Calcium in PDB 6vfv: Crystal Structure of Human Protocadherin 8 EC5-EC6

The structure of Crystal Structure of Human Protocadherin 8 EC5-EC6, PDB code: 6vfv was solved by O.J.Harrison, J.Brasch, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.90 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.658, 29.498, 92.442, 90.00, 98.46, 90.00
R / Rfree (%)	22.5 / 26.4

The structure of Crystal Structure of Human Protocadherin 8 EC5-EC6 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Human Protocadherin 8 EC5-EC6 (pdb code 6vfv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human Protocadherin 8 EC5-EC6, PDB code: 6vfv:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Human Protocadherin 8 EC5-EC6


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 Human Protocadherin 8 EC5-EC6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca707 b:40.0 occ:1.00 OD1 A:ASN462 2.2 62.9 1.0 OD2 A:ASP494 2.3 42.8 1.0 O A:ASN500 2.4 40.6 1.0 O A:ASN464 2.4 50.2 1.0 OD1 A:ASP494 2.5 41.2 1.0 OD1 A:ASP496 2.5 45.5 1.0 CG A:ASP494 2.7 41.8 1.0 OD2 A:ASP554 2.7 35.2 1.0 CG A:ASN462 3.4 63.6 1.0 HB2 A:ASP496 3.4 56.2 1.0 HB3 A:ASP554 3.5 41.3 1.0 CG A:ASP554 3.6 35.1 1.0 HB2 A:ASP554 3.6 41.3 1.0 C A:ASN500 3.6 41.6 1.0 CG A:ASP496 3.6 46.5 1.0 C A:ASN464 3.7 50.2 1.0 HA2 A:GLY501 3.7 42.6 1.0 HD21 A:ASN462 3.8 75.9 1.0 H A:ASN464 3.8 63.1 1.0 CB A:ASP554 3.8 34.4 1.0 HB3 A:ASN500 3.8 53.1 1.0 HA A:ALA465 4.0 36.3 1.0 ND2 A:ASN462 4.0 63.3 1.0 HD12 A:LEU560 4.0 50.9 1.0 CB A:ASP496 4.0 46.9 1.0 HB2 A:ASN464 4.1 62.1 1.0 CB A:ASP494 4.1 41.4 1.0 HA A:ASN462 4.1 79.0 1.0 HB3 A:ASP494 4.3 49.6 1.0 HA A:ASN500 4.4 51.8 1.0 HB2 A:LEU560 4.4 48.9 1.0 HD3 A:PRO466 4.4 46.1 1.0 CA A:ASN500 4.4 43.1 1.0 HB3 A:ASP496 4.5 56.2 1.0 N A:ASN464 4.5 52.6 1.0 N A:GLY501 4.5 36.7 1.0 CA A:GLY501 4.5 35.5 1.0 CA A:ASN464 4.5 51.5 1.0 CB A:ASN462 4.5 65.4 1.0 CB A:ASN500 4.6 44.2 1.0 HB2 A:ASP494 4.6 49.6 1.0 N A:ALA465 4.6 31.4 1.0 OD1 A:ASP554 4.7 35.6 1.0 CA A:ALA465 4.7 30.3 1.0 CA A:ASN462 4.7 65.9 1.0 OD2 A:ASP496 4.7 47.4 1.0 CB A:ASN464 4.7 51.8 1.0 HA A:ASP494 4.8 49.8 1.0 HB2 A:ASN462 4.8 78.5 1.0 HD22 A:ASN462 4.8 75.9 1.0 C A:ASN462 4.9 65.2 1.0 HB3 A:ASN464 4.9 62.1 1.0 HG3 A:PRO466 4.9 45.4 1.0 CD1 A:LEU560 5.0 42.4 1.0 C A:ALA465 5.0 29.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human Protocadherin 8 EC5-EC6


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 Human Protocadherin 8 EC5-EC6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca708 b:32.7 occ:1.00 OE2 A:GLU479 2.2 31.1 1.0 OD1 A:ASP539 2.2 31.9 1.0 OD2 A:ASP575 2.6 35.4 1.0 OE1 A:GLU541 2.6 35.3 1.0 CG A:ASP539 3.1 31.8 1.0 HE1 A:HIS576 3.4 46.2 1.0 CD A:GLU479 3.4 30.4 1.0 CG A:ASP575 3.7 34.2 1.0 OD2 A:ASP539 3.7 33.0 1.0 HB2 A:GLU541 3.8 43.8 1.0 CD A:GLU541 3.9 36.0 1.0 H A:GLU541 3.9 40.7 1.0 HA A:ASP539 3.9 35.3 1.0 CE1 A:HIS576 4.0 38.5 1.0 HD21 A:ASN480 4.1 36.2 1.0 OD1 A:ASP575 4.1 33.8 1.0 CB A:ASP539 4.1 30.4 1.0 HB2 A:ASP539 4.2 36.5 1.0 OE1 A:GLU479 4.2 31.1 1.0 H A:TYR540 4.2 54.2 1.0 OD1 A:ASN480 4.3 29.4 1.0 CG A:GLU479 4.3 29.1 1.0 CA A:ASP539 4.4 29.4 1.0 CB A:GLU541 4.6 36.5 1.0 N A:TYR540 4.6 45.2 1.0 CG A:GLU541 4.7 37.2 1.0 CA A:CA709 4.7 35.3 1.0 N A:GLU541 4.7 33.9 1.0 HG2 A:GLU541 4.7 44.7 1.0 OE2 A:GLU541 4.7 36.0 1.0 ND1 A:HIS576 4.8 37.4 1.0 NE2 A:HIS576 4.8 38.3 1.0 ND2 A:ASN480 4.8 30.1 1.0 HD1 A:HIS576 4.8 44.9 1.0 C A:ASP539 4.9 29.8 1.0 HB2 A:ASP575 4.9 40.3 1.0 CB A:ASP575 4.9 33.6 1.0 CG A:ASN480 5.0 29.3 1.0 HB3 A:ASP539 5.0 36.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human Protocadherin 8 EC5-EC6


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 Human Protocadherin 8 EC5-EC6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca709 b:35.3 occ:1.00 OD1 A:ASP575 2.2 33.8 1.0 OD1 A:ASP572 2.3 40.9 1.0 O A:GLN573 2.5 51.2 1.0 OD1 A:ASP613 2.5 28.3 1.0 OE2 A:GLU541 2.6 36.0 1.0 OE1 A:GLU479 2.8 31.1 1.0 OE1 A:GLU541 3.1 35.3 1.0 H A:GLN573 3.2 64.6 1.0 CD A:GLU541 3.2 36.0 1.0 H A:ASP575 3.3 38.7 1.0 CG A:ASP575 3.3 34.2 1.0 CG A:ASP572 3.4 41.2 1.0 HD1 A:HIS576 3.5 44.9 1.0 CG A:ASP613 3.5 27.5 1.0 HA A:ASP613 3.6 34.5 1.0 CD A:GLU479 3.6 30.4 1.0 C A:GLN573 3.7 51.5 1.0 OE2 A:GLU479 3.7 31.1 1.0 OD2 A:ASP575 3.8 35.4 1.0 N A:GLN573 3.9 53.8 1.0 OD2 A:ASP572 3.9 40.4 1.0 HB3 A:TYR540 3.9 55.2 1.0 HB3 A:ASP613 4.0 33.5 1.0 N A:ASP575 4.1 32.2 1.0 CB A:ASP613 4.2 27.9 1.0 HA A:ASN574 4.3 40.6 1.0 ND1 A:HIS576 4.3 37.4 1.0 HA A:ASP572 4.3 52.4 1.0 HB3 A:GLN573 4.4 64.3 1.0 CA A:ASP613 4.4 28.8 1.0 CA A:GLN573 4.4 53.0 1.0 HD2 A:TYR540 4.4 58.1 1.0 OD2 A:ASP613 4.4 26.7 1.0 CB A:ASP575 4.6 33.6 1.0 HE1 A:HIS576 4.6 46.2 1.0 CB A:ASP572 4.7 42.9 1.0 CG A:GLU541 4.7 37.2 1.0 CA A:CA708 4.7 32.7 1.0 N A:ASN574 4.7 35.1 1.0 HB3 A:ASP575 4.8 40.3 1.0 CA A:ASP575 4.8 32.3 1.0 CA A:ASP572 4.8 43.6 1.0 CE1 A:HIS576 4.8 38.5 1.0 C A:ASP572 4.8 42.8 1.0 CA A:ASN574 4.9 33.9 1.0 H A:GLU541 4.9 40.7 1.0 CB A:TYR540 4.9 46.0 1.0 H A:GLU614 4.9 39.7 1.0 HG2 A:GLU541 4.9 44.7 1.0 HG3 A:GLU541 4.9 44.7 1.0 CB A:GLN573 4.9 53.6 1.0 HB2 A:ASP572 5.0 51.4 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human Protocadherin 8 EC5-EC6


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 Human Protocadherin 8 EC5-EC6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca710 b:35.2 occ:1.00 OD1 A:ASN574 2.3 32.1 1.0 OD2 A:ASP665 2.3 33.5 1.0 OD2 A:ASP611 2.4 25.0 1.0 O A:HIS576 2.4 33.8 1.0 O A:ASN617 2.4 38.7 1.0 OD2 A:ASP613 2.5 26.7 1.0 OD1 A:ASP611 2.8 26.0 1.0 CG A:ASP611 2.9 25.5 1.0 HB2 A:ASP613 3.2 33.5 1.0 CG A:ASN574 3.4 32.5 1.0 HB3 A:ASN617 3.4 48.6 1.0 CG A:ASP665 3.5 33.4 1.0 HD21 A:ASN574 3.5 38.7 1.0 CG A:ASP613 3.5 27.5 1.0 C A:ASN617 3.6 39.4 1.0 C A:HIS576 3.6 34.0 1.0 H A:HIS576 3.7 42.4 1.0 HB2 A:ASP665 3.7 40.0 1.0 HB2 A:HIS576 3.8 42.4 1.0 CB A:ASP613 3.8 27.9 1.0 ND2 A:ASN574 3.8 32.3 1.0 HB3 A:ASP665 3.9 40.0 1.0 CB A:ASP665 3.9 33.3 1.0 HA A:ASN617 4.0 48.0 1.0 HA A:ALA577 4.0 38.0 1.0 HD12 A:LEU671 4.1 36.3 1.0 HD3 A:PRO578 4.1 30.5 1.0 HB2 A:LEU671 4.1 35.5 1.0 CA A:ASN617 4.2 40.0 1.0 CB A:ASN617 4.2 40.5 1.0 HA2 A:GLY618 4.2 60.2 1.0 H A:ASP613 4.2 33.9 1.0 HB3 A:ASP613 4.3 33.5 1.0 CA A:HIS576 4.3 34.9 1.0 HA A:ASN574 4.3 40.6 1.0 CB A:HIS576 4.4 35.3 1.0 N A:HIS576 4.4 35.3 1.0 HB3 A:HIS576 4.4 42.4 1.0 CB A:ASP611 4.4 25.7 1.0 OD1 A:ASP665 4.5 33.6 1.0 N A:ALA577 4.6 32.3 1.0 N A:GLY618 4.6 50.5 1.0 OD1 A:ASP613 4.7 28.3 1.0 CA A:ALA577 4.7 31.7 1.0 HD22 A:ASN574 4.7 38.7 1.0 CB A:ASN574 4.7 33.5 1.0 HB2 A:ASP611 4.8 30.9 1.0 HB3 A:ASP611 4.8 30.9 1.0 HB2 A:ASN617 4.8 48.6 1.0 HG A:LEU671 4.9 36.2 1.0 CD A:PRO578 4.9 25.4 1.0 CA A:GLY618 4.9 50.2 1.0 CA A:ASN574 4.9 33.9 1.0 N A:ASP613 4.9 28.3 1.0 CD1 A:LEU671 5.0 30.3 1.0 C A:ALA577 5.0 31.6 1.0

O.J.Harrison, J.Brasch, P.S.Katsamba, G.Ahlsen, A.J.Noble, H.Dan, R.V.Sampogna, C.S.Potter, B.Carragher, B.Honig, L.Shapiro. Family-Wide Structural and Biophysical Analysis of Binding Interactions Among Non-Clustered Delta-Protocadherins. Cell Rep V. 30 2655 2020.
ISSN: ESSN 2211-1247
PubMed: 32101743
DOI: 10.1016/J.CELREP.2020.02.003