Atomistry » Calcium » PDB 3l7f-3ljt » 3lcp
Atomistry »
  Calcium »
    PDB 3l7f-3ljt »
      3lcp »

Calcium in PDB 3lcp: Crystal Structure of the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2

Protein crystallography data

The structure of Crystal Structure of the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2, PDB code: 3lcp was solved by E.Wigren, J.M.Bourhis, I.Kursula, J.E.Guy, Y.Lindqvist, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.45
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 58.602, 58.602, 396.870, 90.00, 90.00, 120.00
R / Rfree (%) 19.6 / 24.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2 (pdb code 3lcp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2, PDB code: 3lcp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3lcp

Go back to Calcium Binding Sites List in 3lcp
Calcium binding site 1 out of 8 in the Crystal Structure of the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2


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 the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca278

b:37.8
occ:1.00
 OD2 A:ASP181 2.1 21.2 1.0
O A:HOH16 2.3 30.8 1.0
OD1 A:ASN156 2.4 24.3 1.0
O A:HOH17 2.5 28.2 1.0
O A:PHE154 2.5 25.8 1.0
OD2 A:ASP152 2.6 26.2 1.0
OD1 A:ASP152 2.7 25.9 1.0
CG A:ASP152 3.1 21.9 1.0
CG A:ASP181 3.3 21.8 1.0
CG A:ASN156 3.4 24.5 1.0
C A:PHE154 3.7 24.9 1.0
CB A:ASN156 3.9 25.1 1.0
O A:HIS178 3.9 32.2 1.0
N A:ASN156 4.1 25.0 1.0
OD1 A:ASP181 4.2 17.5 1.0
CB A:ASP181 4.2 23.0 1.0
CA A:ASP181 4.2 23.8 1.0
CA A:PHE154 4.3 25.4 1.0
CB A:PHE154 4.4 25.9 1.0
N A:PHE154 4.5 24.3 1.0
ND2 A:ASN156 4.6 25.5 1.0
CB A:ASP152 4.6 19.6 1.0
CA A:ASN156 4.6 25.2 1.0
ND2 A:ASN162 4.7 27.5 1.0
OH A:TYR176 4.7 24.7 1.0
N A:ASP155 4.7 24.3 1.0
CZ A:PHE138 4.7 22.4 1.0
CD2 A:PHE154 4.8 29.9 1.0
N A:ASP181 4.8 25.3 1.0

Calcium binding site 2 out of 8 in 3lcp

Go back to Calcium Binding Sites List in 3lcp
Calcium binding site 2 out of 8 in the Crystal Structure of the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2


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 the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca279

b:27.9
occ:1.00
 OD1 A:ASP181 2.2 17.5 1.0
OD1 A:ASN161 2.2 19.2 1.0
O A:HOH12 2.3 28.3 1.0
OD1 A:ASN162 2.4 29.4 1.0
OD1 A:ASP157 2.5 24.9 1.0
OD1 A:ASP155 2.5 26.6 1.0
O A:HOH288 2.7 27.5 1.0
CG A:ASN161 3.3 25.5 1.0
CG A:ASP181 3.4 21.8 1.0
CG A:ASP157 3.5 27.6 1.0
CG A:ASP155 3.5 25.3 1.0
CG A:ASN162 3.5 28.0 1.0
OD2 A:ASP157 3.8 25.9 1.0
CA A:ASP155 4.0 24.7 1.0
ND2 A:ASN161 4.0 24.8 1.0
ND2 A:ASN162 4.0 27.5 1.0
CB A:ASP181 4.0 23.0 1.0
O A:ASN161 4.1 27.6 1.0
CB A:ASP155 4.2 24.4 1.0
CB A:LYS159 4.3 30.3 1.0
C A:ASN161 4.3 27.0 1.0
OD2 A:ASP155 4.3 25.8 1.0
N A:LYS159 4.4 29.6 1.0
N A:ASN161 4.4 27.8 1.0
OD2 A:ASP181 4.4 21.2 1.0
N A:ASN156 4.4 25.0 1.0
C A:ASP155 4.5 24.8 1.0
CB A:ASN161 4.6 26.2 1.0
N A:ASP157 4.6 26.1 1.0
CA A:ASN161 4.6 27.1 1.0
CA A:LYS159 4.8 29.6 1.0
CB A:ASN162 4.8 26.5 1.0
CB A:ASP157 4.9 26.8 1.0
N A:GLY158 4.9 28.2 1.0
N A:ASN162 5.0 26.4 1.0
N A:LYS160 5.0 29.5 1.0

Calcium binding site 3 out of 8 in 3lcp

Go back to Calcium Binding Sites List in 3lcp
Calcium binding site 3 out of 8 in the Crystal Structure of the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca278

b:36.1
occ:1.00
 OD2 B:ASP181 2.0 21.1 1.0
O B:PHE154 2.3 25.6 1.0
OD1 B:ASN156 2.3 24.7 1.0
O B:HOH16 2.5 30.6 1.0
OD2 B:ASP152 2.6 25.8 1.0
OD1 B:ASP152 2.8 25.9 1.0
O B:HOH17 2.9 28.4 1.0
CG B:ASP152 3.1 21.9 1.0
CG B:ASP181 3.3 21.7 1.0
CG B:ASN156 3.4 24.5 1.0
C B:PHE154 3.5 24.9 1.0
CB B:ASN156 4.0 24.9 1.0
N B:ASN156 4.1 24.9 1.0
CA B:PHE154 4.1 25.5 1.0
OD1 B:ASP181 4.1 17.8 1.0
CB B:ASP181 4.2 22.8 1.0
CB B:PHE154 4.2 26.1 1.0
O B:HIS178 4.3 32.2 1.0
CA B:ASP181 4.3 23.7 1.0
N B:PHE154 4.4 24.2 1.0
N B:ASP155 4.5 24.2 1.0
ND2 B:ASN156 4.6 25.6 1.0
CD2 B:PHE154 4.6 30.0 1.0
CB B:ASP152 4.6 19.7 1.0
ND2 B:ASN162 4.6 26.9 1.0
CA B:ASN156 4.6 24.9 1.0
CZ B:PHE138 4.7 22.6 1.0
OH B:TYR176 4.7 24.0 1.0
CG B:PHE154 4.9 28.4 1.0
CA B:ASP155 4.9 24.4 1.0
C B:ASP155 5.0 24.5 1.0
N B:ASP181 5.0 25.4 1.0
O B:ASP121 5.0 22.2 1.0

Calcium binding site 4 out of 8 in 3lcp

Go back to Calcium Binding Sites List in 3lcp
Calcium binding site 4 out of 8 in the Crystal Structure of the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca279

b:28.5
occ:1.00
 OD1 B:ASP181 2.2 17.8 1.0
OD1 B:ASN161 2.3 18.7 1.0
OD1 B:ASN162 2.3 29.6 1.0
O B:HOH12 2.5 27.9 1.0
OD1 B:ASP157 2.6 25.1 1.0
OD1 B:ASP155 2.6 25.4 1.0
CG B:ASP181 3.4 21.7 1.0
CG B:ASN161 3.4 25.1 1.0
CG B:ASN162 3.4 28.2 1.0
CG B:ASP155 3.6 25.0 1.0
CG B:ASP157 3.7 27.4 1.0
CB B:ASP181 3.9 22.8 1.0
ND2 B:ASN162 3.9 26.9 1.0
ND2 B:ASN161 3.9 24.4 1.0
CA B:ASP155 4.0 24.4 1.0
OD2 B:ASP157 4.0 25.2 1.0
O B:ASN161 4.1 27.3 1.0
CB B:ASP155 4.3 24.3 1.0
C B:ASN161 4.3 27.0 1.0
OD2 B:ASP181 4.4 21.1 1.0
CB B:LYS159 4.4 30.3 1.0
N B:ASN161 4.5 27.8 1.0
N B:ASN156 4.5 24.9 1.0
C B:ASP155 4.5 24.5 1.0
OD2 B:ASP155 4.5 25.6 1.0
CB B:ASN161 4.6 26.1 1.0
N B:LYS159 4.6 29.4 1.0
CA B:ASN161 4.6 27.0 1.0
N B:ASP157 4.7 25.8 1.0
CB B:ASN162 4.8 26.7 1.0
N B:ASN162 4.9 26.3 1.0
CA B:LYS159 5.0 29.6 1.0
O B:HOH282 5.0 17.0 1.0

Calcium binding site 5 out of 8 in 3lcp

Go back to Calcium Binding Sites List in 3lcp
Calcium binding site 5 out of 8 in the Crystal Structure of the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca158

b:22.8
occ:1.00
 OD1 C:ASP83 2.2 15.0 1.0
O C:LEU87 2.2 19.6 1.0
OD1 C:ASN85 2.2 17.8 1.0
O C:HOH4 2.3 21.4 1.0
OE2 C:GLU92 2.5 20.8 1.0
OD2 C:ASP81 2.6 19.2 1.0
OE1 C:GLU92 2.6 15.0 1.0
CD C:GLU92 2.9 16.4 1.0
CG C:ASP83 3.2 17.6 1.0
CG C:ASN85 3.3 19.1 1.0
C C:LEU87 3.4 19.2 1.0
OD2 C:ASP83 3.6 19.4 1.0
CG C:ASP81 3.7 21.7 1.0
ND2 C:ASN85 3.9 18.1 1.0
N C:LEU87 4.0 19.9 1.0
N C:ASN85 4.1 20.0 1.0
CA C:ASP81 4.2 22.2 1.0
CA C:LEU87 4.2 19.6 1.0
CB C:ASP81 4.3 22.0 1.0
CB C:ASN85 4.4 19.0 1.0
N C:LEU88 4.4 18.3 1.0
N C:ASP83 4.4 18.7 1.0
CG C:GLU92 4.4 17.3 1.0
C C:ASP81 4.5 22.0 1.0
CA C:LEU88 4.5 17.7 1.0
OD2 C:ASP89 4.5 16.9 1.0
CB C:ASP83 4.6 17.3 1.0
N C:GLY84 4.6 19.1 1.0
OD1 C:ASP81 4.6 19.5 1.0
CA C:ASN85 4.6 19.8 1.0
C C:ASN85 4.7 19.8 1.0
CB C:LEU87 4.7 19.1 1.0
N C:ASN86 4.7 20.5 1.0
CA C:ASP83 4.8 18.2 1.0
N C:TYR82 4.8 22.1 1.0
N C:ASP89 4.8 16.6 1.0
C C:ASP83 4.8 18.0 1.0
O C:ASP81 4.9 21.4 1.0

Calcium binding site 6 out of 8 in 3lcp

Go back to Calcium Binding Sites List in 3lcp
Calcium binding site 6 out of 8 in the Crystal Structure of the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca159

b:26.2
occ:1.00
 OD1 C:ASP129 2.1 23.2 1.0
OD1 C:ASN131 2.2 28.8 1.0
O C:HOH147 2.3 21.9 1.0
O C:TYR135 2.4 20.0 1.0
OD1 C:ASP133 2.6 21.1 1.0
OE1 C:GLU140 2.6 24.7 1.0
OE2 C:GLU140 2.8 22.6 1.0
CD C:GLU140 3.1 22.8 1.0
CG C:ASN131 3.3 27.4 1.0
CG C:ASP133 3.3 21.3 1.0
CG C:ASP129 3.3 25.2 1.0
C C:TYR135 3.4 19.6 1.0
OD2 C:ASP133 3.6 20.9 1.0
ND2 C:ASN131 3.6 28.4 1.0
OD2 C:ASP129 4.1 23.4 1.0
N C:TYR135 4.1 19.1 1.0
CA C:TYR135 4.2 19.5 1.0
CB C:ASP129 4.2 26.2 1.0
N C:ILE136 4.3 19.8 1.0
CB C:TYR135 4.3 18.9 1.0
CA C:ASP129 4.4 26.3 1.0
N C:ASP133 4.4 22.9 1.0
CA C:ILE136 4.5 19.7 1.0
N C:ASN131 4.5 25.6 1.0
CB C:ASP133 4.5 21.0 1.0
CG C:GLU140 4.6 23.5 1.0
CB C:ASN131 4.6 25.8 1.0
N C:ASP137 4.6 21.2 1.0
N C:LYS130 4.7 25.4 1.0
O C:HOH19 4.7 20.6 1.0
C C:ASP129 4.7 25.9 1.0
N C:ASN132 4.8 25.8 1.0
OD2 C:ASP137 4.9 27.6 1.0
CA C:ASN131 4.9 25.8 1.0
CA C:ASP133 4.9 21.8 1.0

Calcium binding site 7 out of 8 in 3lcp

Go back to Calcium Binding Sites List in 3lcp
Calcium binding site 7 out of 8 in the Crystal Structure of the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca158

b:23.7
occ:1.00
 OD1 D:ASP83 2.2 16.4 1.0
OD1 D:ASN85 2.3 18.5 1.0
O D:LEU87 2.4 19.7 1.0
OE2 D:GLU92 2.4 20.6 1.0
OD1 D:ASP81 2.4 19.9 1.0
OE1 D:GLU92 2.5 14.6 1.0
CD D:GLU92 2.8 16.3 1.0
CG D:ASP83 3.2 18.1 1.0
CG D:ASN85 3.3 19.7 1.0
CG D:ASP81 3.6 21.6 1.0
C D:LEU87 3.6 19.2 1.0
OD2 D:ASP83 3.6 19.1 1.0
ND2 D:ASN85 3.8 18.0 1.0
CA D:ASP81 4.1 22.2 1.0
N D:ASN85 4.1 20.1 1.0
N D:LEU87 4.1 19.7 1.0
OD2 D:ASP81 4.3 19.3 1.0
CG D:GLU92 4.4 17.4 1.0
CB D:ASP81 4.4 22.0 1.0
C D:ASP81 4.4 22.1 1.0
N D:ASP83 4.4 18.9 1.0
CA D:LEU87 4.4 19.4 1.0
CB D:ASN85 4.4 19.4 1.0
OD2 D:ASP89 4.5 17.0 1.0
N D:GLY84 4.5 19.2 1.0
CB D:ASP83 4.5 17.4 1.0
N D:LEU88 4.6 18.6 1.0
CA D:LEU88 4.6 17.7 1.0
CA D:ASN85 4.6 19.9 1.0
N D:TYR82 4.6 21.9 1.0
N D:ASN86 4.7 20.8 1.0
C D:ASN85 4.7 20.1 1.0
CB D:LEU87 4.7 19.4 1.0
C D:ASP83 4.7 18.6 1.0
CA D:ASP83 4.7 18.1 1.0
N D:ASP89 4.8 16.7 1.0
O D:ASP81 4.9 21.8 1.0

Calcium binding site 8 out of 8 in 3lcp

Go back to Calcium Binding Sites List in 3lcp
Calcium binding site 8 out of 8 in the Crystal Structure of the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of the Carbohydrate Recognition Domain of LMAN1 in Complex with MCFD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca159

b:27.7
occ:1.00
 O D:TYR135 2.3 19.9 1.0
OD1 D:ASP129 2.4 23.6 1.0
OD1 D:ASN131 2.4 28.4 1.0
OD1 D:ASP133 2.4 21.6 1.0
OE1 D:GLU140 2.6 25.2 1.0
OE2 D:GLU140 3.0 22.4 1.0
CG D:ASP133 3.2 21.2 1.0
CD D:GLU140 3.2 23.2 1.0
C D:TYR135 3.3 19.5 1.0
CG D:ASN131 3.3 27.5 1.0
OD2 D:ASP133 3.4 20.1 1.0
CG D:ASP129 3.6 25.4 1.0
ND2 D:ASN131 3.6 28.3 1.0
CA D:TYR135 4.1 19.6 1.0
N D:ILE136 4.2 19.6 1.0
N D:TYR135 4.2 19.2 1.0
CB D:TYR135 4.2 19.2 1.0
CA D:ILE136 4.3 19.5 1.0
OD2 D:ASP129 4.4 23.5 1.0
CB D:ASP129 4.4 26.3 1.0
N D:ASP133 4.5 22.8 1.0
N D:ASP137 4.5 21.1 1.0
CB D:ASP133 4.5 20.9 1.0
CA D:ASP129 4.6 26.2 1.0
N D:ASN131 4.7 25.6 1.0
CG D:GLU140 4.7 23.8 1.0
CB D:ASN131 4.7 26.1 1.0
OD2 D:ASP137 4.8 27.3 1.0
C D:ILE136 4.9 19.9 1.0
N D:LYS130 4.9 25.3 1.0
CA D:ASP133 4.9 21.9 1.0
C D:ASP129 5.0 26.0 1.0
N D:ASN132 5.0 25.9 1.0

Reference:

E.Wigren, J.M.Bourhis, I.Kursula, J.E.Guy, Y.Lindqvist. Crystal Structure of the LMAN1-Crd/MCFD2 Transport Receptor Complex Provides Insight Into Combined Deficiency of Factor V and Factor VIII. Febs Lett. V. 584 878 2010.
ISSN: ISSN 0014-5793
PubMed: 20138881
DOI: 10.1016/J.FEBSLET.2010.02.009
Page generated: Sat Jul 13 13:00:21 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy