Calcium in PDB 3v64: Crystal Structure of Agrin and LRP4

The structure of Crystal Structure of Agrin and LRP4, PDB code: 3v64 was solved by Y.Zong, B.Zhang, S.Gu, K.Lee, J.Zhou, G.Yao, D.Figueiedo, K.Perry, L.Mei, R.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.460, 106.070, 112.060, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 27.3

The binding sites of Calcium atom in the Crystal Structure of Agrin and LRP4 (pdb code 3v64). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Agrin and LRP4, PDB code: 3v64:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of Agrin and LRP4


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 Agrin and LRP4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca803 b:66.7 occ:1.00 OH C:TYR720 3.1 45.1 1.0 O C:GLY707 3.3 59.7 1.0 CA C:GLY707 3.5 72.4 1.0 C C:GLY707 3.7 64.3 1.0 O C:ASN706 3.7 91.1 1.0 SG C:CYS709 3.7 46.1 1.0 N C:CYS709 3.8 61.0 1.0 CA C:CYS709 3.9 57.5 1.0 CZ C:TYR720 4.0 43.8 1.0 CE1 C:TYR720 4.1 42.6 1.0 CB C:CYS709 4.3 53.6 1.0 N C:GLY707 4.4 85.6 1.0 C C:ASN706 4.4 94.9 1.0 SG C:CYS722 4.5 30.6 1.0 N C:GLY708 4.7 59.0 1.0 C C:GLY708 5.0 59.7 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of Agrin and LRP4


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 Agrin and LRP4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:50.5 occ:1.00 O A:LEU1837 2.5 44.8 1.0 O A:GLN1887 2.6 42.0 1.0 OD1 A:ASP1889 2.8 68.0 1.0 OD2 A:ASP1820 3.0 39.7 1.0 C A:GLN1887 3.7 41.4 1.0 C A:LEU1837 3.7 43.5 1.0 CG A:ASP1889 3.8 66.1 1.0 CG A:ASP1820 4.1 39.6 1.0 N A:ASP1889 4.4 44.5 1.0 OD2 A:ASP1889 4.4 67.2 1.0 CA A:GLN1887 4.5 41.9 1.0 CA A:LEU1837 4.5 40.7 1.0 CB A:GLN1887 4.5 44.9 1.0 OD1 A:ASP1820 4.5 40.3 1.0 N A:LEU1888 4.5 37.0 1.0 CB A:ALA1885 4.6 45.1 1.0 N A:GLY1838 4.6 43.9 1.0 CA A:LEU1888 4.6 34.4 1.0 CB A:ASP1889 4.7 60.3 1.0 N A:GLN1887 4.7 40.8 1.0 CB A:LEU1837 4.7 40.3 1.0 CA A:GLY1838 4.8 44.6 1.0 C A:LEU1888 4.9 35.5 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of Agrin and LRP4


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 Agrin and LRP4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2001 b:77.2 occ:1.00 O B:GLN1887 2.7 64.8 1.0 O B:LEU1837 2.9 58.1 1.0 OD2 B:ASP1820 2.9 86.1 1.0 OD1 B:ASP1889 3.2 82.1 1.0 C B:GLN1887 3.5 66.6 1.0 CG B:ASP1889 3.6 81.2 1.0 N B:ASP1889 3.8 67.8 1.0 OD2 B:ASP1889 3.8 81.9 1.0 C B:LEU1837 3.9 57.3 1.0 CG B:ASP1820 3.9 86.7 1.0 N B:LEU1888 4.2 62.6 1.0 CA B:LEU1888 4.3 61.0 1.0 CA B:GLN1887 4.3 69.1 1.0 CB B:GLN1887 4.3 71.6 1.0 CB B:ALA1885 4.4 70.9 1.0 C B:LEU1888 4.4 61.3 1.0 OD1 B:ASP1820 4.4 90.0 1.0 N B:GLN1887 4.5 67.4 1.0 CB B:ASP1889 4.6 78.6 1.0 CA B:ASP1889 4.7 74.1 1.0 N B:GLY1838 4.8 61.6 1.0 CA B:LEU1837 4.8 55.3 1.0 CA B:GLY1838 4.9 65.2 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of Agrin and LRP4


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 Agrin and LRP4 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca801 b:85.3 occ:1.00 O D:ASN706 2.5 0.8 1.0 O D:HOH927 2.6 44.4 1.0 N D:CYS709 3.2 80.8 1.0 O D:CYS702 3.3 91.2 1.0 C D:ASN706 3.6 0.1 1.0 N D:ASN706 3.9 1.0 1.0 CA D:CYS709 3.9 75.8 1.0 SG D:CYS709 3.9 70.1 1.0 SG D:CYS713 3.9 69.5 1.0 N D:GLY708 3.9 83.6 1.0 CB D:ASN705 4.2 0.2 1.0 OH D:TYR720 4.2 72.1 1.0 C D:CYS702 4.2 88.6 1.0 C D:GLY708 4.2 76.9 1.0 CB D:CYS713 4.2 62.5 1.0 CZ D:TYR720 4.3 71.0 1.0 CA D:ASN706 4.3 0.6 1.0 CA D:GLY708 4.3 78.2 1.0 CA D:CYS702 4.4 79.8 1.0 CE1 D:TYR720 4.4 68.9 1.0 CB D:CYS709 4.5 73.9 1.0 C D:GLY707 4.6 0.0 1.0 CB D:ASN706 4.6 0.5 1.0 CB D:CYS702 4.6 80.4 1.0 N D:GLY707 4.6 0.3 1.0 O D:HOH928 4.8 57.5 1.0 CE2 D:TYR720 4.8 69.9 1.0 CA D:GLY707 4.8 0.5 1.0 C D:ASN705 5.0 0.6 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of Agrin and LRP4


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 Agrin and LRP4 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca802 b:76.2 occ:1.00 O D:VAL487 2.9 51.5 1.0 OD1 D:ASP490 2.9 75.6 1.0 O D:GLU511 2.9 65.8 1.0 OD2 D:ASP490 3.5 81.9 1.0 CG D:ASP490 3.6 79.5 1.0 C D:GLU511 4.0 64.5 1.0 C D:VAL487 4.1 49.9 1.0 CA D:GLU511 4.6 65.5 1.0 O D:THR488 4.6 48.9 1.0 CA D:THR488 4.8 47.4 1.0 N D:THR488 4.9 48.2 1.0

Y.Zong, B.Zhang, S.Gu, K.Lee, J.Zhou, G.Yao, D.Figueiredo, K.Perry, L.Mei, R.Jin. Structural Basis of Agrin-LRP4-Musk Signaling. Genes Dev. V. 26 247 2012.
ISSN: ISSN 0890-9369
PubMed: 22302937
DOI: 10.1101/GAD.180885.111