Calcium in PDB 4m7z: Unliganded 1 Crystal Structure of S25-26 Fab

The structure of Unliganded 1 Crystal Structure of S25-26 Fab, PDB code: 4m7z was solved by O.Haji-Ghassemi, S.V.Evans, S.Muller-Loennies, R.Saldova, M.Muniyappa, L.Brade, P.M.Rudd, D.J.Harvey, P.Kosma, H.Brade, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.76 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.298, 111.988, 156.925, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 23.8

The binding sites of Calcium atom in the Unliganded 1 Crystal Structure of S25-26 Fab (pdb code 4m7z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Unliganded 1 Crystal Structure of S25-26 Fab, PDB code: 4m7z:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Unliganded 1 Crystal Structure of S25-26 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Unliganded 1 Crystal Structure of S25-26 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca409 b:37.1 occ:1.00 O5 B:PG4404 2.3 37.1 1.0 O3 B:PG4404 2.3 37.1 1.0 OD2 B:ASP58 2.5 34.0 1.0 O4 B:PG4404 2.6 37.1 1.0 O2 B:PG4404 2.7 37.1 1.0 OD1 B:ASP58 2.9 35.2 1.0 CG B:ASP58 3.1 34.0 1.0 C3 B:PG4404 3.2 37.1 1.0 C4 B:PG4404 3.3 37.1 1.0 C8 B:PG4404 3.3 37.1 1.0 C5 B:PG4404 3.4 37.1 1.0 C6 B:PG4404 3.5 37.1 1.0 C7 B:PG4404 3.5 37.1 1.0 C2 B:PG4404 4.0 37.1 1.0 NE1 B:TRP52 4.3 32.7 1.0 O B:THR57 4.5 32.8 1.0 C1 B:PG4404 4.5 37.1 1.0 CB B:ASP58 4.5 33.0 1.0 CD1 B:TRP52 4.8 32.2 1.0 OG B:SER56 4.9 32.9 1.0

Calcium binding site 2 out of 3 in the Unliganded 1 Crystal Structure of S25-26 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Unliganded 1 Crystal Structure of S25-26 Fab within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca404 b:37.1 occ:1.00 O5 H:PG4402 2.4 37.1 1.0 O4 H:PG4402 2.5 37.1 1.0 O3 H:PG4402 2.6 37.1 1.0 OD2 H:ASP58 2.6 31.2 1.0 O2 H:PG4402 2.6 37.1 1.0 OD1 H:ASP58 2.9 32.4 1.0 CG H:ASP58 3.1 31.3 1.0 C4 H:PG4402 3.2 37.1 1.0 C3 H:PG4402 3.2 37.1 1.0 C8 H:PG4402 3.4 37.1 1.0 C7 H:PG4402 3.5 37.1 1.0 C5 H:PG4402 3.6 37.1 1.0 C6 H:PG4402 3.6 37.1 1.0 C2 H:PG4402 3.9 37.1 1.0 O H:THR57 4.4 29.8 1.0 NE1 H:TRP52 4.5 30.0 1.0 CB H:ASP58 4.6 30.5 1.0 OG H:SER56 4.9 29.9 1.0 CD1 H:TRP52 5.0 29.4 1.0 C1 H:PG4402 5.0 37.1 1.0

Calcium binding site 3 out of 3 in the Unliganded 1 Crystal Structure of S25-26 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Unliganded 1 Crystal Structure of S25-26 Fab within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca304 b:37.1 occ:0.50 OE2 L:GLU81 1.7 57.8 1.0 OE2 C:GLU81 2.0 50.7 1.0 OE1 C:GLU81 2.5 54.8 1.0 OE1 L:GLU79 2.5 58.1 1.0 CD C:GLU81 2.5 51.9 1.0 CD L:GLU81 2.8 54.9 1.0 OE1 C:GLU79 3.0 51.8 1.0 O L:HOH418 3.2 37.1 1.0 CD C:GLU79 3.4 52.0 1.0 CG L:GLU81 3.6 54.1 1.0 CD L:GLU79 3.7 58.1 1.0 CB C:GLU79 3.7 48.1 1.0 OE1 L:GLU81 3.7 52.9 1.0 OE2 C:GLU79 3.8 54.4 1.0 CG C:GLU81 4.0 50.0 1.0 CG C:GLU79 4.1 49.5 1.0 N C:ALA80 4.3 48.6 1.0 OE2 L:GLU79 4.4 59.4 1.0 N C:GLU81 4.6 46.9 1.0 CB L:GLU79 4.7 55.2 1.0 CB C:GLU81 4.7 46.8 1.0 CG L:GLU79 4.7 56.7 1.0 O C:HOH433 4.7 37.1 1.0 CA C:GLU79 4.7 47.5 1.0 C C:GLU79 5.0 46.8 1.0

O.Haji-Ghassemi, S.Muller-Loennies, R.Saldova, M.Muniyappa, L.Brade, P.M.Rudd, D.J.Harvey, P.Kosma, H.Brade, S.V.Evans. Groove-Type Recognition of Chlamydiaceae-Specific Lipopolysaccharide Antigen By A Family of Antibodies Possessing An Unusual Variable Heavy Chain N-Linked Glycan. J.Biol.Chem. V. 289 16644 2014.
ISSN: ISSN 0021-9258
PubMed: 24682362
DOI: 10.1074/JBC.M113.528224