Calcium in PDB 5d6c: Structure of 4497 Fab Bound to Synthetic Wall Teichoic Acid Fragment

The structure of Structure of 4497 Fab Bound to Synthetic Wall Teichoic Acid Fragment, PDB code: 5d6c was solved by P.J.Lupardus, R.Fong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.64 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.707, 111.471, 158.412, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 23.8

The binding sites of Calcium atom in the Structure of 4497 Fab Bound to Synthetic Wall Teichoic Acid Fragment (pdb code 5d6c). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of 4497 Fab Bound to Synthetic Wall Teichoic Acid Fragment, PDB code: 5d6c:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of 4497 Fab Bound to Synthetic Wall Teichoic Acid Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of 4497 Fab Bound to Synthetic Wall Teichoic Acid Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:35.2 occ:1.00 O B:HOH489 3.0 39.8 1.0 O B:HOH429 3.1 38.3 1.0 N B:TRP47 3.3 24.9 1.0 N A:PHE98 3.3 28.0 1.0 CA A:THR97 3.6 27.8 1.0 CA B:VAL46 3.8 23.7 1.0 C A:THR97 4.0 32.2 1.0 CG2 A:THR97 4.0 32.7 1.0 CB A:THR97 4.0 34.0 1.0 C B:VAL46 4.0 28.0 1.0 CB B:TRP47 4.0 25.1 1.0 CD2 A:PHE98 4.1 27.0 1.0 CB A:PHE98 4.2 25.8 1.0 CA B:TRP47 4.2 25.3 1.0 O B:LEU45 4.3 24.5 1.0 CA A:PHE98 4.3 25.5 1.0 CG1 B:VAL46 4.3 27.4 1.0 O A:PHE98 4.3 28.3 1.0 O B:TRP47 4.5 26.9 1.0 CB B:VAL46 4.5 27.8 1.0 CG A:PHE98 4.6 25.2 1.0 N A:THR97 4.7 27.1 1.0 C A:PHE98 4.8 27.8 1.0 N B:VAL46 4.8 23.5 1.0 O A:TYR96 4.9 28.7 1.0 C B:TRP47 4.9 26.1 1.0 C B:LEU45 4.9 25.9 1.0 CG2 B:VAL46 5.0 27.6 1.0

Calcium binding site 2 out of 4 in the Structure of 4497 Fab Bound to Synthetic Wall Teichoic Acid Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of 4497 Fab Bound to Synthetic Wall Teichoic Acid Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:33.4 occ:1.00 O A:HOH423 3.1 37.2 1.0 O A:HOH513 3.2 46.5 1.0 NH1 L:ARG67 3.3 29.5 1.0 N A:ALA12 3.4 26.1 1.0 N L:ARG67 3.5 29.0 1.0 CB L:PRO65 3.5 33.4 1.0 CG L:ARG67 3.6 26.8 1.0 CB L:ARG67 3.7 25.7 1.0 CA A:LEU11 3.7 24.6 1.0 O A:SER10 3.9 29.3 1.0 N L:ASP66 3.9 30.1 1.0 CD L:ARG67 4.0 25.6 1.0 C A:LEU11 4.1 28.7 1.0 CD1 A:LEU11 4.1 29.1 1.0 CA L:ARG67 4.2 27.9 1.0 C L:PRO65 4.3 32.7 1.0 CA L:PRO65 4.3 31.8 1.0 CZ L:ARG67 4.4 40.1 1.0 CB A:ALA12 4.4 25.1 1.0 C L:ASP66 4.4 32.5 1.0 CA A:ALA12 4.4 24.2 1.0 N A:LEU11 4.5 26.1 1.0 O A:ALA12 4.5 26.9 1.0 O L:HOH541 4.5 54.1 1.0 C A:SER10 4.5 28.3 1.0 CA L:ASP66 4.6 30.5 1.0 NE L:ARG67 4.6 26.9 1.0 CG L:PRO65 4.8 36.2 1.0 CB A:LEU11 4.8 24.7 1.0 CB L:ASP66 4.8 34.1 1.0 C A:ALA12 4.9 27.7 1.0 CG A:LEU11 4.9 27.6 1.0

Calcium binding site 3 out of 4 in the Structure of 4497 Fab Bound to Synthetic Wall Teichoic Acid Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of 4497 Fab Bound to Synthetic Wall Teichoic Acid Fragment within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca301 b:41.2 occ:1.00 O H:HOH441 3.1 41.6 1.0 O H:HOH487 3.2 45.7 1.0 N H:TRP47 3.2 30.1 1.0 N L:PHE104 3.4 31.6 1.0 CA L:THR103 3.6 34.0 1.0 CA H:VAL46 3.8 28.9 1.0 C H:VAL46 4.0 32.5 1.0 CB H:TRP47 4.0 28.1 1.0 CG2 L:THR103 4.1 36.1 1.0 C L:THR103 4.1 36.8 1.0 CB L:THR103 4.1 39.2 1.0 CD2 L:PHE104 4.1 29.0 1.0 CA H:TRP47 4.2 28.8 1.0 O H:LEU45 4.2 33.1 1.0 CG1 H:VAL46 4.3 31.2 1.0 CB L:PHE104 4.3 29.2 1.0 CA L:PHE104 4.4 29.2 1.0 O L:PHE104 4.5 34.6 1.0 O H:TRP47 4.5 33.3 1.0 CB H:VAL46 4.5 31.4 1.0 N L:THR103 4.6 33.8 1.0 CG L:PHE104 4.7 28.3 1.0 N H:VAL46 4.8 28.3 1.0 C H:TRP47 4.8 34.0 1.0 O L:TYR102 4.9 37.7 1.0 C H:LEU45 4.9 33.6 1.0 C L:PHE104 5.0 34.3 1.0 CG2 H:VAL46 5.0 31.0 1.0

Calcium binding site 4 out of 4 in the Structure of 4497 Fab Bound to Synthetic Wall Teichoic Acid Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of 4497 Fab Bound to Synthetic Wall Teichoic Acid Fragment within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca301 b:44.0 occ:1.00 O L:GLN161 2.6 26.2 1.0 N L:TRP154 2.9 19.7 1.0 CA L:GLN153 3.6 18.6 1.0 O L:HOH435 3.6 22.4 1.0 CB L:TRP154 3.7 18.2 1.0 C L:GLN153 3.7 22.5 1.0 C L:GLN161 3.7 23.4 1.0 CD1 L:LEU160 3.8 25.9 1.0 CA L:TRP154 3.8 18.5 1.0 O L:TRP154 3.9 20.1 1.0 CD1 L:TRP154 4.0 20.2 1.0 O L:VAL152 4.1 24.2 1.0 CG L:TRP154 4.3 18.5 1.0 N L:GLN161 4.3 17.8 1.0 CB L:GLN153 4.3 21.3 1.0 C L:TRP154 4.4 21.9 1.0 CA L:GLN161 4.4 19.0 1.0 CB L:GLN161 4.5 20.8 1.0 OG L:SER165 4.6 21.4 1.0 N L:GLN153 4.7 19.8 1.0 CG L:LEU160 4.8 24.9 1.0 N L:SER162 4.8 18.2 1.0 C L:VAL152 4.8 24.3 1.0 CG L:GLN153 4.9 26.3 1.0 O L:GLN153 4.9 21.9 1.0 CA L:SER162 4.9 18.3 1.0

S.M.Lehar, T.Pillow, M.Xu, L.Staben, K.K.Kajihara, R.Vandlen, L.Depalatis, H.Raab, W.L.Hazenbos, J.H.Morisaki, J.Kim, S.Park, M.Darwish, B.C.Lee, H.Hernandez, K.M.Loyet, P.Lupardus, R.Fong, D.Yan, C.Chalouni, E.Luis, Y.Khalfin, E.Plise, J.Cheong, J.P.Lyssikatos, M.Strandh, K.Koefoed, P.S.Andersen, J.A.Flygare, M.Wah Tan, E.J.Brown, S.Mariathasan. Novel Antibody-Antibiotic Conjugate Eliminates Intracellular S. Aureus. Nature V. 527 323 2015.
ISSN: ESSN 1476-4687
PubMed: 26536114
DOI: 10.1038/NATURE16057