Calcium in PDB 6usc: Structure of Human Intelectin-1 in Complex with Ko

The structure of Structure of Human Intelectin-1 in Complex with Ko, PDB code: 6usc was solved by I.W.Windsor, C.R.Isabella, P.Kosma, R.T.Raines, L.L.Kiessling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.23 / 1.59
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	118.145, 118.145, 118.145, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 18.2

The structure of Structure of Human Intelectin-1 in Complex with Ko also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Structure of Human Intelectin-1 in Complex with Ko (pdb code 6usc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of Human Intelectin-1 in Complex with Ko, PDB code: 6usc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of Human Intelectin-1 in Complex with Ko


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Human Intelectin-1 in Complex with Ko within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:19.4 occ:1.00 O A:HOH591 2.3 21.9 1.0 OD1 A:ASN260 2.4 22.5 1.0 OE2 A:GLU262 2.4 18.2 1.0 O8 A:KO2404 2.4 20.8 1.0 O A:HOH597 2.4 20.5 1.0 OE1 A:GLU274 2.4 20.4 1.0 O7 A:KO2404 2.6 24.0 1.0 CG A:ASN260 3.3 22.1 1.0 CD A:GLU274 3.4 28.8 1.0 C8 A:KO2404 3.4 26.0 1.0 C7 A:KO2404 3.4 23.6 1.0 CD A:GLU262 3.5 18.4 1.0 OE2 A:GLU274 3.7 26.5 1.0 OE1 A:GLU262 3.9 16.6 1.0 CB A:ASN260 4.0 17.8 1.0 NE2 A:GLN279 4.1 20.4 1.0 CA A:ASN260 4.3 14.2 1.0 ND2 A:ASN260 4.3 20.0 1.0 O A:HOH631 4.3 31.6 1.0 OE1 A:GLU244 4.4 20.9 1.0 OE2 A:GLU244 4.4 28.1 1.0 NE2 A:HIS263 4.5 18.7 1.0 CG A:GLU262 4.8 15.3 1.0 CG A:GLU274 4.8 23.4 1.0 C6 A:KO2404 4.8 26.2 1.0 CD A:GLU244 4.9 26.8 1.0 O A:CYS259 5.0 19.8 1.0

Calcium binding site 2 out of 6 in the Structure of Human Intelectin-1 in Complex with Ko


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Human Intelectin-1 in Complex with Ko within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:14.6 occ:1.00 OD2 A:ASP282 2.3 13.8 1.0 O A:HIS86 2.3 16.1 1.0 O A:GLY97 2.4 15.8 1.0 O A:HOH595 2.4 16.5 1.0 O A:HOH552 2.4 16.3 1.0 OD2 A:ASP133 2.5 15.9 1.0 OD1 A:ASP133 2.5 14.3 1.0 CG A:ASP133 2.8 16.8 1.0 CG A:ASP282 3.4 13.3 1.0 C A:HIS86 3.5 15.9 1.0 C A:GLY97 3.5 13.2 1.0 CB A:ASP282 4.0 13.2 1.0 CA A:ASP98 4.2 14.0 1.0 N A:ARG99 4.2 14.0 1.0 CB A:ASP133 4.3 14.7 1.0 N A:ASP98 4.3 13.5 1.0 N A:HIS86 4.3 15.2 1.0 OD1 A:ASP282 4.3 15.3 1.0 OD1 A:ASN88 4.4 19.6 1.0 CA A:HIS86 4.4 14.5 1.0 N A:GLU87 4.5 15.0 1.0 N A:ASN88 4.5 16.4 1.0 CA A:GLU87 4.5 14.8 1.0 NH1 A:ARG99 4.6 18.7 1.0 CA A:GLY97 4.6 14.8 1.0 CB A:HIS86 4.6 19.4 1.0 CD1 A:TRP100 4.6 15.0 1.0 OD1 A:ASP98 4.7 16.3 1.0 ND1 A:HIS86 4.7 15.7 1.0 C A:ASP98 4.7 15.8 1.0 OD1 A:ASP132 4.7 21.3 1.0 N A:ASP133 4.7 15.2 1.0 CA A:ASP133 4.9 16.0 1.0 C A:GLU87 5.0 18.3 1.0

Calcium binding site 3 out of 6 in the Structure of Human Intelectin-1 in Complex with Ko


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Human Intelectin-1 in Complex with Ko within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:15.9 occ:1.00 O A:GLY92 2.4 16.2 1.0 O A:HOH574 2.4 16.6 1.0 O A:HOH585 2.4 15.7 1.0 OE2 A:GLU87 2.4 17.2 1.0 O A:ASP89 2.5 17.8 1.0 OD2 A:ASP98 2.5 15.9 1.0 OD1 A:ASP98 2.5 16.3 1.0 CG A:ASP98 2.9 16.7 1.0 CD A:GLU87 3.4 19.2 1.0 C A:ASP89 3.5 17.2 1.0 C A:GLY92 3.5 19.6 1.0 OE1 A:GLU87 3.6 18.3 1.0 CA A:GLY92 4.2 20.0 1.0 N A:ASP89 4.2 19.1 1.0 O A:HOH552 4.2 16.3 1.0 CA A:ASP89 4.3 17.9 1.0 OD1 A:ASN88 4.3 19.6 1.0 N A:MET90 4.3 18.6 1.0 N A:GLY92 4.3 22.1 1.0 CB A:ASP98 4.4 13.6 1.0 OG1 A:THR95 4.4 19.4 1.0 CA A:MET90 4.5 19.8 1.0 CA A:GLY281 4.5 16.7 1.0 CB A:ASP89 4.5 20.7 1.0 N A:CYS94 4.6 14.8 1.0 N A:LYS93 4.6 17.1 1.0 C A:MET90 4.7 22.1 1.0 N A:ASP282 4.7 15.0 1.0 CG A:GLU87 4.7 16.4 1.0 O A:MET90 4.8 22.2 1.0 O A:HOH564 4.9 18.9 1.0 CA A:LYS93 4.9 17.5 1.0

Calcium binding site 4 out of 6 in the Structure of Human Intelectin-1 in Complex with Ko


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Human Intelectin-1 in Complex with Ko within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:17.5 occ:1.00 OD1 B:ASN260 2.3 17.7 1.0 O8 B:KO2404 2.3 18.5 1.0 OE2 B:GLU262 2.4 16.9 1.0 OE1 B:GLU274 2.4 19.2 1.0 O B:HOH538 2.4 17.6 1.0 O B:HOH542 2.4 18.5 1.0 O7 B:KO2404 2.6 21.4 1.0 C8 B:KO2404 3.3 20.5 1.0 CG B:ASN260 3.4 17.1 1.0 C7 B:KO2404 3.4 19.3 1.0 CD B:GLU274 3.4 25.0 1.0 CD B:GLU262 3.5 17.8 1.0 OE2 B:GLU274 3.7 22.8 1.0 OE1 B:GLU262 3.9 15.9 1.0 CB B:ASN260 4.0 13.7 1.0 NE2 B:GLN279 4.1 21.3 1.0 OE1 B:GLU244 4.2 19.3 1.0 CA B:ASN260 4.3 18.1 1.0 OE2 B:GLU244 4.3 22.7 1.0 ND2 B:ASN243 4.3 26.7 1.0 O B:HOH606 4.4 32.9 1.0 NE2 B:HIS263 4.4 16.3 1.0 ND2 B:ASN260 4.4 18.5 1.0 CD B:GLU244 4.7 25.5 1.0 O B:HOH660 4.7 41.8 1.0 CG B:GLU262 4.7 15.5 1.0 CG B:GLU274 4.8 20.6 1.0 C6 B:KO2404 4.8 25.1 1.0

Calcium binding site 5 out of 6 in the Structure of Human Intelectin-1 in Complex with Ko


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Human Intelectin-1 in Complex with Ko within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:13.4 occ:1.00 OD2 B:ASP282 2.3 13.1 1.0 O B:HIS86 2.3 12.2 1.0 O B:GLY97 2.4 13.3 1.0 O B:HOH566 2.4 13.7 1.0 OD2 B:ASP133 2.4 14.1 1.0 OD1 B:ASP133 2.5 12.3 1.0 O B:HOH544 2.5 13.2 1.0 CG B:ASP133 2.8 13.0 1.0 CG B:ASP282 3.4 12.8 1.0 C B:HIS86 3.5 12.1 1.0 C B:GLY97 3.6 12.8 1.0 CB B:ASP282 4.0 13.2 1.0 N B:ARG99 4.1 12.5 1.0 CA B:ASP98 4.1 12.2 1.0 N B:HIS86 4.2 12.8 1.0 CB B:ASP133 4.3 12.8 1.0 N B:ASP98 4.3 11.6 1.0 CA B:HIS86 4.3 13.0 1.0 OD1 B:ASP282 4.4 12.1 1.0 N B:GLU87 4.4 13.4 1.0 CA B:GLU87 4.5 14.8 1.0 OD1 B:ASN88 4.5 16.3 1.0 CB B:HIS86 4.5 13.6 1.0 N B:ASN88 4.6 14.1 1.0 CA B:GLY97 4.6 14.0 1.0 NH1 B:ARG99 4.6 15.8 1.0 C B:ASP98 4.6 10.7 1.0 ND1 B:HIS86 4.6 14.4 1.0 OD1 B:ASP98 4.7 13.9 1.0 CD1 B:TRP100 4.7 12.6 1.0 OD1 B:ASP132 4.7 21.4 1.0 N B:ASP133 4.7 13.3 1.0 O B:HOH512 4.9 22.1 1.0 CA B:ASP133 4.9 14.0 1.0

Calcium binding site 6 out of 6 in the Structure of Human Intelectin-1 in Complex with Ko


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Human Intelectin-1 in Complex with Ko within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:14.4 occ:1.00 O B:GLY92 2.4 14.4 1.0 O B:HOH547 2.4 14.8 1.0 O B:HOH564 2.4 15.1 1.0 OE2 B:GLU87 2.5 14.4 1.0 O B:ASP89 2.5 13.8 1.0 OD2 B:ASP98 2.5 14.3 1.0 OD1 B:ASP98 2.6 13.9 1.0 CG B:ASP98 2.9 15.3 1.0 CD B:GLU87 3.4 13.9 1.0 C B:GLY92 3.5 15.9 1.0 C B:ASP89 3.5 16.5 1.0 OE1 B:GLU87 3.6 14.2 1.0 CA B:GLY92 4.1 16.9 1.0 N B:ASP89 4.2 16.9 1.0 OD1 B:ASN88 4.2 16.3 1.0 O B:HOH544 4.2 13.2 1.0 CA B:ASP89 4.3 15.9 1.0 N B:GLY92 4.4 15.6 1.0 CB B:ASP98 4.4 12.1 1.0 N B:MET90 4.4 16.2 1.0 OG1 B:THR95 4.4 16.0 1.0 CA B:MET90 4.5 15.6 1.0 CA B:GLY281 4.5 11.2 1.0 N B:CYS94 4.6 15.0 1.0 N B:LYS93 4.6 14.8 1.0 CB B:ASP89 4.6 15.5 1.0 N B:ASP282 4.7 11.8 1.0 CG B:GLU87 4.8 15.0 1.0 C B:MET90 4.8 17.1 1.0 O B:HOH576 4.9 16.1 1.0 O B:MET90 4.9 17.7 1.0 CA B:LYS93 4.9 12.8 1.0

C.M.Mcmahon, C.R.Isabella, I.W.Windsor, P.Kosma, R.T.Raines, L.L.Kiessling. Stereoelectronic Effects Impact Glycan Recognition. J.Am.Chem.Soc. 2020.
ISSN: ESSN 1520-5126
PubMed: 31930911
DOI: 10.1021/JACS.9B11699