Manganese 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:

Calcium

(Ca)

4 atoms

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Discovery of Glycomimetic Ligands Via Genetically-Encoded Library of Phage Displaying Mannose-Peptides, PDB code: 4czs:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese 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 Manganese with other atoms in the Mn 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:Mn1240 b:13.6 occ:1.00 OD2 A:ASP10 2.1 10.8 1.0 OE2 A:GLU8 2.1 12.3 1.0 O A:HOH2018 2.1 14.9 1.0 OD1 A:ASP19 2.2 13.2 1.0 NE2 A:HIS24 2.2 16.0 1.0 O A:HOH2017 2.3 15.8 1.0 CG A:ASP19 3.1 18.2 1.0 CG A:ASP10 3.1 12.1 1.0 CD A:GLU8 3.2 14.9 1.0 CD2 A:HIS24 3.2 17.0 1.0 CE1 A:HIS24 3.2 16.8 1.0 CB A:ASP10 3.5 11.0 1.0 OE1 A:GLU8 3.5 14.0 1.0 OD2 A:ASP19 3.6 15.0 1.0 O A:HOH2021 3.9 12.5 1.0 CA A:CA1239 4.0 13.0 1.0 OG A:SER34 4.1 14.6 1.0 OD1 A:ASP10 4.2 14.3 1.0 O A:HOH2037 4.2 20.5 1.0 CB A:ASP19 4.3 15.4 1.0 ND1 A:HIS24 4.3 15.1 1.0 CG A:HIS24 4.4 13.6 1.0 CG A:GLU8 4.5 13.1 1.0 CA A:ASP19 4.5 17.3 1.0 O A:VAL32 4.6 13.8 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn1240 b:14.1 occ:1.00 OD2 B:ASP10 2.0 9.1 1.0 O B:HOH2015 2.1 16.4 1.0 OE2 B:GLU8 2.2 14.6 1.0 NE2 B:HIS24 2.2 15.2 1.0 OD1 B:ASP19 2.2 14.1 1.0 O B:HOH2014 2.2 15.2 1.0 CG B:ASP10 3.0 11.7 1.0 CG B:ASP19 3.1 18.7 1.0 CE1 B:HIS24 3.1 15.7 1.0 CD2 B:HIS24 3.2 16.7 1.0 CD B:GLU8 3.2 16.2 1.0 CB B:ASP10 3.5 9.4 1.0 OD2 B:ASP19 3.5 17.3 1.0 OE1 B:GLU8 3.5 15.8 1.0 O B:HOH2018 4.0 13.2 1.0 O B:HOH2033 4.0 36.0 1.0 CA B:CA1239 4.1 14.6 1.0 OG B:SER34 4.1 15.7 1.0 OD1 B:ASP10 4.1 16.0 1.0 ND1 B:HIS24 4.3 14.4 1.0 CB B:ASP19 4.3 20.9 1.0 O B:HOH2037 4.3 29.2 1.0 CG B:HIS24 4.3 13.3 1.0 CG B:GLU8 4.5 14.7 1.0 O B:VAL32 4.6 14.9 1.0 CA B:ASP19 4.6 16.6 1.0 CA B:ASP10 5.0 12.0 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn1240 b:17.5 occ:1.00 OD2 C:ASP10 2.1 15.6 1.0 OE2 C:GLU8 2.1 16.4 1.0 NE2 C:HIS24 2.2 18.6 1.0 OD1 C:ASP19 2.2 18.1 1.0 O C:HOH2016 2.2 18.7 1.0 O C:HOH2015 2.4 18.6 1.0 CE1 C:HIS24 3.1 20.1 1.0 CG C:ASP10 3.1 13.4 1.0 CG C:ASP19 3.1 22.5 1.0 CD C:GLU8 3.2 18.4 1.0 CD2 C:HIS24 3.2 17.0 1.0 CB C:ASP10 3.5 13.1 1.0 OE1 C:GLU8 3.5 14.5 1.0 OD2 C:ASP19 3.5 22.3 1.0 O C:HOH2019 3.9 18.0 1.0 CA C:CA1239 4.1 17.9 1.0 OG C:SER34 4.2 17.9 1.0 OD1 C:ASP10 4.2 17.1 1.0 ND1 C:HIS24 4.2 20.5 1.0 CB C:ASP19 4.3 21.6 1.0 O C:HOH2032 4.3 34.8 1.0 CG C:HIS24 4.3 15.7 1.0 O C:HOH2031 4.4 31.3 1.0 CG C:GLU8 4.5 14.1 1.0 O C:VAL32 4.6 20.2 1.0 CA C:ASP19 4.6 20.5 1.0 O C:HOH2034 4.8 36.2 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn1240 b:19.6 occ:1.00 O D:HOH2021 1.8 26.1 1.0 OD2 D:ASP10 2.1 16.5 1.0 OE2 D:GLU8 2.1 17.1 1.0 NE2 D:HIS24 2.2 23.1 1.0 OD1 D:ASP19 2.2 20.8 1.0 O D:HOH2020 2.4 20.9 1.0 CE1 D:HIS24 3.1 21.6 1.0 CG D:ASP10 3.1 17.2 1.0 CD D:GLU8 3.1 19.1 1.0 CG D:ASP19 3.2 23.6 1.0 CD2 D:HIS24 3.2 21.9 1.0 OE1 D:GLU8 3.4 18.5 1.0 CB D:ASP10 3.5 16.6 1.0 OD2 D:ASP19 3.6 20.8 1.0 O D:HOH2023 3.9 16.2 1.0 OG D:SER34 4.0 19.3 1.0 CA D:CA1239 4.1 19.1 1.0 O D:HOH2031 4.2 38.2 1.0 ND1 D:HIS24 4.2 25.9 1.0 O D:HOH2030 4.2 33.9 1.0 OD1 D:ASP10 4.2 21.2 1.0 CG D:HIS24 4.3 19.5 1.0 CB D:ASP19 4.4 25.4 1.0 CG D:GLU8 4.5 11.7 1.0 O D:VAL32 4.6 20.9 1.0 CA D:ASP19 4.7 27.4 1.0 CA D:ASP10 5.0 19.5 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