Calcium in PDB 4n37: Structure of Langerin Crd I313 D288 Complexed with Me-Man

Protein crystallography data

The structure of Structure of Langerin Crd I313 D288 Complexed with Me-Man, PDB code: 4n37 was solved by H.Feinberg, T.J.W.Rowntree, S.L.W.Tan, K.Drickamer, W.I.Weis, M.E.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.33 / 2.00
Space group P 42
Cell size a, b, c (Å), α, β, γ (°) 79.920, 79.920, 90.360, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 24.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Langerin Crd I313 D288 Complexed with Me-Man (pdb code 4n37). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Langerin Crd I313 D288 Complexed with Me-Man, PDB code: 4n37:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4n37

Go back to Calcium Binding Sites List in 4n37
Calcium binding site 1 out of 4 in the Structure of Langerin Crd I313 D288 Complexed with Me-Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Langerin Crd I313 D288 Complexed with Me-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:28.4
occ:1.00
 OE1 A:GLU293 2.4 27.9 1.0
OD1 A:ASP308 2.4 21.3 1.0
OD1 A:ASN307 2.4 24.7 1.0
OE1 A:GLU285 2.4 27.8 1.0
O A:ASP308 2.5 21.3 1.0
O4 A:MMA401 2.5 29.3 1.0
O3 A:MMA401 2.5 27.9 1.0
OD1 A:ASN287 2.5 28.2 1.0
CD A:GLU285 3.3 24.1 1.0
CG A:ASP308 3.3 23.2 1.0
C3 A:MMA401 3.3 29.2 1.0
C4 A:MMA401 3.3 25.9 1.0
CD A:GLU293 3.4 27.9 1.0
CG A:ASN287 3.4 32.8 1.0
CG A:ASN307 3.5 22.8 1.0
C A:ASP308 3.5 25.7 1.0
OE2 A:GLU285 3.6 28.5 1.0
N A:ASP308 3.7 21.5 1.0
OE2 A:GLU293 3.7 29.9 1.0
ND2 A:ASN287 3.8 30.9 1.0
ND2 A:ASN307 3.9 26.9 1.0
CA A:ASP308 4.0 23.0 1.0
OD2 A:ASP308 4.0 25.7 1.0
CB A:ASP308 4.2 26.3 1.0
N A:ASN287 4.3 32.9 1.0
CG A:GLU285 4.6 25.0 1.0
N A:ASP288 4.6 30.9 1.0
C A:ASN307 4.6 20.3 1.0
CG A:GLU293 4.7 28.1 1.0
CB A:ASN287 4.7 32.6 1.0
N A:ALA309 4.7 23.5 1.0
C5 A:MMA401 4.7 28.8 1.0
CB A:ASN307 4.7 21.6 1.0
C2 A:MMA401 4.7 31.9 1.0
CB A:GLU293 4.9 27.1 1.0
CA A:ASN307 4.9 24.0 1.0
CA A:ASN287 4.9 31.5 1.0
CB A:GLU285 4.9 26.6 1.0
N A:ALA289 5.0 35.7 1.0
O2 A:MMA401 5.0 34.2 1.0

Calcium binding site 2 out of 4 in 4n37

Go back to Calcium Binding Sites List in 4n37
Calcium binding site 2 out of 4 in the Structure of Langerin Crd I313 D288 Complexed with Me-Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Langerin Crd I313 D288 Complexed with Me-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:27.2
occ:1.00
 OD1 B:ASN307 2.4 19.3 1.0
OE1 B:GLU293 2.4 21.6 1.0
OD1 B:ASP308 2.4 22.4 1.0
OD1 B:ASN287 2.5 25.7 1.0
OE1 B:GLU285 2.5 26.1 1.0
O B:ASP308 2.5 23.3 1.0
O3 B:MMA401 2.5 29.3 1.0
O4 B:MMA401 2.5 23.4 1.0
C4 B:MMA401 3.2 29.9 1.0
C3 B:MMA401 3.3 27.0 1.0
CD B:GLU293 3.3 23.9 1.0
CG B:ASP308 3.4 24.8 1.0
CD B:GLU285 3.4 27.8 1.0
CG B:ASN287 3.4 26.1 1.0
CG B:ASN307 3.4 20.1 1.0
C B:ASP308 3.5 22.7 1.0
OE2 B:GLU293 3.6 26.2 1.0
OE2 B:GLU285 3.6 29.9 1.0
ND2 B:ASN307 3.7 19.5 1.0
N B:ASP308 3.8 19.7 1.0
ND2 B:ASN287 3.8 29.5 1.0
OD2 B:ASP308 4.0 22.6 1.0
CA B:ASP308 4.0 19.6 1.0
N B:ASN287 4.2 22.8 1.0
CB B:ASP308 4.3 20.8 1.0
CB B:ASN287 4.6 28.9 1.0
CG B:GLU285 4.7 24.7 1.0
CG B:GLU293 4.7 23.0 1.0
C5 B:MMA401 4.7 30.6 1.0
N B:ALA309 4.7 22.5 1.0
C B:ASN307 4.7 18.6 1.0
C2 B:MMA401 4.7 30.4 1.0
CB B:ASN307 4.7 21.7 1.0
N B:ASP288 4.8 24.4 1.0
CB B:ALA289 4.8 27.8 1.0
CA B:ASN287 4.8 29.0 1.0
CB B:GLU293 4.9 23.3 1.0
N B:ALA289 4.9 30.8 1.0
CA B:ASN307 5.0 21.8 1.0

Calcium binding site 3 out of 4 in 4n37

Go back to Calcium Binding Sites List in 4n37
Calcium binding site 3 out of 4 in the Structure of Langerin Crd I313 D288 Complexed with Me-Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Langerin Crd I313 D288 Complexed with Me-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:21.9
occ:1.00
 OD1 C:ASN307 2.4 18.3 1.0
OD1 C:ASP308 2.4 20.7 1.0
OE1 C:GLU293 2.4 21.0 1.0
OD1 C:ASN287 2.4 22.9 1.0
OE1 C:GLU285 2.5 20.8 1.0
O3 C:MMA401 2.5 24.0 1.0
O C:ASP308 2.5 19.8 1.0
O4 C:MMA401 2.5 18.7 1.0
C4 C:MMA401 3.3 23.3 1.0
CD C:GLU285 3.3 21.5 1.0
CD C:GLU293 3.3 19.4 1.0
C3 C:MMA401 3.3 21.8 1.0
CG C:ASN287 3.4 24.7 1.0
CG C:ASN307 3.4 18.0 1.0
CG C:ASP308 3.4 20.4 1.0
C C:ASP308 3.6 19.2 1.0
OE2 C:GLU293 3.6 18.4 1.0
OE2 C:GLU285 3.7 23.6 1.0
N C:ASP308 3.7 22.6 1.0
ND2 C:ASN307 3.8 18.0 1.0
ND2 C:ASN287 3.9 17.8 1.0
CA C:ASP308 4.1 19.3 1.0
OD2 C:ASP308 4.1 19.2 1.0
N C:ASN287 4.2 21.3 1.0
CB C:ASP308 4.3 16.3 1.0
CG C:GLU285 4.5 19.6 1.0
CB C:ASN287 4.5 19.7 1.0
C C:ASN307 4.6 20.4 1.0
CG C:GLU293 4.6 18.4 1.0
N C:ASP288 4.7 19.9 1.0
CB C:ASN307 4.7 19.8 1.0
C2 C:MMA401 4.7 25.2 1.0
N C:ALA309 4.7 18.9 1.0
C5 C:MMA401 4.7 22.4 1.0
CA C:ASN287 4.7 24.8 1.0
CB C:GLU293 4.8 18.8 1.0
CA C:ASN307 4.9 19.9 1.0
N C:ALA289 4.9 19.4 1.0
CB C:GLU285 4.9 19.4 1.0
O2 C:MMA401 4.9 25.7 1.0
CB C:ALA289 5.0 25.9 1.0

Calcium binding site 4 out of 4 in 4n37

Go back to Calcium Binding Sites List in 4n37
Calcium binding site 4 out of 4 in the Structure of Langerin Crd I313 D288 Complexed with Me-Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Langerin Crd I313 D288 Complexed with Me-Man within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:31.8
occ:1.00
 OD1 D:ASP308 2.4 34.0 1.0
OD1 D:ASN307 2.5 28.3 1.0
OE1 D:GLU293 2.5 33.4 1.0
OD1 D:ASN287 2.5 38.1 1.0
OE1 D:GLU285 2.5 33.9 1.0
O D:ASP308 2.5 30.1 1.0
O3 D:MMA401 2.5 37.2 1.0
O4 D:MMA401 2.6 39.6 1.0
C3 D:MMA401 3.3 37.8 1.0
CD D:GLU285 3.3 36.9 1.0
CD D:GLU293 3.3 28.8 1.0
CG D:ASP308 3.3 32.3 1.0
C4 D:MMA401 3.4 35.8 1.0
CG D:ASN307 3.4 25.5 1.0
CG D:ASN287 3.4 31.6 1.0
OE2 D:GLU285 3.5 37.2 1.0
C D:ASP308 3.5 29.3 1.0
OE2 D:GLU293 3.6 33.7 1.0
N D:ASP308 3.7 25.8 1.0
ND2 D:ASN307 3.8 25.1 1.0
ND2 D:ASN287 3.9 36.7 1.0
OD2 D:ASP308 4.0 28.3 1.0
CA D:ASP308 4.0 26.4 1.0
CB D:ASP308 4.3 29.3 1.0
N D:ASN287 4.3 33.6 1.0
CG D:GLU285 4.6 30.8 1.0
C D:ASN307 4.6 26.7 1.0
CG D:GLU293 4.6 32.8 1.0
CB D:ASN287 4.7 38.2 1.0
N D:ASP288 4.7 36.3 1.0
CB D:ASN307 4.7 27.6 1.0
C2 D:MMA401 4.7 42.1 1.0
N D:ALA309 4.7 27.8 1.0
C5 D:MMA401 4.8 41.0 1.0
CB D:GLU293 4.8 29.9 1.0
N D:ALA289 4.8 40.7 1.0
CB D:ALA289 4.8 35.1 1.0
CA D:ASN307 4.9 27.6 1.0
CA D:ASN287 4.9 37.2 1.0

Reference:

H.Feinberg, T.J.Rowntree, S.L.Tan, K.Drickamer, W.I.Weis, M.E.Taylor. Common Polymorphisms in Human Langerin Change Specificity For Glycan Ligands. J.Biol.Chem. V. 288 36762 2013.
ISSN: ISSN 0021-9258
PubMed: 24217250
DOI: 10.1074/JBC.M113.528000
Page generated: Sat Dec 12 05:00:23 2020

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