Calcium in PDB 4wmq: Structure of Human Intelectin-1

The structure of Structure of Human Intelectin-1, PDB code: 4wmq was solved by K.Wangkanont, L.L.Kiessling, K.T.Forest, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.00 / 1.80
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	118.450, 118.450, 118.450, 90.00, 90.00, 90.00
R / Rfree (%)	13.3 / 16.4

The binding sites of Calcium atom in the Structure of Human Intelectin-1 (pdb code 4wmq). 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, PDB code: 4wmq:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:7.5 occ:1.00 OD2 A:ASP282 2.3 7.2 1.0 O A:HIS86 2.3 7.9 1.0 O A:GLY97 2.3 7.4 1.0 O A:HOH663 2.4 7.7 1.0 OD2 A:ASP133 2.4 6.7 1.0 O A:HOH589 2.4 7.6 1.0 OD1 A:ASP133 2.5 8.6 1.0 CG A:ASP133 2.8 9.2 1.0 CG A:ASP282 3.4 6.7 1.0 C A:HIS86 3.5 8.2 1.0 C A:GLY97 3.5 4.9 1.0 CB A:ASP282 4.0 5.8 1.0 CA A:ASP98 4.1 5.4 1.0 N A:ARG99 4.2 5.8 1.0 N A:HIS86 4.2 9.2 1.0 N A:ASP98 4.2 7.1 1.0 CB A:ASP133 4.2 8.5 1.0 CA A:HIS86 4.3 8.3 1.0 OD1 A:ASP282 4.4 7.4 1.0 OD1 A:ASN88 4.4 7.5 1.0 N A:GLU87 4.4 6.3 1.0 N A:ASN88 4.5 9.8 1.0 CA A:GLU87 4.5 7.2 1.0 CB A:HIS86 4.5 6.7 1.0 NH1 A:ARG99 4.6 9.0 1.0 CD1 A:TRP100 4.6 4.9 1.0 CA A:GLY97 4.6 8.2 1.0 OD1 A:ASP132 4.6 11.3 1.0 C A:ASP98 4.6 8.5 1.0 N A:ASP133 4.6 6.3 1.0 OD1 A:ASP98 4.6 8.2 1.0 ND1 A:HIS86 4.7 7.7 1.0 CA A:ASP133 4.9 5.3 1.0 C A:GLU87 4.9 8.2 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:9.1 occ:1.00 O A:GLY92 2.3 7.5 1.0 O A:HOH573 2.4 8.6 1.0 OE2 A:GLU87 2.4 8.9 1.0 O A:ASP89 2.4 8.6 1.0 O A:HOH640 2.4 8.5 1.0 OD2 A:ASP98 2.5 8.0 1.0 OD1 A:ASP98 2.5 8.2 1.0 CG A:ASP98 2.8 12.3 1.0 CD A:GLU87 3.3 10.5 1.0 C A:ASP89 3.4 9.2 1.0 C A:GLY92 3.5 9.7 1.0 OE1 A:GLU87 3.6 10.1 1.0 CA A:GLY92 4.1 11.5 1.0 N A:ASP89 4.2 9.8 1.0 O A:HOH589 4.2 7.6 1.0 CA A:ASP89 4.2 10.0 1.0 OD1 A:ASN88 4.3 7.5 1.0 N A:GLY92 4.3 11.0 1.0 N A:MET90 4.3 9.2 1.0 CB A:ASP98 4.4 8.3 1.0 OG1 A:THR95 4.4 9.9 1.0 CA A:MET90 4.5 14.7 1.0 CB A:ASP89 4.5 9.0 1.0 CA A:GLY281 4.5 9.2 1.0 N A:CYS94 4.5 7.1 1.0 N A:LYS93 4.6 8.8 1.0 CG A:GLU87 4.7 8.1 1.0 C A:MET90 4.7 17.1 1.0 N A:ASP282 4.7 6.9 1.0 O A:MET90 4.7 13.8 1.0 CA A:LYS93 4.9 7.4 1.0 O A:HOH556 4.9 9.0 1.0 N A:THR95 5.0 9.3 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:14.8 occ:1.00 O A:HOH632 2.3 15.6 1.0 O A:HOH619 2.3 21.0 1.0 O A:HOH611 2.4 13.5 1.0 OD1 A:ASN260 2.4 9.8 1.0 OE1 A:GLU274 2.4 18.6 1.0 OE2 A:GLU262 2.4 12.3 1.0 O A:HOH534 2.5 20.6 1.0 CG A:ASN260 3.4 15.2 1.0 CD A:GLU274 3.4 25.2 1.0 CD A:GLU262 3.6 13.6 1.0 OE2 A:GLU274 3.6 21.4 1.0 CB A:ASN260 4.0 13.2 1.0 OE1 A:GLU262 4.0 9.7 1.0 ND2 A:ASN243 4.0 16.3 0.2 NE2 A:GLN279 4.1 14.6 1.0 CA A:ASN260 4.3 9.3 1.0 OE1 A:GLU244 4.3 15.5 1.0 ND2 A:ASN260 4.4 13.8 1.0 NE2 A:HIS263 4.4 14.0 1.0 OE2 A:GLU244 4.5 20.6 1.0 O A:HOH689 4.6 24.9 1.0 CG A:GLU274 4.8 17.2 1.0 CG A:GLU262 4.8 10.1 1.0 CD A:GLU244 4.8 22.3 1.0 O A:CYS259 4.9 12.9 1.0 O A:HOH501 4.9 20.6 1.0 O A:HOH790 5.0 45.1 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:7.4 occ:1.00 O B:HIS86 2.2 6.8 1.0 OD2 B:ASP282 2.3 8.8 1.0 O B:GLY97 2.3 8.1 1.0 O B:HOH632 2.4 7.7 1.0 OD2 B:ASP133 2.4 8.4 1.0 O B:HOH563 2.4 7.0 1.0 OD1 B:ASP133 2.5 7.1 1.0 CG B:ASP133 2.7 6.7 1.0 CG B:ASP282 3.4 8.3 1.0 C B:HIS86 3.4 7.7 1.0 C B:GLY97 3.5 8.1 1.0 CB B:ASP282 4.0 7.2 1.0 CA B:ASP98 4.1 5.6 1.0 N B:ARG99 4.1 7.8 0.3 N B:ARG99 4.1 7.7 0.7 N B:HIS86 4.2 6.8 1.0 CB B:ASP133 4.2 7.5 1.0 N B:ASP98 4.2 6.1 1.0 CA B:HIS86 4.3 8.4 1.0 N B:GLU87 4.4 8.4 1.0 OD1 B:ASP282 4.4 6.1 1.0 CA B:GLU87 4.4 7.6 1.0 OD1 B:ASN88 4.5 9.1 1.0 CB B:HIS86 4.5 7.1 1.0 N B:ASN88 4.5 6.1 1.0 CA B:GLY97 4.6 11.1 1.0 CD1 B:TRP100 4.6 6.3 1.0 C B:ASP98 4.6 8.3 1.0 NH1 B:ARG99 4.6 5.5 0.7 ND1 B:HIS86 4.6 8.3 1.0 OD1 B:ASP98 4.6 6.7 1.0 OD1 B:ASP132 4.7 12.0 1.0 N B:ASP133 4.7 7.6 1.0 CA B:ASP133 4.9 9.7 1.0 C B:GLU87 5.0 7.1 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:8.2 occ:1.00 O B:GLY92 2.3 7.3 1.0 O B:ASP89 2.4 8.7 1.0 O B:HOH581 2.4 6.8 1.0 OE2 B:GLU87 2.4 8.9 1.0 O B:HOH582 2.4 7.8 1.0 OD2 B:ASP98 2.5 8.4 1.0 OD1 B:ASP98 2.6 6.7 1.0 CG B:ASP98 2.9 7.3 1.0 CD B:GLU87 3.4 6.4 1.0 C B:ASP89 3.4 8.7 1.0 C B:GLY92 3.5 8.7 1.0 OE1 B:GLU87 3.6 7.2 1.0 CA B:GLY92 4.1 8.4 1.0 N B:ASP89 4.2 10.3 1.0 OD1 B:ASN88 4.2 9.1 1.0 O B:HOH563 4.2 7.0 1.0 CA B:ASP89 4.3 8.0 1.0 N B:MET90 4.3 8.6 1.0 N B:GLY92 4.4 9.0 1.0 CA B:MET90 4.4 8.1 1.0 CB B:ASP98 4.4 5.7 1.0 OG1 B:THR95 4.4 9.2 1.0 CA B:GLY281 4.5 6.5 1.0 N B:CYS94 4.6 6.1 1.0 N B:LYS93 4.6 6.6 1.0 CB B:ASP89 4.6 8.4 1.0 CG B:GLU87 4.7 5.1 1.0 N B:ASP282 4.7 7.2 1.0 C B:MET90 4.7 8.5 1.0 O B:HOH569 4.9 8.1 1.0 O B:MET90 4.9 12.4 1.0 CA B:LYS93 4.9 7.8 1.0 N B:THR95 5.0 7.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:13.3 occ:1.00 OD1 B:ASN260 2.3 11.5 1.0 O B:HOH558 2.4 14.5 1.0 O B:HOH578 2.4 17.5 1.0 OE2 B:GLU262 2.4 11.3 1.0 O B:HOH605 2.4 11.7 1.0 OE1 B:GLU274 2.4 16.3 1.0 O B:HOH534 2.5 18.4 1.0 CG B:ASN260 3.4 16.9 1.0 CD B:GLU274 3.4 22.7 1.0 CD B:GLU262 3.5 12.7 1.0 OE2 B:GLU274 3.6 26.7 1.0 OE1 B:GLU262 3.9 9.1 1.0 CB B:ASN260 4.0 11.6 1.0 O B:HOH783 4.1 43.2 1.0 OE1 B:GLU244 4.3 16.1 1.0 NE2 B:GLN279 4.3 11.0 1.0 ND2 B:ASN243 4.3 16.3 1.0 CA B:ASN260 4.3 9.7 1.0 OE2 B:GLU244 4.3 15.5 1.0 NE2 B:HIS263 4.4 12.1 1.0 ND2 B:ASN260 4.5 15.1 1.0 O B:HOH776 4.6 48.3 1.0 CD B:GLU244 4.7 20.2 1.0 CG B:GLU262 4.7 9.8 1.0 CG B:GLU274 4.8 16.7 1.0

D.A.Wesener, K.Wangkanont, R.Mcbride, X.Song, M.B.Kraft, H.L.Hodges, L.C.Zarling, R.A.Splain, D.F.Smith, R.D.Cummings, J.C.Paulson, K.T.Forest, L.L.Kiessling. Recognition of Microbial Glycans By Human Intelectin-1. Nat.Struct.Mol.Biol. V. 22 603 2015.
ISSN: ESSN 1545-9985
PubMed: 26148048
DOI: 10.1038/NSMB.3053