Calcium in PDB 7p2d: Structure of ALPHAMBETA2/CD11BCD18 Headpiece in Complex with A Nanobody

The structure of Structure of ALPHAMBETA2/CD11BCD18 Headpiece in Complex with A Nanobody, PDB code: 7p2d was solved by R.K.Jensen, G.R.Andersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.95 / 3.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.1, 114.1, 250.12, 90, 90, 120
R / Rfree (%)	26.1 / 29.5

The binding sites of Calcium atom in the Structure of ALPHAMBETA2/CD11BCD18 Headpiece in Complex with A Nanobody (pdb code 7p2d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of ALPHAMBETA2/CD11BCD18 Headpiece in Complex with A Nanobody, PDB code: 7p2d:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of ALPHAMBETA2/CD11BCD18 Headpiece in Complex with A Nanobody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of ALPHAMBETA2/CD11BCD18 Headpiece in Complex with A Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:100.0 occ:1.00 OD1 A:ASP518 2.3 88.6 1.0 OD2 A:ASP522 2.3 91.0 1.0 O A:LEU520 2.3 78.5 1.0 OD1 A:ASP522 2.4 76.2 1.0 OD1 A:ASP514 2.4 92.5 1.0 OD1 A:ASN516 2.5 88.6 1.0 CG A:ASP522 2.5 74.3 1.0 CG A:ASP518 3.1 84.4 1.0 OD2 A:ASP518 3.2 73.2 1.0 CG A:ASP514 3.4 87.7 1.0 C A:LEU520 3.5 80.9 1.0 CG A:ASN516 3.6 77.3 1.0 CA A:ASP514 3.7 73.6 1.0 CB A:ASP522 3.8 43.8 1.0 N A:VAL515 3.9 60.6 1.0 N A:ASP522 3.9 59.5 1.0 CB A:ASP514 4.0 73.3 1.0 ND2 A:ASN516 4.1 78.6 1.0 N A:ASN516 4.2 73.8 1.0 C A:THR521 4.3 63.0 1.0 C A:ASP514 4.3 86.6 1.0 OD2 A:ASP514 4.3 94.6 1.0 N A:LEU520 4.3 78.5 1.0 CA A:ASP522 4.4 45.9 1.0 CA A:LEU520 4.4 55.6 1.0 O A:GLY513 4.4 59.0 1.0 CB A:ASP518 4.5 80.6 1.0 N A:ASP518 4.5 83.1 1.0 N A:THR521 4.5 81.9 1.0 CA A:THR521 4.6 68.1 1.0 CB A:LEU520 4.7 59.7 1.0 CB A:ASN516 4.8 65.1 1.0 N A:ASP514 4.8 49.9 1.0 O A:THR521 4.8 62.3 1.0 N A:GLY517 4.8 90.8 1.0 ND1 A:HIS541 4.8 70.0 1.0 N A:GLY542 4.9 71.1 1.0 CG1 A:VAL515 4.9 67.0 1.0 CA A:ASN516 4.9 77.7 1.0 CA A:ASP518 4.9 81.2 1.0 CA A:VAL515 5.0 79.9 1.0

Calcium binding site 2 out of 2 in the Structure of ALPHAMBETA2/CD11BCD18 Headpiece in Complex with A Nanobody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of ALPHAMBETA2/CD11BCD18 Headpiece in Complex with A Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:78.2 occ:1.00 OD1 A:ASP581 2.2 110.0 1.0 OD1 A:ASP585 2.3 83.4 1.0 OG1 A:THR579 2.4 91.9 1.0 OD2 A:ASP581 2.5 94.0 1.0 CG A:ASP581 2.7 107.5 1.0 O A:LEU583 2.7 76.6 1.0 CG A:ASP585 3.0 77.2 1.0 CB A:LEU583 3.0 106.8 1.0 OD2 A:ASP585 3.0 70.3 1.0 OD1 A:ASP577 3.3 83.7 1.0 C A:LEU583 3.4 84.7 1.0 CA A:LEU583 3.6 92.3 1.0 CB A:THR579 3.7 88.1 1.0 CG2 A:THR579 3.7 78.4 1.0 N A:LEU583 3.8 104.9 1.0 CB A:ASP581 4.2 125.5 1.0 CG A:LEU583 4.2 119.1 1.0 CG A:ASP577 4.3 86.0 1.0 CB A:ASP585 4.4 69.4 1.0 N A:THR579 4.4 87.6 1.0 CD1 A:LEU583 4.4 125.3 1.0 N A:VAL584 4.5 70.4 1.0 CB A:ARG598 4.6 68.7 1.0 N A:ASP585 4.6 80.8 1.0 CA A:THR579 4.6 96.9 1.0 N A:ASP581 4.7 102.2 1.0 OD2 A:ASP577 4.8 94.4 1.0 N A:SER599 4.8 60.7 1.0 CA A:ASP585 4.8 66.5 1.0 C A:VAL584 4.8 73.4 1.0 CD A:ARG598 4.8 91.1 1.0 CA A:ASP581 4.9 113.8 1.0 OG A:SER599 4.9 96.7 1.0 O A:SER599 4.9 54.4 1.0 CA A:ARG598 5.0 61.8 1.0

R.K.Jensen, H.Pedersen, J.Lorentzen, N.S.Laursen, T.Vorup-Jensen, G.R.Andersen. Structural Insights Into the Function-Modulating Effects of Nanobody Binding to the Integrin Receptor Alpha M Beta 2. J.Biol.Chem. V. 298 02168 2022.
ISSN: ESSN 1083-351X
PubMed: 35738398
DOI: 10.1016/J.JBC.2022.102168