Zinc in PDB 3bpc: Co-Crystal Structure of S25-2 Fab in Complex with 5-Deoxy-4-Epi-2,3- Dehydro Kdo (4.8) Kdo

The structure of Co-Crystal Structure of S25-2 Fab in Complex with 5-Deoxy-4-Epi-2,3- Dehydro Kdo (4.8) Kdo, PDB code: 3bpc was solved by C.L.Brooks, S.V.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.850, 81.290, 132.340, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 27.3

The structure of Co-Crystal Structure of S25-2 Fab in Complex with 5-Deoxy-4-Epi-2,3- Dehydro Kdo (4.8) Kdo also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Co-Crystal Structure of S25-2 Fab in Complex with 5-Deoxy-4-Epi-2,3- Dehydro Kdo (4.8) Kdo (pdb code 3bpc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Co-Crystal Structure of S25-2 Fab in Complex with 5-Deoxy-4-Epi-2,3- Dehydro Kdo (4.8) Kdo, PDB code: 3bpc:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Co-Crystal Structure of S25-2 Fab in Complex with 5-Deoxy-4-Epi-2,3- Dehydro Kdo (4.8) Kdo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Co-Crystal Structure of S25-2 Fab in Complex with 5-Deoxy-4-Epi-2,3- Dehydro Kdo (4.8) Kdo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn215 b:44.0 occ:1.00 ND1 A:HIS188 1.9 19.1 1.0 OD2 A:ASP150 2.4 22.1 1.0 CE1 A:HIS188 2.7 20.7 1.0 CG A:HIS188 3.0 19.2 1.0 CG A:ASP150 3.4 24.2 1.0 CB A:HIS188 3.5 18.7 1.0 O A:ARG187 3.5 20.6 1.0 CB A:ASP150 3.7 24.2 1.0 CA A:HIS188 3.7 18.6 1.0 NE2 A:HIS188 3.9 16.1 1.0 CD2 A:HIS188 4.1 18.3 1.0 C A:ARG187 4.3 20.0 1.0 N A:HIS188 4.5 18.2 1.0 OD1 A:ASP150 4.5 21.1 1.0 C A:HIS188 4.9 17.5 1.0 O A:HOH282 4.9 34.8 1.0 N A:ASN189 4.9 17.2 1.0

Zinc binding site 2 out of 2 in the Co-Crystal Structure of S25-2 Fab in Complex with 5-Deoxy-4-Epi-2,3- Dehydro Kdo (4.8) Kdo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Co-Crystal Structure of S25-2 Fab in Complex with 5-Deoxy-4-Epi-2,3- Dehydro Kdo (4.8) Kdo within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn217 b:23.6 occ:1.00 OE2 B:GLU56 2.0 18.8 1.0 O B:HOH329 2.4 21.4 1.0 CD B:GLU56 2.8 17.9 1.0 OE1 B:GLU56 3.0 18.0 1.0 O B:HOH523 3.5 28.1 1.0 NH1 B:ARG52 4.0 21.1 1.0 CG B:GLU56 4.2 19.1 1.0 O B:THR55 4.5 18.8 1.0 NH2 B:ARG52 4.5 19.9 1.0 CZ B:ARG52 4.7 19.1 1.0

C.L.Brooks, S.Muller-Loennies, L.Brade, P.Kosma, T.Hirama, C.R.Mackenzie, H.Brade, S.V.Evans. Exploration of Specificity in Germline Monoclonal Antibody Recognition of A Range of Natural and Synthetic Epitopes. J.Mol.Biol. V. 377 450 2008.
ISSN: ISSN 0022-2836
PubMed: 18272175
DOI: 10.1016/J.JMB.2008.01.018