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

The structure of Catalytic Antibody D2.3 Complex, PDB code: 1yek 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 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.730, 78.730, 159.030, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 23.7

The binding sites of Zinc atom in the Catalytic Antibody D2.3 Complex (pdb code 1yek). 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: 1yek:
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:Zn605 b:28.4 occ:1.00 O L:HOH654 1.7 47.9 1.0 O L:HOH641 1.7 22.3 1.0 OD2 L:ASP151 1.9 22.0 1.0 ND1 L:HIS189 2.3 28.2 1.0 CG L:ASP151 3.0 16.3 1.0 CE1 L:HIS189 3.1 27.1 1.0 ZN L:ZN606 3.2 29.4 1.0 CG L:HIS189 3.3 28.2 1.0 ZN L:ZN601 3.4 36.7 1.0 CB L:ASP151 3.4 14.4 1.0 O L:HOH655 3.6 25.0 1.0 O L:HOH674 3.6 47.5 1.0 CB L:HIS189 3.6 27.5 1.0 CA L:HIS189 3.8 28.1 1.0 O L:HOH679 3.9 40.8 1.0 O L:HOH616 3.9 30.0 1.0 OD1 L:ASP151 4.0 20.5 1.0 O L:HOH675 4.1 24.7 1.0 NE2 L:HIS189 4.2 31.9 1.0 O L:ARG188 4.2 32.6 1.0 CD2 L:HIS189 4.3 28.2 1.0 CG2 L:ILE150 4.5 18.6 1.0 O L:HOH680 4.5 41.5 1.0 N L:HIS189 4.7 30.6 1.0 N L:ASN190 4.8 29.7 1.0 C L:ARG188 4.8 30.7 1.0 CA L:ASP151 4.8 19.3 1.0 O L:ILE150 4.9 21.6 1.0 ZN L:ZN607 4.9 30.8 1.0 C L:HIS189 4.9 28.5 1.0 O L:HOH628 4.9 20.8 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:30.8 occ:1.00 O L:HOH655 1.9 25.0 1.0 O L:HOH656 1.9 21.0 1.0 O L:HOH675 2.0 24.7 1.0 O L:HOH679 3.3 40.8 1.0 ZN L:ZN606 3.4 29.4 1.0 ZN L:ZN601 3.4 36.7 1.0 O L:HOH628 3.8 20.8 1.0 O L:HOH674 3.8 47.5 1.0 O L:HOH680 4.4 41.5 1.0 O L:HOH641 4.6 22.3 1.0 O L:HOH654 4.8 47.9 1.0 ZN L:ZN605 4.9 28.4 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:36.7 occ:1.00 O L:HOH675 1.6 24.7 1.0 O L:HOH674 1.7 47.5 1.0 O L:HOH654 2.2 47.9 1.0 ZN L:ZN607 3.4 30.8 1.0 ZN L:ZN605 3.4 28.4 1.0 O L:HOH655 3.6 25.0 1.0 O L:ARG188 3.8 32.6 1.0 OD2 L:ASP151 3.9 22.0 1.0 O L:HOH641 4.4 22.3 1.0 O L:HOH679 4.5 40.8 1.0 ZN L:ZN606 4.6 29.4 1.0 CG L:ASP151 4.7 16.3 1.0 O L:HOH656 4.8 21.0 1.0 ND1 L:HIS189 4.9 28.2 1.0 ND2 L:ASN190 4.9 52.0 1.0 OD1 L:ASN190 4.9 51.9 1.0 C L:ARG188 5.0 30.7 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:33.5 occ:1.00 O L:HOH676 1.6 32.6 1.0 O L:HOH663 1.9 34.3 1.0 O L:HOH678 2.3 37.7 1.0 ZN L:ZN604 3.4 20.8 1.0 O L:HOH635 4.0 36.8 1.0 O L:HOH660 4.1 52.5 1.0 O L:HOH643 4.3 10.0 1.0 ND1 L:HIS93 4.9 23.1 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:Zn603 b:28.4 occ:1.00 O L:HOH677 1.6 42.2 1.0 O H:HOH611 1.7 30.5 1.0 OD1 H:ASP100C 2.1 33.7 1.0 NE2 L:HIS49 2.4 15.1 1.0 CG H:ASP100C 2.9 32.7 1.0 OD2 H:ASP100C 3.1 35.3 1.0 CE1 L:HIS49 3.2 13.2 1.0 CD2 L:HIS49 3.4 13.1 1.0 CB L:LYS53 4.3 22.5 1.0 ND1 L:HIS49 4.3 15.9 1.0 N H:TYR100D 4.3 26.3 1.0 CB H:ASP100C 4.4 32.2 1.0 CG L:HIS49 4.4 15.1 1.0 CG L:LYS53 4.5 28.5 1.0 O H:TYR100D 4.6 30.1 1.0 CA H:ASP100C 4.8 26.5 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:Zn604 b:20.8 occ:1.00 O L:HOH678 1.6 37.7 1.0 O L:HOH643 2.0 10.0 1.0 ND1 L:HIS93 2.5 23.1 1.0 CG L:HIS93 3.3 23.6 1.0 ZN L:ZN602 3.4 33.5 1.0 CB L:HIS93 3.4 18.9 1.0 CE1 L:HIS93 3.5 23.1 1.0 O L:HOH635 3.6 36.8 1.0 O L:HOH663 3.8 34.3 1.0 CA L:HIS93 3.9 17.3 1.0 O L:HOH676 3.9 32.6 1.0 CD2 L:HIS93 4.5 22.3 1.0 O L:HOH620 4.5 26.2 1.0 NE2 L:HIS93 4.5 25.7 1.0 O L:THR92 4.7 18.5 1.0 N L:PHE94 4.8 21.6 1.0 C L:HIS93 4.9 19.8 1.0 N L:HIS93 4.9 16.4 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:29.4 occ:1.00 O L:HOH680 1.6 41.5 1.0 O L:HOH679 1.6 40.8 1.0 O L:HOH655 1.9 25.0 1.0 O L:HOH641 1.9 22.3 1.0 ZN L:ZN605 3.2 28.4 1.0 ZN L:ZN607 3.4 30.8 1.0 O L:HOH628 3.4 20.8 1.0 O L:HOH616 3.5 30.0 1.0 O L:HOH656 4.1 21.0 1.0 O L:HOH675 4.1 24.7 1.0 CB L:ASP151 4.3 14.4 1.0 O L:HOH654 4.3 47.9 1.0 OD2 L:ASP151 4.5 22.0 1.0 ZN L:ZN601 4.6 36.7 1.0 O L:HOH674 4.6 47.5 1.0 OG L:SER153 4.7 37.0 1.0 CG L:ASP151 4.9 16.3 1.0 O L:ASP151 4.9 24.1 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