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Calcium in PDB 3p5b: The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation

Protein crystallography data

The structure of The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation, PDB code: 3p5b was solved by P.Lo Surdo, M.J.Bottomley, A.Calzetta, E.C.Settembre, A.Cirillo, S.Pandit, Y.Ni, B.Hubbard, A.Sitlani, A.Carfi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.000, 109.701, 178.456, 90.00, 90.00, 90.00
R / Rfree (%) 27.1 / 29.8

Calcium Binding Sites:

The binding sites of Calcium atom in the The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation (pdb code 3p5b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation, PDB code: 3p5b:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3p5b

Go back to Calcium Binding Sites List in 3p5b
Calcium binding site 1 out of 3 in the The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:78.8
occ:1.00
OG1 A:THR335 2.7 52.1 1.0
O A:CYS358 2.7 54.2 1.0
O A:ALA330 2.7 54.9 1.0
O A:VAL333 3.0 57.2 1.0
OD2 A:ASP360 3.1 57.5 1.0
O A:ALA328 3.5 45.0 1.0
CB A:THR335 3.7 51.2 1.0
C A:ALA330 3.7 54.1 1.0
C A:CYS358 3.8 53.5 1.0
CG A:ASP360 3.9 57.9 1.0
CA A:PRO331 4.0 56.0 1.0
O A:PRO331 4.1 58.1 1.0
OD1 A:ASP360 4.1 59.9 1.0
N A:THR335 4.1 50.6 1.0
C A:VAL333 4.2 56.0 1.0
C A:PRO331 4.3 56.9 1.0
N A:PRO331 4.3 55.2 1.0
CA A:CYS358 4.4 54.3 1.0
CA A:THR335 4.5 50.4 1.0
C A:ALA328 4.6 44.3 1.0
CB A:CYS358 4.6 57.2 1.0
N A:ALA330 4.8 50.0 1.0
CG2 A:THR335 4.8 51.4 1.0
CA A:ALA330 4.9 52.1 1.0
C A:SER329 4.9 48.9 1.0
N A:VAL359 5.0 51.9 1.0
N A:VAL333 5.0 56.8 1.0
C A:ILE334 5.0 51.0 1.0

Calcium binding site 2 out of 3 in 3p5b

Go back to Calcium Binding Sites List in 3p5b
Calcium binding site 2 out of 3 in the The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1

b:64.3
occ:1.00
OD2 L:ASP333 2.2 94.8 1.0
O L:LEU350 2.3 98.2 1.0
O L:ILE334 2.3 87.6 1.0
O L:GLY353 3.1 99.5 1.0
CG L:ASP333 3.1 94.1 1.0
C L:LEU350 3.3 97.5 1.0
OD1 L:ASP333 3.4 93.7 1.0
C L:ILE334 3.4 87.5 1.0
N L:LEU350 3.5 95.2 1.0
CA L:ASP335 3.8 86.9 1.0
CA L:LEU350 3.9 96.7 1.0
OE1 L:GLU336 3.9 85.7 1.0
N L:ASP335 4.0 87.4 1.0
C L:GLY353 4.1 99.7 1.0
O L:GLY352 4.3 0.6 1.0
N L:ILE334 4.4 88.9 1.0
OD1 L:ASP335 4.4 86.0 1.0
CB L:ASP333 4.5 93.2 1.0
CB L:LEU350 4.5 97.1 1.0
N L:GLU351 4.5 98.6 1.0
CA L:ILE334 4.5 87.4 1.0
CD L:GLU336 4.6 85.7 1.0
C L:ASN349 4.6 94.0 1.0
OE2 L:GLU336 4.6 85.3 1.0
N L:GLU336 4.6 87.0 1.0
CA L:GLY353 4.6 0.5 1.0
C L:ASP333 4.7 90.6 1.0
CB L:ASP335 4.7 87.0 1.0
C L:ASP335 4.8 86.5 1.0
C L:GLY352 4.8 0.6 1.0
CA L:ASN349 4.9 93.2 1.0
C L:GLU351 5.0 99.5 1.0
CA L:GLU351 5.0 99.7 1.0
N L:GLY353 5.0 0.8 1.0

Calcium binding site 3 out of 3 in 3p5b

Go back to Calcium Binding Sites List in 3p5b
Calcium binding site 3 out of 3 in the The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structure of the Ldlr/PCSK9 Complex Reveals the Receptor in An Extended Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca3

b:0.8
occ:1.00
OD2 L:ASP310 3.0 89.8 1.0
OE1 L:GLU296 3.5 0.8 1.0
OE2 L:GLU296 3.6 0.2 1.0
O L:LEU311 3.7 94.3 1.0
CD L:GLU296 3.9 0.5 1.0
CA L:ASN295 3.9 97.0 1.0
O L:GLY314 4.0 92.4 1.0
CG L:ASP310 4.2 90.1 1.0
N L:ASN295 4.3 96.8 1.0
C L:LEU311 4.4 94.4 1.0
N L:GLU296 4.6 96.5 1.0
C L:ASN295 4.6 96.7 1.0
N L:LEU311 4.7 93.2 1.0
OD1 L:ASP310 4.8 89.0 1.0
OD1 L:ASN295 4.9 0.9 1.0
CB L:ASN295 4.9 98.2 1.0
O L:LYS312 4.9 95.3 1.0
C L:LYS312 4.9 95.5 1.0

Reference:

P.Lo Surdo, M.J.Bottomley, A.Calzetta, E.C.Settembre, A.Cirillo, S.Pandit, Y.G.Ni, B.Hubbard, A.Sitlani, A.Carfi. Mechanistic Implications For Ldl Receptor Degradation From the PCSK9/Ldlr Structure at Neutral pH. Embo Rep. V. 12 1300 2011.
ISSN: ISSN 1469-221X
PubMed: 22081141
DOI: 10.1038/EMBOR.2011.205
Page generated: Sat Jul 13 16:29:38 2024

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