalytic Antibody D2.3 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 D2.3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn605 b:28.4 occ:1.00 O L:HOH685 1.6 22.6 1.0 O L:HOH684 1.7 21.4 1.0 ZN L:ZN603 3.3 25.4 1.0 ZN L:ZN604 3.4 27.8 1.0 O L:HOH650 3.5 35.9 1.0 O L:HOH608 3.9 28.8 1.0 O L:HOH686 3.9 48.5 1.0 O L:HOH683 4.1 24.8 1.0 CB L:ASP151 4.4 17.7 1.0 ZN L:ZN606 4.5 27.8 1.0 OD2 L:ASP151 4.7 19.1 1.0 OG L:SER153 4.8 33.2 1.0

Zinc binding site 7 out of 7 in the Catalytic Antibody D2.3 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 D2.3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn606 b:27.8 occ:1.00 O L:HOH686 1.6 48.5 1.0 O L:HOH683 1.7 24.8 1.0 O L:HOH658 2.2 32.6 1.0 ZN L:ZN604 3.2 27.8 1.0 ZN L:ZN603 3.4 25.4 1.0 O L:HOH685 3.8 22.6 1.0 OD1 L:ASN190 4.0 50.4 1.0 OD2 L:ASP151 4.0 19.1 1.0 O L:ARG188 4.1 29.6 1.0 O L:HOH684 4.1 21.4 1.0 ZN L:ZN605 4.5 28.4 1.0 O L:HOH608 4.6 28.8 1.0 CG L:ASP151 4.7 15.4 1.0 O L:HOH680 4.9 53.5 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