Zinc in PDB 1kn2: Catalytic Antibody D2.3 Complex

The structure of Catalytic Antibody D2.3 Complex, PDB code: 1kn2 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)	20.00 / 1.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.275, 78.275, 158.952, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 23.8

The binding sites of Zinc atom in the Catalytic Antibody D2.3 Complex (pdb code 1kn2). 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: 1kn2:
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:Zn553 b:29.8 occ:1.00 O L:HOH581 1.6 51.6 1.0 OD1 H:ASP100C 2.1 32.1 1.0 NE2 L:HIS49 2.3 23.2 1.0 CG H:ASP100C 2.9 31.8 1.0 OD2 H:ASP100C 2.9 32.9 1.0 NZ L:LYS53 3.2 54.9 1.0 CD2 L:HIS49 3.2 21.9 1.0 CE1 L:HIS49 3.2 21.3 1.0 CD L:LYS53 3.5 43.2 1.0 CE L:LYS53 3.6 50.4 1.0 ND1 L:HIS49 4.3 22.4 1.0 CG L:HIS49 4.3 20.7 1.0 N H:TYR100D 4.3 26.9 1.0 CB H:ASP100C 4.3 29.1 1.0 CB L:LYS53 4.4 28.6 1.0 O H:TYR100D 4.5 28.9 1.0 CG L:LYS53 4.6 35.1 1.0 CA H:ASP100C 4.9 27.4 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:Zn554 b:25.7 occ:1.00 O L:HOH561 1.7 39.6 1.0 O L:HOH571 1.7 44.3 1.0 ND1 L:HIS93 2.3 23.5 1.0 CG L:HIS93 3.2 22.9 1.0 CE1 L:HIS93 3.3 22.6 1.0 ZN L:ZN559 3.4 35.6 1.0 CB L:HIS93 3.4 20.4 1.0 O L:HOH591 3.5 55.0 1.0 O L:HOH620 3.5 40.0 1.0 CA L:HIS93 3.9 19.4 1.0 CD2 L:HIS93 4.3 22.7 1.0 NE2 L:HIS93 4.3 24.7 1.0 O L:HOH577 4.6 38.6 1.0 O L:THR92 4.6 22.2 1.0 N L:PHE94 4.7 23.9 1.0 C L:HIS93 4.8 22.4 1.0 N L:HIS93 4.9 18.4 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:Zn555 b:38.5 occ:1.00 O L:HOH601 1.5 55.4 1.0 O L:HOH602 1.9 43.7 1.0 OD1 L:ASP151 2.1 28.9 1.0 ND1 L:HIS189 2.4 33.0 1.0 CG L:ASP151 3.1 23.2 1.0 CG L:HIS189 3.2 33.2 1.0 CE1 L:HIS189 3.3 32.8 1.0 ZN L:ZN557 3.4 40.2 1.0 CB L:ASP151 3.4 23.6 1.0 CB L:HIS189 3.5 30.8 1.0 ZN L:ZN558 3.5 39.7 1.0 O L:HOH604 3.6 48.2 1.0 CA L:HIS189 3.7 30.4 1.0 O L:HOH612 4.0 55.1 1.0 O L:HOH603 4.0 41.0 1.0 CD2 L:HIS189 4.2 35.5 1.0 OD2 L:ASP151 4.2 27.3 1.0 NE2 L:HIS189 4.2 36.1 1.0 O L:ARG188 4.2 34.6 1.0 CG2 L:ILE150 4.3 26.4 1.0 O L:HOH619 4.5 39.4 1.0 N L:ASN190 4.6 32.6 1.0 N L:HIS189 4.6 30.2 1.0 C L:HIS189 4.7 31.5 1.0 O L:ILE150 4.8 24.9 1.0 CA L:ASP151 4.8 24.2 1.0 C L:ARG188 4.8 32.7 1.0 C L:ILE150 5.0 25.2 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:Zn556 b:41.5 occ:1.00 O L:HOH619 1.7 39.4 1.0 O L:HOH560 1.9 43.4 1.0 O L:HOH603 1.9 41.0 1.0 ZN L:ZN558 3.3 39.7 1.0 ZN L:ZN557 3.5 40.2 1.0 O L:HOH612 3.5 55.1 1.0 O L:HOH602 4.2 43.7 1.0 O L:HOH601 4.3 55.4 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:Zn557 b:40.2 occ:1.00 O L:HOH603 1.6 41.0 1.0 O L:HOH602 1.7 43.7 1.0 O L:HOH604 3.3 48.2 1.0 ZN L:ZN555 3.4 38.5 1.0 ZN L:ZN556 3.5 41.5 1.0 O L:HOH560 3.9 43.4 1.0 O L:HOH601 3.9 55.4 1.0 O L:HOH619 4.2 39.4 1.0 CB L:ASP151 4.5 23.6 1.0 ZN L:ZN558 4.6 39.7 1.0 OD1 L:ASP151 4.9 28.9 1.0 OG L:SER153 4.9 36.0 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:Zn558 b:39.7 occ:1.00 O L:HOH612 1.7 55.1 1.0 O L:HOH619 1.8 39.4 1.0 O L:HOH601 2.0 55.4 1.0 ZN L:ZN556 3.3 41.5 1.0 ZN L:ZN555 3.5 38.5 1.0 O L:HOH603 3.9 41.0 1.0 O L:HOH602 4.0 43.7 1.0 OD1 L:ASP151 4.0 28.9 1.0 O L:ARG188 4.0 34.6 1.0 O L:HOH560 4.6 43.4 1.0 ZN L:ZN557 4.6 40.2 1.0 CG L:ASP151 4.7 23.2 1.0 ND1 L:HIS189 5.0 33.0 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:Zn559 b:35.6 occ:1.00 O L:HOH620 1.8 40.0 1.0 O L:HOH571 2.0 44.3 1.0 ZN L:ZN554 3.4 25.7 1.0 O L:HOH624 4.1 50.6 1.0 O L:HOH561 4.2 39.6 1.0 O L:HOH591 4.3 55.0 1.0 O L:HOH608 4.4 55.9 1.0 ND1 L:HIS93 4.8 23.5 1.0

L.J.D'souza, B.Gigant, M.Knossow, B.S.Green. Remarkable Remote Chiral Recognition in A Reaction Mediated By A Catalytic Antibody. J.Am.Chem.Soc. V. 124 2114 2002.
ISSN: ISSN 0002-7863
PubMed: 11878955
DOI: 10.1021/JA0170504