Calcium in PDB 4czs: Discovery of Glycomimetic Ligands Via Genetically-Encoded Library of Phage Displaying Mannose-Peptides

The structure of Discovery of Glycomimetic Ligands Via Genetically-Encoded Library of Phage Displaying Mannose-Peptides, PDB code: 4czs was solved by S.Ng, E.Lin, K.F.Tjhung, O.Gerlits, A.Sood, B.Kasper, L.Deng, P.I.Kitov, W.L.Matochko, B.M.Paschal, C.J.Noren, J.Klassen, L.K.Mahal, L.Coates, R.J.Woods, R.Derda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.489 / 1.73
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.995, 62.761, 124.827, 90.00, 96.10, 90.00
R / Rfree (%)	19.16 / 23.74

The structure of Discovery of Glycomimetic Ligands Via Genetically-Encoded Library of Phage Displaying Mannose-Peptides also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Discovery of Glycomimetic Ligands Via Genetically-Encoded Library of Phage Displaying Mannose-Peptides (pdb code 4czs). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Discovery of Glycomimetic Ligands Via Genetically-Encoded Library of Phage Displaying Mannose-Peptides, PDB code: 4czs:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Discovery of Glycomimetic Ligands Via Genetically-Encoded Library of Phage Displaying Mannose-Peptides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Discovery of Glycomimetic Ligands Via Genetically-Encoded Library of Phage Displaying Mannose-Peptides within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1239 b:13.0 occ:1.00 O A:TYR12 2.3 14.5 1.0 OD2 A:ASP19 2.3 15.0 1.0 OD1 A:ASN14 2.4 16.1 1.0 O A:HOH2021 2.4 12.5 1.0 OD2 A:ASP10 2.4 10.8 1.0 O A:HOH2020 2.4 15.1 1.0 OD1 A:ASP10 2.5 14.3 1.0 CG A:ASP10 2.8 12.1 1.0 CG A:ASP19 3.4 18.2 1.0 CG A:ASN14 3.5 15.7 1.0 C A:TYR12 3.5 13.9 1.0 OD1 A:ASP19 3.8 13.2 1.0 N A:ASN14 3.9 12.6 1.0 CB A:ASN14 4.0 17.7 1.0 MN A:MN1240 4.0 13.6 1.0 CB A:ASP10 4.3 11.0 1.0 CA A:TYR12 4.3 16.0 1.0 O A:HOH2017 4.4 15.8 1.0 N A:TYR12 4.4 14.9 1.0 CE1 A:HIS24 4.4 16.8 1.0 CB A:TYR12 4.4 11.7 1.0 N A:PRO13 4.5 13.8 1.0 CA A:ASN14 4.6 16.0 1.0 ND2 A:ASN14 4.6 11.6 1.0 CB A:ASP19 4.6 15.4 1.0 C A:PRO13 4.6 17.5 1.0 CD2 A:TYR12 4.6 14.0 1.0 CA A:PRO13 4.6 12.6 1.0 CB A:ARG228 4.7 11.1 1.0 O A:ASP208 4.7 12.0 1.0 NE2 A:HIS24 4.7 16.0 1.0 OD2 A:ASP208 4.7 14.1 1.0 CA A:ARG228 4.8 8.3 1.0 O A:ARG228 4.9 11.5 1.0

Calcium binding site 2 out of 4 in the Discovery of Glycomimetic Ligands Via Genetically-Encoded Library of Phage Displaying Mannose-Peptides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Discovery of Glycomimetic Ligands Via Genetically-Encoded Library of Phage Displaying Mannose-Peptides within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1239 b:14.6 occ:1.00 OD2 B:ASP19 2.3 17.3 1.0 O B:TYR12 2.3 16.8 1.0 O B:HOH2017 2.4 15.7 1.0 ND2 B:ASN14 2.4 13.3 1.0 OD1 B:ASP10 2.4 16.0 1.0 OD2 B:ASP10 2.4 9.1 1.0 O B:HOH2018 2.5 13.2 1.0 CG B:ASP10 2.7 11.7 1.0 CG B:ASP19 3.4 18.7 1.0 C B:TYR12 3.5 13.2 1.0 CG B:ASN14 3.6 22.5 1.0 N B:ASN14 3.9 16.8 1.0 OD1 B:ASP19 3.9 14.1 1.0 MN B:MN1240 4.1 14.1 1.0 CB B:ASN14 4.1 19.8 1.0 O B:HOH2014 4.2 15.2 1.0 CB B:ASP10 4.2 9.4 1.0 CA B:TYR12 4.3 16.6 1.0 CB B:TYR12 4.4 11.4 1.0 N B:TYR12 4.5 16.7 1.0 N B:PRO13 4.5 16.0 1.0 CE1 B:HIS24 4.5 15.7 1.0 CA B:PRO13 4.6 17.1 1.0 O B:ASP208 4.6 13.2 1.0 C B:PRO13 4.6 18.6 1.0 OD1 B:ASN14 4.6 22.3 1.0 CA B:ASN14 4.6 15.0 1.0 CB B:ASP19 4.6 20.9 1.0 CD2 B:TYR12 4.7 16.4 1.0 OD2 B:ASP208 4.7 13.5 1.0 CB B:ARG228 4.7 14.4 1.0 CA B:ARG228 4.8 16.8 1.0 O B:ARG228 4.8 14.0 1.0 NE2 B:HIS24 4.8 15.2 1.0

Calcium binding site 3 out of 4 in the Discovery of Glycomimetic Ligands Via Genetically-Encoded Library of Phage Displaying Mannose-Peptides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Discovery of Glycomimetic Ligands Via Genetically-Encoded Library of Phage Displaying Mannose-Peptides within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1239 b:17.9 occ:1.00 O C:TYR12 2.2 19.9 1.0 O C:HOH2019 2.3 18.0 1.0 OD2 C:ASP19 2.3 22.3 1.0 OD1 C:ASN14 2.3 17.2 1.0 OD2 C:ASP10 2.4 15.6 1.0 O C:HOH2018 2.4 18.3 1.0 OD1 C:ASP10 2.4 17.1 1.0 CG C:ASP10 2.7 13.4 1.0 C C:TYR12 3.4 16.9 1.0 CG C:ASP19 3.4 22.5 1.0 CG C:ASN14 3.5 27.3 1.0 N C:ASN14 3.9 20.1 1.0 OD1 C:ASP19 3.9 18.1 1.0 CB C:ASN14 4.1 27.5 1.0 MN C:MN1240 4.1 17.5 1.0 CA C:TYR12 4.2 19.7 1.0 CB C:ASP10 4.3 13.1 1.0 N C:TYR12 4.4 16.3 1.0 CB C:TYR12 4.4 23.0 1.0 N C:PRO13 4.4 22.0 1.0 O C:HOH2015 4.5 18.6 1.0 CE1 C:HIS24 4.5 20.1 1.0 CA C:PRO13 4.5 21.9 1.0 C C:PRO13 4.5 26.6 1.0 ND2 C:ASN14 4.6 17.0 1.0 O C:ASP208 4.6 21.8 1.0 CA C:ASN14 4.6 23.7 1.0 CB C:ASP19 4.6 21.6 1.0 CD2 C:TYR12 4.7 22.8 1.0 OD2 C:ASP208 4.7 18.4 1.0 CB C:ARG228 4.8 18.0 1.0 CA C:ARG228 4.8 16.6 1.0 NE2 C:HIS24 4.8 18.6 1.0 O C:ARG228 4.9 14.7 1.0

Calcium binding site 4 out of 4 in the Discovery of Glycomimetic Ligands Via Genetically-Encoded Library of Phage Displaying Mannose-Peptides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Discovery of Glycomimetic Ligands Via Genetically-Encoded Library of Phage Displaying Mannose-Peptides within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1239 b:19.1 occ:1.00 OD2 D:ASP19 2.3 20.8 1.0 ND2 D:ASN14 2.4 18.9 1.0 O D:TYR12 2.4 18.9 1.0 OD2 D:ASP10 2.4 16.5 1.0 O D:HOH2022 2.4 23.3 1.0 OD1 D:ASP10 2.4 21.2 1.0 O D:HOH2023 2.5 16.2 1.0 CG D:ASP10 2.7 17.2 1.0 CG D:ASP19 3.4 23.6 1.0 C D:TYR12 3.6 18.4 1.0 CG D:ASN14 3.6 30.9 1.0 N D:ASN14 3.8 25.7 1.0 OD1 D:ASP19 3.8 20.8 1.0 MN D:MN1240 4.1 19.6 1.0 CB D:ASN14 4.1 28.6 1.0 CB D:ASP10 4.2 16.6 1.0 CA D:TYR12 4.4 24.7 1.0 CB D:TYR12 4.5 23.6 1.0 N D:PRO13 4.6 24.7 1.0 CE1 D:HIS24 4.6 21.6 1.0 O D:HOH2020 4.6 20.9 1.0 N D:TYR12 4.6 19.0 1.0 C D:PRO13 4.6 30.4 1.0 O D:ASP208 4.6 18.2 1.0 OD1 D:ASN14 4.6 29.8 1.0 CA D:PRO13 4.6 26.6 1.0 CA D:ASN14 4.6 31.9 1.0 CB D:ARG228 4.7 20.1 1.0 CB D:ASP19 4.7 25.4 1.0 CA D:ARG228 4.7 24.1 1.0 O D:ARG228 4.7 20.4 1.0 CD1 D:TYR12 4.8 25.3 1.0 OD1 D:ASP208 4.8 17.7 1.0 NE2 D:HIS24 4.9 23.1 1.0

S.Ng, E.Lin, P.I.Kitov, K.F.Tjhung, O.O.Gerlits, L.Deng, B.Kasper, A.Sood, B.M.Paschal, P.Zhang, C.C.Ling, J.S.Klassen, C.J.Noren, L.K.Mahal, R.J.Woods, L.Coates, R.Derda. Genetically-Encoded Fragment-Based Discovery of Glycopeptide Ligands For Carbohydrate-Binding Proteins. J.Am.Chem.Soc. V. 137 5248 2015.
ISSN: ISSN 0002-7863
PubMed: 25860443
DOI: 10.1021/JA511237N