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Calcium in PDB 4wmy: Structure of Human Intelectin-1 in Complex with Allyl-Beta- Galactofuranose

Protein crystallography data

The structure of Structure of Human Intelectin-1 in Complex with Allyl-Beta- Galactofuranose, PDB code: 4wmy 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) 28.59 / 1.60
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 117.865, 117.865, 117.865, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 18

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Human Intelectin-1 in Complex with Allyl-Beta- Galactofuranose (pdb code 4wmy). 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 Allyl-Beta- Galactofuranose, PDB code: 4wmy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4wmy

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Calcium binding site 1 out of 6 in the Structure of Human Intelectin-1 in Complex with Allyl-Beta- Galactofuranose


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 Allyl-Beta- Galactofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:15.3
occ:0.92
 OD2 A:ASP282 2.3 17.2 1.0
O A:HIS86 2.3 18.0 1.0
O A:GLY97 2.4 17.0 1.0
O A:HOH648 2.4 18.0 1.0
OD1 A:ASP133 2.4 17.6 1.0
OD2 A:ASP133 2.4 16.7 1.0
O A:HOH607 2.4 16.7 1.0
CG A:ASP133 2.7 18.0 1.0
CG A:ASP282 3.4 19.1 1.0
C A:HIS86 3.5 19.6 1.0
C A:GLY97 3.5 16.3 1.0
CB A:ASP282 4.0 16.5 1.0
CA A:ASP98 4.1 14.6 1.0
CB A:ASP133 4.2 16.4 1.0
N A:ARG99 4.2 17.0 1.0
N A:ASP98 4.2 16.9 1.0
N A:HIS86 4.3 20.2 1.0
CA A:HIS86 4.4 16.9 1.0
OD1 A:ASP282 4.4 17.2 1.0
OD1 A:ASN88 4.4 18.2 1.0
N A:GLU87 4.4 17.3 1.0
CA A:GLU87 4.5 18.2 1.0
N A:ASN88 4.5 17.4 1.0
N A:ASP133 4.5 19.2 1.0
NH1 A:ARG99 4.6 17.3 1.0
CB A:HIS86 4.6 18.4 1.0
CA A:GLY97 4.6 17.4 1.0
OD1 A:ASP132 4.6 20.5 1.0
C A:ASP98 4.6 16.0 1.0
CD1 A:TRP100 4.6 15.2 1.0
ND1 A:HIS86 4.7 17.8 1.0
OD1 A:ASP98 4.7 15.7 1.0
CA A:ASP133 4.8 16.3 1.0
C A:GLU87 5.0 18.2 1.0

Calcium binding site 2 out of 6 in 4wmy

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


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 Allyl-Beta- Galactofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:15.4
occ:0.90
 O A:GLY92 2.3 16.8 1.0
O A:HOH596 2.3 17.5 1.0
O A:HOH658 2.4 16.7 1.0
O A:ASP89 2.5 16.4 1.0
OD2 A:ASP98 2.5 16.1 1.0
OE2 A:GLU87 2.5 18.9 1.0
OD1 A:ASP98 2.5 15.7 1.0
CG A:ASP98 2.8 13.6 1.0
CD A:GLU87 3.4 21.1 1.0
C A:ASP89 3.5 18.3 1.0
C A:GLY92 3.5 19.2 1.0
OE1 A:GLU87 3.6 18.5 1.0
CA A:GLY92 4.1 17.8 1.0
N A:ASP89 4.2 16.7 1.0
O A:HOH607 4.2 16.7 1.0
OD1 A:ASN88 4.3 18.2 1.0
CA A:ASP89 4.3 16.8 1.0
N A:GLY92 4.3 19.4 1.0
N A:MET90 4.3 19.4 1.0
CB A:ASP98 4.4 14.5 1.0
OG1 A:THR95 4.4 19.4 1.0
CA A:MET90 4.5 20.8 1.0
CA A:GLY281 4.5 19.0 1.0
N A:CYS94 4.5 16.4 1.0
N A:LYS93 4.6 18.9 1.0
CB A:ASP89 4.6 18.1 1.0
C A:MET90 4.7 24.4 1.0
N A:ASP282 4.7 17.4 1.0
O A:MET90 4.7 24.0 1.0
CG A:GLU87 4.8 15.8 1.0
CA A:LYS93 4.9 17.9 1.0
O A:HOH545 4.9 18.3 1.0
N A:THR95 5.0 19.0 1.0

Calcium binding site 3 out of 6 in 4wmy

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


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 Allyl-Beta- Galactofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:17.7
occ:0.80
 O A:HOH678 2.3 23.8 1.0
OAB A:3S6404 2.3 24.3 1.0
OE1 A:GLU274 2.4 25.9 1.0
OE2 A:GLU262 2.4 20.1 1.0
O A:HOH606 2.4 23.5 1.0
OD1 A:ASN260 2.4 19.6 1.0
OAC A:3S6404 2.6 24.6 1.0
CAG A:3S6404 3.4 23.7 1.0
CD A:GLU274 3.4 27.6 1.0
CG A:ASN260 3.4 17.8 1.0
CAK A:3S6404 3.4 23.6 1.0
CD A:GLU262 3.5 22.2 1.0
OE2 A:GLU274 3.7 27.2 1.0
CB A:ASN260 4.0 19.2 1.0
OE1 A:GLU262 4.0 18.4 1.0
NE2 A:GLN279 4.1 20.4 1.0
ND2 A:ASN243 4.1 19.5 0.3
CA A:ASN260 4.2 19.1 1.0
OE1 A:GLU244 4.3 22.9 1.0
ND2 A:ASN260 4.4 23.3 1.0
OE2 A:GLU244 4.5 23.9 1.0
NE2 A:HIS263 4.5 22.0 1.0
CG A:GLU274 4.7 27.9 1.0
O A:HOH623 4.8 30.3 1.0
CG A:GLU262 4.8 18.4 1.0
CAO A:3S6404 4.8 38.7 1.0
CD A:GLU244 4.8 25.7 1.0
O A:CYS259 4.8 18.7 1.0
O A:HOH501 4.9 24.6 1.0

Calcium binding site 4 out of 6 in 4wmy

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


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 Allyl-Beta- Galactofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:11.3
occ:1.00
 O B:HIS86 2.3 11.3 1.0
OD2 B:ASP282 2.3 11.4 1.0
O B:GLY97 2.4 10.3 1.0
O B:HOH633 2.4 10.8 1.0
OD2 B:ASP133 2.4 11.6 1.0
O B:HOH595 2.4 11.3 1.0
OD1 B:ASP133 2.5 11.6 1.0
CG B:ASP133 2.8 11.7 1.0
CG B:ASP282 3.4 10.2 1.0
C B:HIS86 3.5 13.2 1.0
C B:GLY97 3.5 10.3 1.0
CB B:ASP282 4.0 10.1 1.0
CA B:ASP98 4.1 9.2 1.0
N B:ARG99 4.2 10.1 0.7
N B:ARG99 4.2 10.2 0.3
N B:HIS86 4.2 10.4 1.0
CB B:ASP133 4.3 10.4 1.0
N B:ASP98 4.3 9.1 1.0
CA B:HIS86 4.3 11.4 1.0
OD1 B:ASP282 4.4 9.6 1.0
N B:GLU87 4.4 11.0 1.0
CA B:GLU87 4.4 11.6 1.0
OD1 B:ASN88 4.5 13.5 1.0
N B:ASN88 4.5 11.6 1.0
CB B:HIS86 4.5 10.6 1.0
NH1 B:ARG99 4.6 7.9 0.7
CA B:GLY97 4.6 12.6 1.0
C B:ASP98 4.6 9.9 1.0
CD1 B:TRP100 4.6 10.5 1.0
ND1 B:HIS86 4.6 11.6 1.0
OD1 B:ASP132 4.7 15.4 1.0
OD1 B:ASP98 4.7 11.6 1.0
N B:ASP133 4.7 10.9 1.0
CA B:ASP133 4.9 10.3 1.0
C B:GLU87 5.0 11.8 1.0

Calcium binding site 5 out of 6 in 4wmy

Go back to Calcium Binding Sites List in 4wmy
Calcium binding site 5 out of 6 in the Structure of Human Intelectin-1 in Complex with Allyl-Beta- Galactofuranose


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 Allyl-Beta- Galactofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:11.0
occ:1.00
 O B:HOH597 2.3 11.8 1.0
O B:GLY92 2.4 12.2 1.0
OE2 B:GLU87 2.4 11.9 1.0
O B:ASP89 2.4 11.5 1.0
O B:HOH576 2.4 10.9 1.0
OD2 B:ASP98 2.5 10.4 1.0
OD1 B:ASP98 2.5 11.6 1.0
CG B:ASP98 2.9 10.4 1.0
CD B:GLU87 3.3 9.5 1.0
C B:ASP89 3.4 10.6 1.0
C B:GLY92 3.5 11.1 1.0
OE1 B:GLU87 3.6 11.3 1.0
CA B:GLY92 4.1 12.5 1.0
N B:ASP89 4.2 12.6 1.0
OD1 B:ASN88 4.2 13.5 1.0
O B:HOH595 4.2 11.3 1.0
CA B:ASP89 4.3 11.4 1.0
N B:MET90 4.3 12.0 1.0
N B:GLY92 4.4 11.8 1.0
CB B:ASP98 4.4 9.8 1.0
OG1 B:THR95 4.4 11.5 1.0
CA B:MET90 4.4 12.4 1.0
CA B:GLY281 4.5 9.7 1.0
N B:CYS94 4.6 9.6 1.0
CB B:ASP89 4.6 11.0 1.0
N B:LYS93 4.6 11.0 1.0
N B:ASP282 4.6 10.7 1.0
CG B:GLU87 4.7 11.6 1.0
C B:MET90 4.7 14.2 1.0
O B:HOH590 4.9 12.5 1.0
O B:MET90 4.9 15.9 1.0
CA B:LYS93 4.9 10.5 1.0
N B:THR95 5.0 9.5 1.0

Calcium binding site 6 out of 6 in 4wmy

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Calcium binding site 6 out of 6 in the Structure of Human Intelectin-1 in Complex with Allyl-Beta- Galactofuranose


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 Allyl-Beta- Galactofuranose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:15.9
occ:1.00
 OD1 B:ASN260 2.3 16.4 1.0
OE1 B:GLU274 2.3 17.2 1.0
OE2 B:GLU262 2.4 14.1 1.0
OAB B:3S6404 2.4 18.4 1.0
O B:HOH598 2.4 15.9 1.0
O B:HOH573 2.5 17.1 1.0
OAC B:3S6404 2.6 18.0 1.0
CD B:GLU274 3.3 18.8 1.0
CAG B:3S6404 3.4 20.5 1.0
CG B:ASN260 3.4 15.8 1.0
CAK B:3S6404 3.5 18.8 1.0
CD B:GLU262 3.5 13.8 1.0
OE2 B:GLU274 3.6 18.2 1.0
CB B:ASN260 3.9 14.2 1.0
OE1 B:GLU262 4.0 13.8 1.0
O B:HOH575 4.0 34.5 1.0
NE2 B:GLN279 4.2 15.8 1.0
OE1 B:GLU244 4.3 17.2 1.0
CA B:ASN260 4.3 16.9 1.0
OE2 B:GLU244 4.3 19.4 1.0
ND2 B:ASN243 4.3 20.6 1.0
NE2 B:HIS263 4.4 15.2 1.0
ND2 B:ASN260 4.5 17.2 1.0
CG B:GLU274 4.7 16.5 1.0
CD B:GLU244 4.7 21.5 1.0
O B:HOH776 4.8 36.2 1.0
CG B:GLU262 4.8 13.9 1.0
CAO B:3S6404 4.8 21.5 1.0
OAJ B:3S6404 5.0 28.4 1.0

Reference:

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
Page generated: Wed Jul 9 02:39:46 2025

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