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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

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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

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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

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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

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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

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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

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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

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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

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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

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