Atomistry » Calcium » PDB 1scr-1spj » 1sl5
Atomistry »
  Calcium »
    PDB 1scr-1spj »
      1sl5 »

Calcium in PDB 1sl5: Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with Lnfp III (Dextra L504).

Protein crystallography data

The structure of Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with Lnfp III (Dextra L504)., PDB code: 1sl5 was solved by Y.Guo, H.Feinberg, E.Conroy, D.A.Mitchell, R.Alvarez, O.Blixt, M.E.Taylor, W.I.Weis, K.Drickamer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.02 / 1.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 72.570, 55.370, 29.630, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 22.3

Other elements in 1sl5:

The structure of Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with Lnfp III (Dextra L504). also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with Lnfp III (Dextra L504). (pdb code 1sl5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with Lnfp III (Dextra L504)., PDB code: 1sl5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1sl5

Go back to Calcium Binding Sites List in 1sl5
Calcium binding site 1 out of 2 in the Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with Lnfp III (Dextra L504).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with Lnfp III (Dextra L504). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:12.5
occ:1.00
O A:HOH407 2.2 7.8 1.0
OE1 A:GLU324 2.4 15.3 1.0
OD1 A:ASN350 2.4 16.2 1.0
OE2 A:GLU324 2.5 14.3 1.0
OD2 A:ASP320 2.5 13.7 1.0
OD1 A:ASP355 2.5 12.5 1.0
O A:GLU354 2.5 12.0 1.0
OD1 A:ASP320 2.7 16.7 1.0
CD A:GLU324 2.8 15.3 1.0
CG A:ASP320 2.9 15.4 1.0
CG A:ASN350 3.2 16.3 1.0
C A:GLU354 3.4 13.0 1.0
CG A:ASP355 3.6 13.2 1.0
CA A:ASP355 3.7 11.0 1.0
CB A:ASN350 3.9 16.1 1.0
N A:ASP355 3.9 12.2 1.0
O A:HOH405 4.1 12.8 1.0
CB A:ASP355 4.1 12.4 1.0
ND2 A:ASN350 4.1 15.7 1.0
O A:HOH461 4.1 25.5 1.0
CZ2 A:TRP327 4.2 12.4 1.0
N A:GLU354 4.2 12.4 1.0
CG A:GLU324 4.3 17.2 1.0
O A:HOH404 4.3 14.8 1.0
CB A:ASP320 4.5 16.3 1.0
CA A:GLU354 4.5 12.3 1.0
CA A:ASN350 4.5 16.6 1.0
OD2 A:ASP355 4.6 13.8 1.0
OD2 A:ASP366 4.6 13.9 1.0
CH2 A:TRP327 4.7 10.9 1.0
O A:ASP320 4.8 16.8 1.0
N A:GLY325 4.9 19.3 1.0
CA A:GLU324 4.9 20.1 1.0
C A:ASP355 5.0 10.6 1.0
CE2 A:TRP327 5.0 10.9 1.0

Calcium binding site 2 out of 2 in 1sl5

Go back to Calcium Binding Sites List in 1sl5
Calcium binding site 2 out of 2 in the Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with Lnfp III (Dextra L504).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with Lnfp III (Dextra L504). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:11.8
occ:1.00
OD1 A:ASN349 2.3 12.7 1.0
OD1 A:ASP366 2.3 11.7 1.0
OE1 A:GLU354 2.3 13.3 1.0
O4 A:FUC3 2.4 11.7 1.0
OD1 A:ASN365 2.4 11.4 1.0
O A:ASP366 2.5 12.2 1.0
O3 A:FUC3 2.5 12.5 1.0
OE1 A:GLU347 2.5 12.7 1.0
C4 A:FUC3 3.3 10.6 1.0
C3 A:FUC3 3.3 12.1 1.0
CG A:ASN349 3.3 12.8 1.0
CG A:ASP366 3.3 12.4 1.0
CD A:GLU354 3.3 16.9 1.0
CD A:GLU347 3.4 13.3 1.0
CG A:ASN365 3.5 10.5 1.0
C A:ASP366 3.6 10.7 1.0
ND2 A:ASN349 3.7 9.4 1.0
C2 A:FUC3 3.7 12.5 1.0
N A:ASP366 3.7 10.8 1.0
OE2 A:GLU347 3.8 12.8 1.0
OE2 A:GLU354 3.8 19.4 1.0
ND2 A:ASN365 3.9 9.4 1.0
OD2 A:ASP366 4.0 13.9 1.0
CA A:ASP366 4.1 11.3 1.0
N A:ASN349 4.1 14.1 1.0
CB A:ASP366 4.3 12.5 1.0
O2 A:FUC3 4.5 12.3 1.0
CB A:ASN349 4.6 14.2 1.0
CG A:GLU354 4.6 15.3 1.0
N A:ASN350 4.6 16.5 1.0
C5 A:FUC3 4.6 14.1 1.0
N A:ASP367 4.7 9.7 1.0
CB A:GLU354 4.7 13.9 1.0
C A:ASN365 4.7 11.9 1.0
CG A:GLU347 4.7 11.7 1.0
CA A:ASN349 4.8 14.5 1.0
CB A:ASN365 4.8 9.7 1.0
O5 A:FUC3 4.8 14.7 1.0
C1 A:FUC3 4.9 13.3 1.0
CA A:ASP367 5.0 8.2 1.0
CA A:ASN365 5.0 10.5 1.0

Reference:

Y.Guo, H.Feinberg, E.Conroy, D.A.Mitchell, R.Alvarez, O.Blixt, M.E.Taylor, W.I.Weis, K.Drickamer. Structural Basis For Distinct Ligand-Binding and Targeting Properties of the Receptors Dc-Sign and Dc-Signr Nat.Struct.Mol.Biol. V. 11 591 2004.
ISSN: ISSN 1545-9993
PubMed: 15195147
DOI: 10.1038/NSMB784
Page generated: Thu Jul 11 22:40:21 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy