Nickel in PDB 6c5i: Unliganded S25-5 Fab

The structure of Unliganded S25-5 Fab, PDB code: 6c5i was solved by S.V.Evans, O.Haji-Ghassemi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.635, 72.877, 109.015, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.1

The structure of Unliganded S25-5 Fab also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Nickel atom in the Unliganded S25-5 Fab (pdb code 6c5i). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Unliganded S25-5 Fab, PDB code: 6c5i:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Unliganded S25-5 Fab


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Unliganded S25-5 Fab within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni301 b:32.5 occ:1.00 NE2 L:HIS189 2.1 32.2 1.0 CD2 L:HIS189 3.0 32.7 1.0 CE1 L:HIS189 3.0 34.7 1.0 ND1 L:HIS189 4.1 32.1 1.0 CG L:HIS189 4.2 33.6 1.0 O L:HOH527 4.4 44.1 1.0 O L:HOH461 4.6 38.2 1.0

Nickel binding site 2 out of 2 in the Unliganded S25-5 Fab


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Unliganded S25-5 Fab within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni302 b:73.1 occ:0.50 SG L:CYS214 2.6 65.6 1.0 CA L:CYS214 3.5 68.8 1.0 CB L:CYS214 3.5 69.0 1.0 O L:HOH507 3.9 40.4 1.0 N L:CYS214 3.9 68.5 1.0 CG L:PRO119 4.1 35.2 1.0 OG H:SER128 4.1 66.4 1.0 CB L:PHE209 4.2 33.6 1.0 O L:ASN210 4.2 36.0 1.0 O L:GLU213 4.3 62.8 1.0 C L:GLU213 4.3 64.4 1.0 CD2 L:PHE209 4.3 33.8 1.0 CG L:PHE209 4.5 32.0 1.0 N H:SER128 4.5 68.1 1.0 CA H:GLY127 4.7 62.7 1.0 O H:SER128 4.8 78.3 1.0 C L:CYS214 4.8 72.0 1.0 C H:GLY127 5.0 64.2 1.0

O.Haji-Ghassemi, S.Muller-Loennies, C.L.Brooks, C.R.Mackenzie, N.Caveney, F.Van Petegem, L.Brade, P.Kosma, H.Brade, S.V.Evans. Subtle Changes in the Combining Site of the Chlamydiaceae-Specific Mab S25-23 Increase the Antibody-Carbohydrate Binding Affinity By An Order of Magnitude. Biochemistry V. 58 714 2019.
ISSN: ISSN 1520-4995
PubMed: 30571096
DOI: 10.1021/ACS.BIOCHEM.8B00318