Calcium in PDB 7do4: Crystal Structure of CD97-CD55 Complex

The structure of Crystal Structure of CD97-CD55 Complex, PDB code: 7do4 was solved by M.Niu, G.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.23 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.8, 44.25, 116.53, 90, 98.7, 90
R / Rfree (%)	26.7 / 30.4

The binding sites of Calcium atom in the Crystal Structure of CD97-CD55 Complex (pdb code 7do4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of CD97-CD55 Complex, PDB code: 7do4:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of CD97-CD55 Complex


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 CD97-CD55 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:73.1 occ:1.00 O A:THR85 2.3 79.5 1.0 OE1 A:GLU67 2.4 88.0 1.0 OD1 A:ASP64 2.5 99.5 1.0 OD1 A:ASN84 2.5 93.4 1.0 OD2 A:ASP64 2.7 89.4 1.0 O A:ILE65 2.8 83.3 1.0 CG A:ASP64 3.0 92.1 1.0 OE2 A:GLU67 3.0 89.0 1.0 CD A:GLU67 3.0 91.9 1.0 O A:SER88 3.1 81.9 1.0 C A:THR85 3.5 79.7 1.0 N A:SER88 3.5 90.8 1.0 CG A:ASN84 3.6 85.7 1.0 N A:GLY87 3.7 81.0 1.0 C A:SER88 3.8 83.9 1.0 N A:THR85 4.0 80.0 1.0 C A:ILE65 4.1 92.8 1.0 ND2 A:ASN84 4.1 86.3 1.0 CA A:SER88 4.3 89.8 1.0 C A:GLU86 4.3 86.0 1.0 C A:GLY87 4.3 82.7 1.0 CA A:GLY87 4.4 82.9 1.0 CA A:THR85 4.4 79.2 1.0 N A:GLU86 4.4 77.4 1.0 CA A:GLU86 4.4 81.7 1.0 CB A:ASP64 4.5 87.6 1.0 N A:ILE65 4.5 95.4 1.0 CG A:GLU67 4.5 94.1 1.0 O A:GLY47 4.6 80.1 1.0 N A:GLU67 4.7 93.8 1.0 CG2 A:ILE65 4.7 99.1 1.0 N A:TYR89 4.8 92.3 1.0 C A:ASN84 4.8 85.6 1.0 CB A:ASN84 4.8 83.0 1.0 CA A:ILE65 4.9 92.5 1.0 OG1 A:THR85 4.9 82.6 1.0 CA A:ASN84 4.9 83.0 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of CD97-CD55 Complex


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 CD97-CD55 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:88.0 occ:1.00 OD1 A:ASN135 2.5 86.3 1.0 OE1 A:GLU119 2.5 88.8 1.0 OD1 A:ASP116 2.5 89.3 1.0 OD2 A:ASP116 2.6 87.1 1.0 O A:SER139 2.6 84.6 1.0 O A:THR136 2.6 79.4 1.0 OE2 A:GLU119 2.7 83.4 1.0 CG A:ASP116 2.9 85.7 1.0 O A:VAL117 2.9 85.5 1.0 CD A:GLU119 3.0 87.5 1.0 C A:THR136 3.3 79.0 1.0 N A:SER139 3.6 80.0 1.0 N A:THR136 3.6 91.2 1.0 C A:SER139 3.6 83.0 1.0 CG A:ASN135 3.7 88.2 1.0 N A:GLY138 3.8 80.1 1.0 N A:VAL137 4.0 86.9 1.0 CA A:SER139 4.0 83.8 1.0 CA A:THR136 4.1 84.3 1.0 C A:VAL117 4.1 93.6 1.0 C A:GLY138 4.2 81.5 1.0 CA A:VAL137 4.3 81.8 1.0 C A:VAL137 4.4 82.5 1.0 CA A:GLY138 4.4 82.0 1.0 CB A:ASP116 4.4 83.3 1.0 OG1 A:THR136 4.4 89.2 1.0 C A:ASN135 4.4 87.1 1.0 ND2 A:ASN135 4.5 91.6 1.0 N A:VAL117 4.5 83.2 1.0 CG A:GLU119 4.5 89.5 1.0 CA A:ASN135 4.5 87.3 1.0 CB A:ASN135 4.7 89.8 1.0 N A:TYR140 4.8 83.1 1.0 CA A:VAL117 4.8 89.3 1.0 O A:GLY96 4.8 96.6 1.0 CB A:THR136 4.9 87.2 1.0 N A:GLU119 5.0 95.7 1.0 O A:GLY138 5.0 82.9 1.0

M.Niu, S.Xu, J.Yang, D.Yao, N.Li, J.Yan, G.Zhong, G.Song. Structural Basis For CD97 Recognition of the Decay-Accelerating Factor CD55 Suggests Mechanosensitive Activation of Adhesion Gpcrs. J.Biol.Chem. V. 296 00776 2021.
ISSN: ESSN 1083-351X
PubMed: 33992645
DOI: 10.1016/J.JBC.2021.100776