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Calcium in PDB 2w2n: Wt PCSK9-Deltac Bound to Egf-A H306Y Mutant of Ldlr

Protein crystallography data

The structure of Wt PCSK9-Deltac Bound to Egf-A H306Y Mutant of Ldlr, PDB code: 2w2n was solved by M.J.Bottomley, A.Cirillo, L.Orsatti, L.Ruggeri, T.S.Fisher, J.C.Santoro, R.T.Cummings, R.M.Cubbon, P.Lo Surdo, A.Calzetta, A.Noto, J.Baysarowich, M.Mattu, F.Talamo, R.De Francesco, C.P.Sparrow, A.Sitlani, A.Carfi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 83.940, 83.940, 209.933, 90.00, 90.00, 90.00
R / Rfree (%) 21.332 / 25.393

Calcium Binding Sites:

The binding sites of Calcium atom in the Wt PCSK9-Deltac Bound to Egf-A H306Y Mutant of Ldlr (pdb code 2w2n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Wt PCSK9-Deltac Bound to Egf-A H306Y Mutant of Ldlr, PDB code: 2w2n:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2w2n

Go back to Calcium Binding Sites List in 2w2n
Calcium binding site 1 out of 3 in the Wt PCSK9-Deltac Bound to Egf-A H306Y Mutant of Ldlr


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Wt PCSK9-Deltac Bound to Egf-A H306Y Mutant of Ldlr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1447

b:81.0
occ:1.00
OG1 A:THR335 2.7 22.6 1.0
O A:VAL333 2.7 26.5 1.0
O A:ALA330 2.8 25.4 1.0
O A:HOH2054 3.1 44.4 1.0
O A:CYS358 3.1 26.2 1.0
OD2 A:ASP360 3.2 26.1 1.0
O A:ALA328 3.4 21.8 1.0
CB A:THR335 3.5 22.9 1.0
O A:HOH2072 3.5 51.8 1.0
C A:ALA330 3.8 25.1 1.0
C A:VAL333 3.8 26.3 1.0
N A:THR335 4.0 23.4 1.0
CG A:ASP360 4.0 25.2 1.0
CA A:PRO331 4.0 26.5 1.0
OD1 A:ASP360 4.1 29.0 1.0
NH2 A:ARG412 4.1 40.2 1.0
C A:CYS358 4.2 25.8 1.0
O A:PRO331 4.3 27.2 1.0
C A:PRO331 4.3 27.0 1.0
CA A:THR335 4.3 22.9 1.0
N A:PRO331 4.4 26.0 1.0
N A:VAL333 4.5 26.8 1.0
C A:ALA328 4.5 21.8 1.0
CA A:VAL333 4.5 26.7 1.0
CB A:VAL333 4.6 26.6 1.0
CG2 A:THR335 4.6 22.5 1.0
N A:ALA330 4.7 23.8 1.0
CA A:CYS358 4.8 26.4 1.0
C A:ILE334 4.8 24.2 1.0
N A:ILE334 4.8 25.7 1.0
C A:SER329 4.8 23.1 1.0
CA A:ALA330 4.9 24.4 1.0
CA A:ILE334 4.9 24.8 1.0
CB A:CYS358 5.0 26.5 1.0

Calcium binding site 2 out of 3 in 2w2n

Go back to Calcium Binding Sites List in 2w2n
Calcium binding site 2 out of 3 in the Wt PCSK9-Deltac Bound to Egf-A H306Y Mutant of Ldlr


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Wt PCSK9-Deltac Bound to Egf-A H306Y Mutant of Ldlr within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1334

b:35.8
occ:1.00
OD2 E:ASP310 2.3 28.2 1.0
O E:LEU311 2.4 26.6 1.0
O E:THR294 2.4 27.1 1.0
O E:HOH2006 2.4 34.0 1.0
O E:GLY314 2.4 26.8 1.0
OE1 E:GLU296 2.7 27.2 1.0
CG E:ASP310 3.5 26.3 1.0
C E:GLY314 3.5 27.1 1.0
CD E:GLU296 3.5 27.4 1.0
C E:LEU311 3.6 26.6 1.0
C E:THR294 3.6 26.9 1.0
OE2 E:GLU296 3.6 28.1 1.0
N E:GLY314 3.9 27.0 1.0
N E:LEU311 4.0 26.4 1.0
OD1 E:ASP310 4.0 27.4 1.0
O E:LYS312 4.0 27.0 1.0
CA E:GLY314 4.0 27.1 1.0
C E:ASP310 4.2 26.2 1.0
N E:THR294 4.3 27.7 1.0
C E:LYS312 4.3 27.2 1.0
O A:HOH2008 4.3 46.3 1.0
CA E:LEU311 4.4 26.2 1.0
CA E:THR294 4.5 27.4 1.0
CA E:ASP310 4.5 26.2 1.0
C E:ILE313 4.5 27.0 1.0
N E:ASN295 4.5 26.3 1.0
O E:HOH2015 4.6 38.0 1.0
CB E:ASP310 4.6 26.3 1.0
N E:LYS312 4.6 27.1 1.0
CA E:ASN295 4.6 26.0 1.0
N E:TYR315 4.6 26.9 1.0
N E:GLU296 4.6 25.9 1.0
O E:ALA291 4.7 28.3 1.0
CA E:LYS312 4.7 27.4 1.0
N E:ILE313 4.8 27.0 1.0
CB E:TYR315 4.8 26.4 1.0
O E:ASP310 4.8 26.4 1.0
CB E:THR294 4.9 27.4 1.0
CG E:GLU296 5.0 26.8 1.0
CA E:TYR315 5.0 26.9 1.0
CA E:ILE313 5.0 27.1 1.0

Calcium binding site 3 out of 3 in 2w2n

Go back to Calcium Binding Sites List in 2w2n
Calcium binding site 3 out of 3 in the Wt PCSK9-Deltac Bound to Egf-A H306Y Mutant of Ldlr


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Wt PCSK9-Deltac Bound to Egf-A H306Y Mutant of Ldlr within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1335

b:93.6
occ:1.00
O E:ASP333 2.8 41.4 1.0
OD1 E:ASP333 3.1 42.0 1.0
C E:ASP333 3.9 41.5 1.0
CG E:ASP333 4.0 41.7 1.0
OD2 E:ASP333 4.5 41.8 1.0
CA E:ASP333 4.6 41.5 1.0
O E:GLY322 4.7 36.4 1.0
CB E:ASP333 4.9 41.4 1.0

Reference:

M.J.Bottomley, A.Cirillo, L.Orsatti, L.Ruggeri, T.S.Fisher, J.C.Santoro, R.T.Cummings, R.M.Cubbon, P.Lo Surdo, A.Calzetta, A.Noto, J.Baysarowich, M.Mattu, F.Talamo, R.De Francesco, C.P.Sparrow, A.Sitlani, A.Carfi. Structural and Biochemical Characterization of the Wild Type PCSK9/Egf-Ab Complex and Natural Fh Mutants. J.Biol.Chem. V. 284 1313 2009.
ISSN: ISSN 0021-9258
PubMed: 19001363
DOI: 10.1074/JBC.M808363200
Page generated: Sat Dec 12 03:55:00 2020

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