Zinc in PDB 1i9r: Structure of CD40L in Complex with the Fab Fragment of Humanized 5C8 Antibody

The structure of Structure of CD40L in Complex with the Fab Fragment of Humanized 5C8 Antibody, PDB code: 1i9r was solved by M.Karpusas, J.Lucci, J.Ferrant, C.Benjamin, Y.-M.Hsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.00 / 3.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	224.480, 129.910, 96.490, 90.00, 109.60, 90.00
R / Rfree (%)	23.3 / 28.5

The binding sites of Zinc atom in the Structure of CD40L in Complex with the Fab Fragment of Humanized 5C8 Antibody (pdb code 1i9r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of CD40L in Complex with the Fab Fragment of Humanized 5C8 Antibody, PDB code: 1i9r:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of CD40L in Complex with the Fab Fragment of Humanized 5C8 Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of CD40L in Complex with the Fab Fragment of Humanized 5C8 Antibody within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn498 b:39.9 occ:1.00 OD2 H:ASP106 2.4 2.0 1.0 OE1 L:GLU59 2.8 12.3 1.0 OD1 H:ASP100 3.1 21.3 1.0 CG H:ASP106 3.3 2.0 1.0 CB H:ASP106 3.4 2.0 1.0 OE2 L:GLU59 3.5 12.6 1.0 CD L:GLU59 3.5 8.0 1.0 NZ L:LYS53 3.6 27.4 1.0 CG H:ASP100 3.6 20.6 1.0 OD1 H:ASP104 3.6 12.6 1.0 CB H:ASP100 4.0 18.5 1.0 CE L:LYS53 4.1 25.7 1.0 OD2 H:ASP100 4.3 12.2 1.0 OD1 H:ASP106 4.5 2.0 1.0 NH1 H:ARG98 4.6 12.8 1.0 CG H:ASP104 4.8 12.6 1.0 CD2 L:LEU50 4.8 2.0 1.0 CA H:ASP106 4.9 8.4 1.0 CG L:GLU59 5.0 3.5 1.0

Zinc binding site 2 out of 3 in the Structure of CD40L in Complex with the Fab Fragment of Humanized 5C8 Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of CD40L in Complex with the Fab Fragment of Humanized 5C8 Antibody within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn499 b:38.3 occ:1.00 OD2 K:ASP106 2.4 8.9 1.0 OD1 K:ASP100 2.9 22.6 1.0 OD1 K:ASP104 3.2 8.5 1.0 CG K:ASP100 3.3 20.3 1.0 CG K:ASP106 3.3 7.0 1.0 OE1 M:GLU59 3.3 27.4 1.0 CB K:ASP106 3.4 6.9 1.0 NZ M:LYS53 3.5 33.3 1.0 CB K:ASP100 3.6 18.8 1.0 OE2 M:GLU59 3.8 15.7 1.0 CD M:GLU59 3.9 16.0 1.0 OD2 K:ASP100 4.0 24.1 1.0 CE M:LYS53 4.0 27.1 1.0 CG K:ASP104 4.4 9.3 1.0 OD1 K:ASP106 4.5 2.0 1.0 NH1 K:ARG98 4.6 6.3 1.0 OD2 K:ASP104 4.8 14.2 1.0 CA K:ASP106 4.9 9.9 1.0 CD2 M:LEU50 4.9 13.4 1.0

Zinc binding site 3 out of 3 in the Structure of CD40L in Complex with the Fab Fragment of Humanized 5C8 Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of CD40L in Complex with the Fab Fragment of Humanized 5C8 Antibody within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn500 b:38.5 occ:1.00 OD2 X:ASP106 2.5 20.2 1.0 OE1 Y:GLU59 2.9 17.2 1.0 OD1 X:ASP100 2.9 22.1 1.0 OD1 X:ASP104 3.3 7.6 1.0 CG X:ASP106 3.4 12.7 1.0 CG X:ASP100 3.4 22.5 1.0 CB X:ASP106 3.5 7.7 1.0 NZ Y:LYS53 3.5 22.5 1.0 OE2 Y:GLU59 3.5 10.1 1.0 CD Y:GLU59 3.6 8.8 1.0 CB X:ASP100 3.8 22.6 1.0 CE Y:LYS53 4.0 26.2 1.0 OD2 X:ASP100 4.1 29.2 1.0 CG X:ASP104 4.5 15.3 1.0 NH1 X:ARG98 4.6 7.6 1.0 OD1 X:ASP106 4.6 7.2 1.0 CD2 Y:LEU50 4.8 10.1 1.0 CA X:ASP106 5.0 7.5 1.0 OD2 X:ASP104 5.0 23.0 1.0

M.Karpusas, J.Lucci, J.Ferrant, C.Benjamin, F.R.Taylor, K.Strauch, E.Garber, Y.M.Hsu. Structure of CD40 Ligand in Complex with the Fab Fragment of A Neutralizing Humanized Antibody. Structure V. 9 321 2001.
ISSN: ISSN 0969-2126
PubMed: 11525169
DOI: 10.1016/S0969-2126(01)00590-1