Calcium in PDB 4ymd: Cl-K1 Trimer Bound to Man(ALPHA1-2)Man

The structure of Cl-K1 Trimer Bound to Man(ALPHA1-2)Man, PDB code: 4ymd was solved by R.Wallis, U.Venkatraman Girija, A.R.Gingras, P.C.E.Moody, J.E.Marshall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.08 / 2.87
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.850, 106.650, 78.390, 90.00, 92.17, 90.00
R / Rfree (%)	21.3 / 26.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Cl-K1 Trimer Bound to Man(ALPHA1-2)Man (pdb code 4ymd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Cl-K1 Trimer Bound to Man(ALPHA1-2)Man, PDB code: 4ymd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in the Cl-K1 Trimer Bound to Man(ALPHA1-2)Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cl-K1 Trimer Bound to Man(ALPHA1-2)Man within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:78.7 occ:1.00 OE2 A:GLU211 2.4 0.2 1.0 OD1 A:ASP241 2.4 93.3 1.0 O A:GLU240 2.5 61.5 1.0 O A:HOH403 2.5 69.0 1.0 OD2 A:ASP207 2.5 75.2 1.0 OD1 A:ASN235 2.6 80.4 1.0 OE1 A:GLU211 2.6 99.1 1.0 CD A:GLU211 2.8 96.9 1.0 OD1 A:ASP207 3.0 87.5 1.0 CG A:ASP207 3.1 85.3 1.0 CG A:ASN235 3.2 81.3 1.0 C A:GLU240 3.5 64.8 1.0 CG A:ASP241 3.6 84.3 1.0 CB A:ASN235 3.9 72.8 1.0 CA A:CA305 3.9 0.1 1.0 CA A:ASP241 3.9 64.2 1.0 ND2 A:ASN235 4.0 86.6 1.0 N A:ASP241 4.1 67.4 1.0 CB A:ASP241 4.3 76.5 1.0 CG A:GLU211 4.3 87.2 1.0 CA A:ASN235 4.4 75.8 1.0 O A:HOH404 4.4 65.7 1.0 O2 A:GOL306 4.5 88.5 1.0 CZ A:PHE214 4.5 89.5 1.0 CA A:GLU240 4.6 64.1 1.0 OD2 A:ASP241 4.6 82.1 1.0 CB A:ASP207 4.6 88.7 1.0 OD2 A:ASP253 4.7 71.8 1.0 N A:GLU240 4.7 71.1 1.0 N A:GLY212 4.7 0.2 1.0 CA A:GLU211 4.9 0.4 1.0 O A:ASP207 5.0 83.7 1.0 CB A:GLU211 5.0 95.1 1.0 CB A:GLU240 5.0 58.0 1.0

Calcium binding site 2 out of 18 in the Cl-K1 Trimer Bound to Man(ALPHA1-2)Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cl-K1 Trimer Bound to Man(ALPHA1-2)Man within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:73.5 occ:1.00 OD1 A:ASP253 2.2 56.4 1.0 O4 A:MAN302 2.3 0.6 1.0 O3 A:MAN302 2.4 85.8 1.0 OD1 A:ASN252 2.4 64.4 1.0 OD1 A:ASN234 2.5 84.3 1.0 OE1 A:GLU240 2.6 72.7 1.0 OE1 A:GLU232 2.7 73.5 1.0 O A:ASP253 2.7 61.6 1.0 C3 A:MAN302 3.0 94.1 1.0 C4 A:MAN302 3.1 0.3 1.0 CG A:ASP253 3.3 67.0 1.0 CG A:ASN234 3.4 72.8 1.0 CD A:GLU232 3.4 84.7 1.0 CG A:ASN252 3.5 61.1 1.0 CD A:GLU240 3.6 64.1 1.0 C A:ASP253 3.7 61.4 1.0 OE2 A:GLU232 3.7 85.4 1.0 N A:ASP253 3.8 66.0 1.0 OD2 A:ASP253 3.9 71.8 1.0 OE2 A:GLU240 3.9 60.8 1.0 ND2 A:ASN234 3.9 57.1 1.0 ND2 A:ASN252 4.0 67.0 1.0 CA A:ASP253 4.1 67.7 1.0 N A:ASN234 4.1 66.6 1.0 CB A:ASP253 4.3 69.6 1.0 C5 A:MAN302 4.4 0.2 1.0 C2 A:MAN302 4.5 91.5 1.0 CB A:ASN234 4.5 79.1 1.0 C A:ASN252 4.7 68.1 1.0 CB A:ALA236 4.7 54.4 1.0 CA A:ASN234 4.7 77.5 1.0 CG A:GLU232 4.7 87.7 1.0 N A:ASN235 4.7 82.8 1.0 N A:ALA236 4.7 62.7 1.0 O2 A:MAN302 4.8 84.5 1.0 N A:VAL254 4.8 68.8 1.0 CB A:ASN252 4.8 54.5 1.0 CG A:GLU240 4.9 54.2 1.0 C A:ASN234 4.9 84.8 1.0

Calcium binding site 3 out of 18 in the Cl-K1 Trimer Bound to Man(ALPHA1-2)Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cl-K1 Trimer Bound to Man(ALPHA1-2)Man within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:0.1 occ:1.00 O A:HOH404 2.4 65.7 1.0 OD1 A:ASP241 2.4 93.3 1.0 O3 A:GOL306 2.5 0.3 1.0 OD2 A:ASP241 2.6 82.1 1.0 CG A:ASP241 2.8 84.3 1.0 O2 A:GOL306 3.1 88.5 1.0 OE2 A:GLU211 3.2 0.2 1.0 OD1 A:ASN235 3.4 80.4 1.0 O A:ASP238 3.6 91.4 1.0 C3 A:GOL306 3.7 0.7 1.0 C2 A:GOL306 3.9 0.1 1.0 OD1 A:ASP238 3.9 0.0 1.0 N A:GLU240 3.9 71.1 1.0 CA A:CA303 3.9 78.7 1.0 C A:ASP238 3.9 76.5 1.0 CA A:GLU239 4.0 81.7 1.0 N A:GLU239 4.1 72.8 1.0 C A:GLU239 4.2 80.3 1.0 CB A:ASP241 4.2 76.5 1.0 CG A:ASN235 4.2 81.3 1.0 ND2 A:ASN235 4.2 86.6 1.0 CD A:GLU211 4.3 96.9 1.0 C A:GLU240 4.3 64.8 1.0 O A:GLU240 4.4 61.5 1.0 N A:ASP241 4.5 67.4 1.0 CA A:GLU240 4.7 64.1 1.0 CA A:ASP238 4.8 75.2 1.0 CA A:ASP241 4.8 64.2 1.0 CG A:ASP238 4.8 99.4 1.0 OE1 A:GLU211 4.9 99.1 1.0

Calcium binding site 4 out of 18 in the Cl-K1 Trimer Bound to Man(ALPHA1-2)Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cl-K1 Trimer Bound to Man(ALPHA1-2)Man within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:59.1 occ:1.00 OD1 B:ASP241 2.4 80.8 1.0 O B:GLU240 2.4 81.9 1.0 OD2 B:ASP207 2.5 80.7 1.0 O B:HOH401 2.5 76.6 1.0 OE2 B:GLU211 2.5 74.8 1.0 OD1 B:ASN235 2.8 74.4 1.0 OD1 B:ASP207 2.8 74.4 1.0 OE1 B:GLU211 2.8 63.9 1.0 CG B:ASP207 3.0 74.3 1.0 CD B:GLU211 3.0 68.1 1.0 CG B:ASN235 3.4 74.0 1.0 C B:GLU240 3.4 75.2 1.0 CG B:ASP241 3.5 85.7 1.0 CA B:ASP241 3.7 72.0 1.0 CA B:CA305 4.0 82.5 1.0 N B:ASP241 4.0 73.5 1.0 CB B:ASN235 4.0 70.6 1.0 ND2 B:ASN235 4.2 66.8 1.0 CB B:ASP241 4.2 78.5 1.0 O2 B:GOL306 4.3 43.1 1.0 CZ B:PHE214 4.3 74.5 1.0 CG B:GLU211 4.5 64.3 1.0 CB B:ASP207 4.5 71.4 1.0 CA B:ASN235 4.5 66.7 1.0 OD2 B:ASP241 4.5 93.7 1.0 CA B:GLU240 4.6 63.0 1.0 N B:GLY212 4.7 68.3 1.0 OD2 B:ASP253 4.7 63.4 1.0 N B:GLU240 4.8 67.2 1.0 O B:ASP207 4.9 85.6 1.0 CE2 B:PHE214 4.9 71.4 1.0 CA B:GLU211 4.9 77.0 1.0 C B:ASP241 5.0 67.3 1.0 CB B:GLU240 5.0 48.6 1.0

Calcium binding site 5 out of 18 in the Cl-K1 Trimer Bound to Man(ALPHA1-2)Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cl-K1 Trimer Bound to Man(ALPHA1-2)Man within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:60.5 occ:1.00 OD1 B:ASP253 2.4 42.9 1.0 O4 B:MAN302 2.4 79.5 1.0 OD1 B:ASN252 2.4 68.3 1.0 OE1 B:GLU240 2.4 62.5 1.0 O3 B:MAN302 2.5 57.5 1.0 OD1 B:ASN234 2.5 81.0 1.0 O B:ASP253 2.6 50.8 1.0 OE1 B:GLU232 2.7 67.4 1.0 C3 B:MAN302 3.2 75.5 1.0 C4 B:MAN302 3.2 87.5 1.0 CG B:ASP253 3.4 57.3 1.0 CD B:GLU240 3.4 65.9 1.0 CG B:ASN234 3.4 78.3 1.0 CG B:ASN252 3.5 55.6 1.0 CD B:GLU232 3.5 61.6 1.0 OE2 B:GLU240 3.6 69.7 1.0 OE2 B:GLU232 3.7 67.0 1.0 C B:ASP253 3.7 57.8 1.0 ND2 B:ASN252 3.9 51.5 1.0 ND2 B:ASN234 3.9 75.3 1.0 N B:ASP253 4.0 41.5 1.0 OD2 B:ASP253 4.0 63.4 1.0 CA B:ASP253 4.2 57.9 1.0 N B:ASN234 4.3 64.5 1.0 CB B:ASP253 4.4 65.6 1.0 CB B:ASN234 4.6 80.6 1.0 C5 B:MAN302 4.6 0.3 1.0 C2 B:MAN302 4.6 0.3 1.0 CB B:ALA236 4.7 46.0 1.0 C B:ASN252 4.7 51.1 1.0 CG B:GLU240 4.7 58.5 1.0 CG B:GLU232 4.8 49.8 1.0 N B:VAL254 4.8 56.3 1.0 CB B:ASN252 4.8 44.3 1.0 CA B:ASN234 4.8 66.0 1.0 N B:ALA236 4.8 63.2 1.0 O2 B:MAN302 4.9 0.1 1.0 N B:ASN235 4.9 46.6 1.0

Calcium binding site 6 out of 18 in the Cl-K1 Trimer Bound to Man(ALPHA1-2)Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cl-K1 Trimer Bound to Man(ALPHA1-2)Man within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca305 b:82.5 occ:1.00 O2 B:GOL306 2.3 43.1 1.0 O3 B:GOL306 2.5 74.8 1.0 OE2 B:GLU211 2.8 74.8 1.0 OD1 B:ASP241 2.9 80.8 1.0 OD1 B:ASP238 3.0 74.1 1.0 C3 B:GOL306 3.0 75.9 1.0 OD1 B:ASN235 3.1 74.4 1.0 C2 B:GOL306 3.1 70.0 1.0 OD2 B:ASP241 3.2 93.7 1.0 CG B:ASP241 3.4 85.7 1.0 O B:ASP238 3.4 73.8 1.0 ND2 B:ASN235 3.6 66.8 1.0 C B:ASP238 3.7 61.9 1.0 CG B:ASN235 3.8 74.0 1.0 CD B:GLU211 3.8 68.1 1.0 CA B:CA303 4.0 59.1 1.0 CG B:ASP238 4.0 67.2 1.0 N B:GLU239 4.1 67.1 1.0 N B:GLU240 4.3 67.2 1.0 CA B:ASP238 4.3 60.9 1.0 CA B:GLU239 4.3 77.7 1.0 C1 B:GOL306 4.4 70.6 1.0 OE1 B:GLU211 4.5 63.9 1.0 CG B:GLU211 4.6 64.3 1.0 C B:GLU239 4.6 76.3 1.0 O B:GLU240 4.7 81.9 1.0 O1 B:GOL306 4.7 78.2 1.0 CB B:ASP238 4.8 53.3 1.0 C B:GLU240 4.8 75.2 1.0 OD2 B:ASP238 4.8 75.1 1.0 CB B:ASP241 4.8 78.5 1.0 CB B:GLU211 4.9 63.7 1.0

Calcium binding site 7 out of 18 in the Cl-K1 Trimer Bound to Man(ALPHA1-2)Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cl-K1 Trimer Bound to Man(ALPHA1-2)Man within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca303 b:58.3 occ:1.00 OD2 D:ASP207 2.4 73.8 1.0 OD1 D:ASP241 2.4 89.2 1.0 OE1 D:GLU211 2.5 75.1 1.0 O D:GLU240 2.5 63.4 1.0 OE2 D:GLU211 2.7 80.4 1.0 OD1 D:ASN235 2.7 73.7 1.0 OD1 D:ASP207 2.8 79.5 1.0 CD D:GLU211 2.9 76.5 1.0 CG D:ASP207 2.9 72.7 1.0 CG D:ASN235 3.3 78.1 1.0 C D:GLU240 3.5 67.8 1.0 CG D:ASP241 3.6 80.9 1.0 CA D:ASP241 3.8 70.8 1.0 CA D:CA305 3.9 71.2 1.0 CB D:ASN235 3.9 73.7 1.0 N D:ASP241 4.0 75.2 1.0 ND2 D:ASN235 4.1 58.2 1.0 CB D:ASP241 4.2 79.5 1.0 CG D:GLU211 4.4 67.7 1.0 CB D:ASP207 4.4 75.4 1.0 CA D:ASN235 4.4 69.6 1.0 O2 D:GOL306 4.5 47.1 1.0 CZ D:PHE214 4.5 0.5 1.0 OD2 D:ASP241 4.6 80.3 1.0 CA D:GLU240 4.6 57.8 1.0 OD2 D:ASP253 4.7 64.1 1.0 N D:GLY212 4.7 73.5 1.0 N D:GLU240 4.8 73.8 1.0 O D:ASP207 4.8 80.3 1.0 CA D:GLU211 4.9 78.9 1.0 C D:ASP241 5.0 64.6 1.0

Calcium binding site 8 out of 18 in the Cl-K1 Trimer Bound to Man(ALPHA1-2)Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cl-K1 Trimer Bound to Man(ALPHA1-2)Man within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca304 b:72.9 occ:1.00 OD1 D:ASP253 2.2 76.5 1.0 O3 D:MAN302 2.4 86.7 1.0 OD1 D:ASN234 2.4 89.3 1.0 O4 D:MAN302 2.4 81.8 1.0 OE1 D:GLU240 2.5 63.1 1.0 OD1 D:ASN252 2.6 72.5 1.0 OE1 D:GLU232 2.7 78.6 1.0 O D:ASP253 2.7 79.3 1.0 C3 D:MAN302 2.9 94.1 1.0 C4 D:MAN302 3.2 90.6 1.0 CG D:ASP253 3.3 73.2 1.0 CG D:ASN234 3.3 70.0 1.0 CD D:GLU232 3.4 80.3 1.0 CD D:GLU240 3.6 66.9 1.0 OE2 D:GLU232 3.7 81.6 1.0 C D:ASP253 3.7 73.4 1.0 CG D:ASN252 3.7 64.0 1.0 ND2 D:ASN234 3.8 77.1 1.0 OD2 D:ASP253 3.9 64.1 1.0 N D:ASP253 3.9 62.2 1.0 OE2 D:GLU240 4.0 71.8 1.0 N D:ASN234 4.1 59.6 1.0 CA D:ASP253 4.1 68.1 1.0 ND2 D:ASN252 4.2 58.5 1.0 C5 D:MAN302 4.2 0.1 1.0 CB D:ASP253 4.3 73.3 1.0 C2 D:MAN302 4.3 0.3 1.0 CB D:ASN234 4.4 73.6 1.0 CA D:ASN234 4.6 74.1 1.0 CB D:ALA236 4.7 61.0 1.0 N D:ASN235 4.7 59.0 1.0 N D:ALA236 4.7 68.7 1.0 C D:ASN252 4.7 69.1 1.0 CG D:GLU232 4.7 75.3 1.0 N D:VAL254 4.8 75.2 1.0 C D:ASN234 4.9 61.6 1.0 CG D:GLU240 4.9 68.4 1.0 O2 D:MAN302 4.9 0.0 1.0 CB D:ASN252 4.9 69.6 1.0

Calcium binding site 9 out of 18 in the Cl-K1 Trimer Bound to Man(ALPHA1-2)Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cl-K1 Trimer Bound to Man(ALPHA1-2)Man within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca305 b:71.2 occ:1.00 O3 D:GOL306 2.3 85.6 1.0 O2 D:GOL306 2.4 47.1 1.0 OD1 D:ASP241 2.5 89.2 1.0 OE1 D:GLU211 2.6 75.1 1.0 OD2 D:ASP241 2.6 80.3 1.0 CG D:ASP241 2.9 80.9 1.0 C3 D:GOL306 3.0 87.3 1.0 C2 D:GOL306 3.0 79.8 1.0 OD1 D:ASP238 3.5 85.4 1.0 CD D:GLU211 3.6 76.5 1.0 OD1 D:ASN235 3.7 73.7 1.0 CA D:CA303 3.9 58.3 1.0 ND2 D:ASN235 4.1 58.2 1.0 O D:ASP238 4.2 85.8 1.0 CG D:ASN235 4.3 78.1 1.0 CG D:GLU211 4.3 67.7 1.0 CB D:ASP241 4.4 79.5 1.0 CB D:GLU211 4.5 71.0 1.0 C1 D:GOL306 4.5 89.0 1.0 OE2 D:GLU211 4.5 80.4 1.0 C D:ASP238 4.6 71.5 1.0 CG D:ASP238 4.6 78.8 1.0 O D:GLU240 4.9 63.4 1.0 N D:GLU240 4.9 73.8 1.0 N D:GLU239 5.0 59.5 1.0

Calcium binding site 10 out of 18 in the Cl-K1 Trimer Bound to Man(ALPHA1-2)Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Cl-K1 Trimer Bound to Man(ALPHA1-2)Man within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca303 b:72.2 occ:1.00 OD2 F:ASP207 2.4 77.2 1.0 O F:GLU240 2.6 79.2 1.0 OE2 F:GLU211 2.6 82.4 1.0 OE1 F:GLU211 2.6 92.9 1.0 OD1 F:ASN235 2.7 81.3 1.0 OD1 F:ASP241 2.7 71.7 1.0 OD1 F:ASP207 2.9 89.5 1.0 CD F:GLU211 3.0 84.5 1.0 CG F:ASP207 3.0 76.1 1.0 CG F:ASN235 3.3 67.5 1.0 C F:GLU240 3.7 76.4 1.0 CB F:ASN235 3.8 54.4 1.0 CG F:ASP241 3.9 87.4 1.0 CA F:CA305 4.0 0.9 1.0 CA F:ASP241 4.0 86.2 1.0 ND2 F:ASN235 4.1 63.0 1.0 CZ F:PHE214 4.2 84.4 1.0 CA F:ASN235 4.3 62.6 1.0 N F:ASP241 4.3 88.8 1.0 CG F:GLU211 4.4 76.2 1.0 O2 F:GOL306 4.5 60.6 1.0 CB F:ASP207 4.5 66.0 1.0 CB F:ASP241 4.5 88.3 1.0 OD2 F:ASP253 4.5 54.0 1.0 N F:GLY212 4.6 79.7 1.0 CE1 F:PHE214 4.7 75.8 1.0 CA F:GLU240 4.8 60.6 1.0 CE2 F:PHE214 4.9 78.1 1.0 OD2 F:ASP241 4.9 95.3 1.0 N F:GLU240 5.0 80.2 1.0 CA F:GLU211 5.0 75.5 1.0

U.V.Girija, C.M.Furze, A.R.Gingras, T.Yoshizaki, K.Ohtani, J.E.Marshall, A.K.Wallis, W.J.Schwaeble, M.El-Mezgueldi, D.A.Mitchell, P.C.E.Moody, N.Wakamiya, R.Wallis. Molecular Basis of Sugar Recognition By Collectin-K1 and the Effects of Mutations Associated with 3MC Syndrome To Be Published.