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Calcium in PDB 7ytq: Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand

Protein crystallography data

The structure of Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand, PDB code: 7ytq was solved by K.Wangkanont, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.94 / 1.60
Space group P 42
Cell size a, b, c (Å), α, β, γ (°) 80.03, 80.03, 90.07, 90, 90, 90
R / Rfree (%) 18.3 / 21.3

Other elements in 7ytq:

The structure of Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand (pdb code 7ytq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand, PDB code: 7ytq:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7ytq

Go back to Calcium Binding Sites List in 7ytq
Calcium binding site 1 out of 4 in the Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:23.7
occ:1.00
 OD1 A:ASP308 2.3 22.6 1.0
OD1 A:ASN307 2.3 24.5 1.0
OE1 A:GLU285 2.3 29.3 1.0
O3 A:JMI402 2.4 25.6 0.9
OD1 A:ASN287 2.5 27.8 1.0
OE1 A:GLU293 2.5 25.2 1.0
O4 A:JMI402 2.5 25.8 0.9
O A:ASP308 2.6 25.2 1.0
CD A:GLU285 3.3 30.2 1.0
C3 A:JMI402 3.3 26.9 0.9
CG A:ASP308 3.3 30.4 1.0
C4 A:JMI402 3.3 26.5 0.9
CG A:ASN307 3.4 22.2 1.0
CG A:ASN287 3.4 26.5 1.0
CD A:GLU293 3.5 22.6 1.0
OE2 A:GLU285 3.6 32.4 1.0
C A:ASP308 3.6 20.0 1.0
N A:ASP308 3.7 22.0 1.0
ND2 A:ASN307 3.8 19.6 1.0
OE2 A:GLU293 3.8 30.6 1.0
ND2 A:ASN287 3.9 30.3 1.0
OD2 A:ASP308 4.0 26.6 1.0
CA A:ASP308 4.0 19.6 1.0
N A:ASN287 4.1 27.9 1.0
CB A:ASP308 4.3 21.1 1.0
CG A:GLU285 4.5 25.6 1.0
CB A:ASN287 4.6 25.4 1.0
N A:ASN288 4.6 28.1 1.0
C2 A:JMI402 4.7 28.0 0.9
CB A:ASN307 4.7 22.7 1.0
C A:ASN307 4.7 25.1 1.0
C5 A:JMI402 4.7 30.8 0.9
CA A:ASN287 4.8 29.4 1.0
CG A:GLU293 4.8 26.6 1.0
N A:ALA289 4.8 31.3 1.0
N A:ALA309 4.8 18.0 1.0
CB A:ALA289 4.8 34.8 1.0
CA A:ASN307 4.9 23.9 1.0
O2 A:JMI402 4.9 37.6 0.9
CB A:GLU285 4.9 25.9 1.0
CB A:GLU293 4.9 25.0 1.0
C A:ASN287 5.0 35.0 1.0

Calcium binding site 2 out of 4 in 7ytq

Go back to Calcium Binding Sites List in 7ytq
Calcium binding site 2 out of 4 in the Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:24.7
occ:1.00
 OD1 B:ASP308 2.3 22.4 1.0
O3 B:JMI402 2.4 28.5 0.8
OE1 B:GLU293 2.4 29.8 1.0
OD1 B:ASN287 2.4 29.5 1.0
OD1 B:ASN307 2.5 24.5 1.0
OE1 B:GLU285 2.5 25.9 1.0
O B:ASP308 2.6 25.3 1.0
O4 B:JMI402 2.7 24.3 0.8
CG B:ASN287 3.2 27.7 1.0
C3 B:JMI402 3.3 29.9 0.8
CG B:ASP308 3.3 24.7 1.0
CD B:GLU293 3.3 27.8 1.0
C4 B:JMI402 3.4 24.1 0.8
CD B:GLU285 3.4 27.9 1.0
CG B:ASN307 3.5 19.9 1.0
ND2 B:ASN287 3.6 38.6 1.0
OE2 B:GLU293 3.6 26.5 1.0
C B:ASP308 3.6 21.1 1.0
OE2 B:GLU285 3.8 30.3 1.0
N B:ASP308 3.8 19.4 1.0
ND2 B:ASN307 3.8 20.3 1.0
OD2 B:ASP308 3.9 29.6 1.0
CA B:ASP308 4.1 17.0 1.0
N B:ASN287 4.1 27.5 1.0
CB B:ASP308 4.3 22.2 1.0
CB B:ASN287 4.5 29.5 1.0
N B:ASN288 4.6 29.6 1.0
CG B:GLU293 4.6 24.8 1.0
CB B:ALA289 4.6 36.7 1.0
N B:ALA289 4.6 32.4 1.0
C2 B:JMI402 4.7 31.7 0.8
CG B:GLU285 4.7 24.9 1.0
CA B:ASN287 4.7 32.2 1.0
C B:ASN307 4.7 22.1 1.0
N B:ALA309 4.8 22.4 1.0
CB B:ASN307 4.8 22.8 1.0
CB B:GLU293 4.8 25.1 1.0
C5 B:JMI402 4.8 31.7 0.8
C B:ASN287 4.9 35.0 1.0
CA B:ASN307 5.0 22.8 1.0
CB B:GLU285 5.0 27.3 1.0

Calcium binding site 3 out of 4 in 7ytq

Go back to Calcium Binding Sites List in 7ytq
Calcium binding site 3 out of 4 in the Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:21.0
occ:1.00
 OD1 C:ASP308 2.3 18.0 1.0
OD1 C:ASN307 2.4 19.8 1.0
OE1 C:GLU293 2.4 22.5 1.0
OD1 C:ASN287 2.5 26.2 1.0
OE1 C:GLU285 2.5 24.9 1.0
O3 C:JMI403 2.5 26.0 0.9
O C:ASP308 2.5 20.9 1.0
O4 C:JMI403 2.6 21.2 0.9
CG C:ASP308 3.3 21.5 1.0
CD C:GLU293 3.3 18.3 1.0
C4 C:JMI403 3.4 20.2 0.9
C3 C:JMI403 3.4 26.3 0.9
CG C:ASN307 3.4 13.0 1.0
CD C:GLU285 3.4 25.1 1.0
CG C:ASN287 3.5 29.0 1.0
C C:ASP308 3.6 18.2 1.0
OE2 C:GLU293 3.6 23.5 1.0
ND2 C:ASN307 3.7 17.7 1.0
OE2 C:GLU285 3.8 26.9 1.0
N C:ASP308 3.8 16.6 1.0
ND2 C:ASN287 4.0 29.2 1.0
OD2 C:ASP308 4.0 21.5 1.0
CA C:ASP308 4.1 15.2 1.0
N C:ASN287 4.2 20.8 1.0
CB C:ASP308 4.3 18.6 1.0
CG C:GLU285 4.6 20.7 1.0
N C:ASN288 4.6 26.9 1.0
CB C:ASN287 4.7 25.8 1.0
CG C:GLU293 4.7 19.8 1.0
CB C:ASN307 4.7 21.8 1.0
C C:ASN307 4.7 17.9 1.0
C2 C:JMI403 4.8 26.0 0.9
N C:ALA309 4.8 17.1 1.0
N C:ALA289 4.8 24.5 1.0
C5 C:JMI403 4.8 28.1 0.9
CB C:ALA289 4.8 27.6 1.0
CA C:ASN287 4.8 24.9 1.0
CB C:GLU293 4.9 19.9 1.0
CA C:ASN307 4.9 16.0 1.0

Calcium binding site 4 out of 4 in 7ytq

Go back to Calcium Binding Sites List in 7ytq
Calcium binding site 4 out of 4 in the Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Langerin Carbohydrate Recognition Domain in Complex with An Alpha-Mannoside Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:17.6
occ:1.00
 OD1 D:ASP308 2.3 15.3 1.0
OD1 D:ASN307 2.4 16.3 1.0
OD1 D:ASN287 2.4 21.5 1.0
O4 D:JMI403 2.5 17.9 0.8
OE1 D:GLU285 2.5 20.8 1.0
O3 D:JMI403 2.5 18.2 0.8
O D:ASP308 2.5 18.3 1.0
OE1 D:GLU293 2.5 18.2 1.0
C4 D:JMI403 3.3 22.1 0.8
C3 D:JMI403 3.3 24.1 0.8
CG D:ASP308 3.3 18.0 1.0
CD D:GLU285 3.4 21.0 1.0
CG D:ASN307 3.4 14.0 1.0
CD D:GLU293 3.4 16.4 1.0
CG D:ASN287 3.4 22.1 1.0
C D:ASP308 3.6 13.3 1.0
ND2 D:ASN307 3.7 17.8 1.0
OE2 D:GLU293 3.7 19.6 1.0
OE2 D:GLU285 3.8 20.4 1.0
N D:ASP308 3.8 16.3 1.0
ND2 D:ASN287 4.0 25.3 1.0
CA D:ASP308 4.0 14.5 1.0
OD2 D:ASP308 4.1 19.2 1.0
N D:ASN287 4.2 21.6 1.0
CB D:ASP308 4.3 16.1 1.0
CG D:GLU285 4.6 15.4 1.0
CB D:ASN287 4.6 19.6 1.0
C2 D:JMI403 4.7 23.5 0.8
C5 D:JMI403 4.7 26.3 0.8
N D:ASN288 4.7 24.1 1.0
N D:ALA309 4.7 13.5 1.0
CB D:ASN307 4.7 15.3 1.0
C D:ASN307 4.7 16.1 1.0
CG D:GLU293 4.8 17.7 1.0
CA D:ASN287 4.8 18.9 1.0
N D:ALA289 4.8 23.8 1.0
CB D:ALA289 4.9 26.9 1.0
CB D:GLU293 5.0 18.6 1.0
CA D:ASN307 5.0 12.5 1.0
O2 D:JMI403 5.0 23.0 0.8
CB D:GLU285 5.0 17.8 1.0

Reference:

K.Wangkanont, K.Wangkanont. N/A N/A.
Page generated: Fri Jul 19 06:22:38 2024

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