Calcium in PDB 1n7d: Extracellular Domain of the Ldl Receptor

Protein crystallography data

The structure of Extracellular Domain of the Ldl Receptor, PDB code: 1n7d was solved by G.Rudenko, L.Henry, K.Henderson, K.Ichtchenko, M.S.Brown, J.L.Goldstein, J.Deisenhofer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.30 / 3.70
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 185.290, 185.290, 85.186, 90.00, 90.00, 120.00
R / Rfree (%) 38.1 / 38.2

Other elements in 1n7d:

The structure of Extracellular Domain of the Ldl Receptor also contains other interesting chemical elements:

Tungsten (W) 31 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Extracellular Domain of the Ldl Receptor (pdb code 1n7d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Extracellular Domain of the Ldl Receptor, PDB code: 1n7d:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1n7d

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Calcium binding site 1 out of 8 in the Extracellular Domain of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Extracellular Domain of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:0.7
occ:1.00
O A:LEU311 2.0 0.7 1.0
OD1 A:ASP310 2.4 0.7 1.0
N A:ASN295 2.5 0.7 1.0
OE2 A:GLU296 2.8 0.7 1.0
N A:ILE313 2.9 0.7 1.0
OG1 A:THR294 2.9 0.7 1.0
C A:LEU311 3.0 0.7 1.0
CA A:THR294 3.1 0.7 1.0
CB A:TYR315 3.2 0.7 1.0
C A:THR294 3.3 0.7 1.0
CG A:ASP310 3.4 0.7 1.0
CB A:THR294 3.4 0.7 1.0
CA A:ASN295 3.5 0.7 1.0
CA A:LYS312 3.5 0.7 1.0
CA A:ILE313 3.5 0.7 1.0
CD A:GLU296 3.6 0.7 1.0
N A:LYS312 3.6 0.7 1.0
OD2 A:ASP310 3.6 0.7 1.0
OE1 A:GLU296 3.7 0.7 1.0
C A:LYS312 3.7 0.7 1.0
CA A:TYR315 3.9 0.7 1.0
CD2 A:TYR315 3.9 0.7 1.0
N A:LEU311 4.0 0.7 1.0
CG A:TYR315 4.0 0.7 1.0
N A:TYR315 4.1 0.7 1.0
CA A:LEU311 4.1 0.7 1.0
O A:GLY293 4.2 0.7 1.0
CG1 A:ILE313 4.3 0.7 1.0
N A:THR294 4.4 0.7 1.0
CB A:ASN295 4.4 0.7 1.0
O A:THR294 4.5 0.7 1.0
CB A:ILE313 4.5 0.7 1.0
N A:GLY314 4.5 0.7 1.0
N A:GLU296 4.6 0.7 1.0
C A:ASN295 4.6 0.7 1.0
C A:ILE313 4.6 0.7 1.0
CB A:ASP310 4.7 0.7 1.0
C A:GLY293 4.7 0.7 1.0
CG2 A:THR294 4.9 0.7 1.0
CB A:LYS312 4.9 0.7 1.0
O A:LYS312 4.9 0.7 1.0
CG A:GLU296 5.0 0.7 1.0
C A:ASP310 5.0 0.7 1.0

Calcium binding site 2 out of 8 in 1n7d

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Calcium binding site 2 out of 8 in the Extracellular Domain of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Extracellular Domain of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:0.7
occ:1.00
O A:LEU350 2.1 0.7 1.0
OD1 A:ASN349 2.2 0.7 1.0
O A:ILE334 2.4 0.7 1.0
CD A:GLU336 2.8 0.7 1.0
OE1 A:GLU336 2.8 0.7 1.0
OE2 A:GLU336 2.8 0.7 1.0
OD2 A:ASP333 2.9 0.7 1.0
OD1 A:ASP333 3.0 0.7 1.0
C A:LEU350 3.3 0.7 1.0
CG A:ASP333 3.3 0.7 1.0
CG A:ASN349 3.4 0.7 1.0
C A:ILE334 3.5 0.7 1.0
N A:GLU336 3.5 0.7 1.0
CG A:GLU336 3.7 0.7 1.0
N A:LEU350 3.8 0.7 1.0
CA A:ASP335 4.0 0.7 1.0
N A:ASP335 4.1 0.7 1.0
N A:GLU351 4.2 0.7 1.0
ND2 A:ASN349 4.2 0.7 1.0
CA A:GLU351 4.2 0.7 1.0
CA A:LEU350 4.3 0.7 1.0
C A:ASP335 4.3 0.7 1.0
CB A:GLU336 4.3 0.7 1.0
N A:GLY352 4.4 0.7 1.0
C A:ASN349 4.4 0.7 1.0
CA A:GLU336 4.5 0.7 1.0
CB A:ASN349 4.5 0.7 1.0
O A:GLY353 4.5 0.7 1.0
CB A:TYR354 4.6 0.7 1.0
CA A:ASN349 4.6 0.7 1.0
CA A:ILE334 4.6 0.7 1.0
N A:ILE334 4.7 0.7 1.0
CB A:ASP333 4.8 0.7 1.0
C A:GLU351 4.9 0.7 1.0
C A:ASP333 4.9 0.7 1.0
CG2 A:ILE334 5.0 0.7 1.0

Calcium binding site 3 out of 8 in 1n7d

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Calcium binding site 3 out of 8 in the Extracellular Domain of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Extracellular Domain of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:0.7
occ:1.00
OD1 A:ASP200 2.1 0.7 1.0
O A:GLY198 2.2 0.7 1.0
OE1 A:GLU207 2.4 0.7 1.0
OD1 A:ASP196 2.5 0.7 1.0
CG A:ASP200 2.8 0.7 1.0
OD2 A:ASP206 2.9 0.7 1.0
NZ A:LYS582 3.0 0.7 1.0
O A:TRP193 3.0 0.7 1.0
C A:GLY198 3.2 0.7 1.0
N A:ASP200 3.3 0.7 1.0
CD A:GLU207 3.3 0.7 1.0
CG A:ASP196 3.4 0.7 1.0
CB A:ASP200 3.4 0.7 1.0
OD2 A:ASP200 3.5 0.7 1.0
OD2 A:ASP196 3.7 0.7 1.0
OE2 A:GLU207 3.7 0.7 1.0
CG A:ASP206 3.8 0.7 1.0
CA A:ASP200 3.9 0.7 1.0
CA A:GLY198 3.9 0.7 1.0
OD1 A:ASP206 3.9 0.7 1.0
CB A:TRP193 4.1 0.7 1.0
N A:PRO199 4.1 0.7 1.0
C A:TRP193 4.2 0.7 1.0
N A:GLY198 4.2 0.7 1.0
C A:PRO199 4.2 0.7 1.0
CE A:LYS582 4.4 0.7 1.0
CG A:GLU207 4.6 0.7 1.0
CA A:PRO199 4.6 0.7 1.0
CB A:ASP196 4.6 0.7 1.0
C A:ASP200 4.7 0.7 1.0
CA A:TRP193 4.8 0.7 1.0
N A:ASP196 4.8 0.7 1.0

Calcium binding site 4 out of 8 in 1n7d

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Calcium binding site 4 out of 8 in the Extracellular Domain of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Extracellular Domain of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:0.7
occ:1.00
OE2 A:GLU246 1.8 0.7 1.0
OD1 A:ASP245 2.0 0.7 1.0
O A:ARG232 2.2 0.7 1.0
CD A:GLU246 2.6 0.7 1.0
CG A:ASP245 2.6 0.7 1.0
O A:GLU237 2.7 0.7 1.0
O A:GLN233 2.8 0.7 1.0
OE1 A:GLU246 2.8 0.7 1.0
C A:GLN233 2.8 0.7 1.0
CA A:GLN233 2.9 0.7 1.0
C A:ARG232 3.0 0.7 1.0
CB A:ASP245 3.2 0.7 1.0
N A:GLN233 3.3 0.7 1.0
OD2 A:ASP245 3.5 0.7 1.0
OD1 A:ASP235 3.5 0.7 1.0
N A:CYS234 3.6 0.7 1.0
OD2 A:ASP239 3.7 0.7 1.0
C A:GLU237 3.8 0.7 1.0
CG A:GLU246 4.0 0.7 1.0
CA A:ASP245 4.1 0.7 1.0
CB A:GLU237 4.1 0.7 1.0
CG A:ASP239 4.1 0.7 1.0
C A:ASP245 4.3 0.7 1.0
N A:GLU237 4.3 0.7 1.0
CA A:GLU237 4.3 0.7 1.0
CB A:GLN233 4.3 0.7 1.0
CA A:CYS234 4.4 0.7 1.0
N A:GLU246 4.4 0.7 1.0
CB A:ASP239 4.4 0.7 1.0
CG A:ASP235 4.4 0.7 1.0
N A:ASP239 4.5 0.7 1.0
CA A:ARG232 4.5 0.7 1.0
N A:ASP235 4.5 0.7 1.0
OD1 A:ASP239 4.8 0.7 1.0
OD2 A:ASP235 4.9 0.7 1.0
O A:ASP245 4.9 0.7 1.0
N A:TYR238 4.9 0.7 1.0
CB A:GLU246 4.9 0.7 1.0
CB A:ARG232 5.0 0.7 1.0

Calcium binding site 5 out of 8 in 1n7d

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Calcium binding site 5 out of 8 in the Extracellular Domain of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Extracellular Domain of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:0.7
occ:1.00
OD1 A:ASP286 2.6 0.7 1.0
O A:LYS273 2.6 0.7 1.0
OE2 A:GLU287 2.7 0.7 1.0
OD2 A:ASP280 2.7 0.7 1.0
CG A:LYS273 2.9 0.7 1.0
OD1 A:ASN276 3.0 0.7 1.0
OD2 A:ASP286 3.1 0.7 1.0
CG A:ASP286 3.2 0.7 1.0
CD A:LYS273 3.4 0.7 1.0
CG A:ASP280 3.6 0.7 1.0
CB A:ASP280 3.6 0.7 1.0
C A:LYS273 3.7 0.7 1.0
CD A:GLU287 3.7 0.7 1.0
O A:ALA278 3.8 0.7 1.0
CG A:ASN276 3.9 0.7 1.0
CB A:LYS273 4.0 0.7 1.0
ND2 A:ASN276 4.2 0.7 1.0
CG A:GLU287 4.2 0.7 1.0
CE A:LYS273 4.3 0.7 1.0
CB A:ALA278 4.3 0.7 1.0
CA A:LYS273 4.4 0.7 1.0
C A:ALA278 4.5 0.7 1.0
N A:ASP280 4.5 0.7 1.0
N A:CYS275 4.5 0.7 1.0
N A:ASN276 4.5 0.7 1.0
CB A:ASP286 4.6 0.7 1.0
CA A:ASP280 4.6 0.7 1.0
OE1 A:GLU287 4.7 0.7 1.0
OD1 A:ASP280 4.7 0.7 1.0
N A:VAL274 4.8 0.7 1.0
O A:ASN276 4.8 0.7 1.0
CA A:ALA278 4.9 0.7 1.0

Calcium binding site 6 out of 8 in 1n7d

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Calcium binding site 6 out of 8 in the Extracellular Domain of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Extracellular Domain of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:0.7
occ:1.00
OD2 A:ASP151 1.8 0.7 1.0
O A:ASP149 2.1 0.7 1.0
OD1 A:ASP147 2.4 0.7 1.0
OD2 A:ASP147 2.5 0.7 1.0
CG A:ASP151 2.7 0.7 1.0
CG A:ASP147 2.7 0.7 1.0
OD2 A:ASP157 2.8 0.7 1.0
CB A:ASP151 3.2 0.7 1.0
C A:ASP149 3.3 0.7 1.0
OD1 A:ASP151 3.7 0.7 1.0
CB A:TRP144 3.7 0.7 1.0
CG A:ASP157 3.8 0.7 1.0
OE2 A:GLU158 3.8 0.7 1.0
O A:TRP144 3.9 0.7 1.0
C A:PRO150 3.9 0.7 1.0
N A:ASP151 4.0 0.7 1.0
O A:PRO150 4.0 0.7 1.0
CA A:ASP149 4.1 0.7 1.0
CB A:ASP147 4.1 0.7 1.0
CB A:ASP149 4.2 0.7 1.0
NZ A:LYS560 4.2 0.7 1.0
OD1 A:ASP149 4.2 0.7 1.0
CA A:ASP151 4.2 0.7 1.0
CE A:LYS560 4.2 0.7 1.0
N A:PRO150 4.2 0.7 1.0
N A:ASP149 4.3 0.7 1.0
OD1 A:ASP157 4.3 0.7 1.0
CD A:LYS560 4.3 0.7 1.0
CA A:PRO150 4.4 0.7 1.0
CA A:TRP144 4.4 0.7 1.0
O A:ASP147 4.5 0.7 1.0
C A:TRP144 4.6 0.7 1.0
CG A:ASP149 4.6 0.7 1.0
CD A:GLU158 4.6 0.7 1.0
N A:ASP147 4.6 0.7 1.0
CG A:TRP144 4.8 0.7 1.0
CA A:ASP147 4.8 0.7 1.0
CZ3 A:TRP541 4.8 0.7 1.0
OE1 A:GLU158 4.9 0.7 1.0
CB A:ASP157 4.9 0.7 1.0
CG A:LYS560 4.9 0.7 1.0
C A:ASP147 4.9 0.7 1.0
CE3 A:TRP144 5.0 0.7 1.0

Calcium binding site 7 out of 8 in 1n7d

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Calcium binding site 7 out of 8 in the Extracellular Domain of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Extracellular Domain of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:0.7
occ:1.00
OD2 A:ASP112 2.0 0.7 1.0
OD1 A:ASP108 2.6 0.7 1.0
CB A:PHE105 2.8 0.7 1.0
OD1 A:ASP118 2.9 0.7 1.0
CG A:ASP112 3.0 0.7 1.0
OD2 A:ASP118 3.0 0.7 1.0
OE2 A:GLU119 3.1 0.7 1.0
O A:PHE105 3.1 0.7 1.0
CB A:ASP112 3.2 0.7 1.0
CG A:ASP118 3.3 0.7 1.0
O A:ASP110 3.5 0.7 1.0
CG A:ASP108 3.7 0.7 1.0
OE1 A:GLU119 3.8 0.7 1.0
CD A:GLU119 3.8 0.7 1.0
CG A:PHE105 3.8 0.7 1.0
C A:PHE105 3.9 0.7 1.0
CA A:PHE105 3.9 0.7 1.0
OD1 A:ASP112 4.2 0.7 1.0
OD2 A:ASP108 4.2 0.7 1.0
N A:ASP108 4.3 0.7 1.0
CA A:ASP112 4.5 0.7 1.0
CA A:CYS107 4.5 0.7 1.0
CD2 A:PHE105 4.6 0.7 1.0
C A:ASP110 4.6 0.7 1.0
N A:ASP112 4.6 0.7 1.0
N A:CYS107 4.6 0.7 1.0
N A:PHE105 4.6 0.7 1.0
CD1 A:PHE105 4.7 0.7 1.0
CB A:ASP118 4.8 0.7 1.0
CB A:ASP108 4.9 0.7 1.0
O A:ASP112 4.9 0.7 1.0
N A:ASP110 5.0 0.7 1.0

Calcium binding site 8 out of 8 in 1n7d

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Calcium binding site 8 out of 8 in the Extracellular Domain of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Extracellular Domain of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1008

b:0.7
occ:1.00
OD1 A:ASP69 1.9 0.7 1.0
O A:TRP66 2.2 0.7 1.0
OE1 A:GLU80 2.6 0.7 1.0
OD2 A:ASP79 2.6 0.7 1.0
CG A:ASP69 2.7 0.7 1.0
O A:ASP79 2.8 0.7 1.0
O A:GLN71 2.9 0.7 1.0
C A:TRP66 3.0 0.7 1.0
OD2 A:ASP69 3.1 0.7 1.0
CA A:TRP66 3.2 0.7 1.0
CG A:ASP79 3.4 0.7 1.0
CB A:TRP66 3.5 0.7 1.0
OD1 A:ASP73 3.6 0.7 1.0
CB A:GLN71 3.7 0.7 1.0
C A:GLN71 3.8 0.7 1.0
CE3 A:TRP66 3.8 0.7 1.0
CD A:GLU80 3.8 0.7 1.0
N A:GLN71 3.9 0.7 1.0
C A:ASP79 3.9 0.7 1.0
CB A:ASP79 3.9 0.7 1.0
CB A:ASP69 3.9 0.7 1.0
CA A:GLN71 4.0 0.7 1.0
N A:ARG67 4.3 0.7 1.0
N A:ASP69 4.3 0.7 1.0
OD1 A:ASP79 4.3 0.7 1.0
CG A:TRP66 4.4 0.7 1.0
CD2 A:TRP66 4.4 0.7 1.0
CB A:ASP73 4.4 0.7 1.0
CG A:ASP73 4.4 0.7 1.0
CB A:GLU80 4.5 0.7 1.0
C A:GLY70 4.5 0.7 1.0
N A:GLY70 4.5 0.7 1.0
O A:PHE65 4.5 0.7 1.0
N A:TRP66 4.6 0.7 1.0
C A:ASP69 4.6 0.7 1.0
CA A:ASP69 4.6 0.7 1.0
CA A:ASP79 4.6 0.7 1.0
OE2 A:GLU80 4.7 0.7 1.0
CG A:GLU80 4.7 0.7 1.0
N A:ASP73 4.8 0.7 1.0
CZ3 A:TRP66 4.9 0.7 1.0
N A:CYS68 4.9 0.7 1.0
N A:GLU80 4.9 0.7 1.0
O A:ASP73 4.9 0.7 1.0
N A:VAL72 5.0 0.7 1.0
O A:GLY70 5.0 0.7 1.0
C A:PHE65 5.0 0.7 1.0

Reference:

G.Rudenko, L.Henry, K.Henderson, K.Ichtchenko, M.S.Brown, J.L.Goldstein, J.Deisenhofer. Structure of the Ldl Receptor Extracellular Domain at Endosomal pH Science V. 298 2353 2002.
ISSN: ISSN 0036-8075
PubMed: 12459547
DOI: 10.1126/SCIENCE.1078124
Page generated: Sat Dec 12 03:08:18 2020

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