Calcium in PDB 7op2: CHADOX1/ Chimpanzee Adenovirus Y25 Fiber Knob Protein

The structure of CHADOX1/ Chimpanzee Adenovirus Y25 Fiber Knob Protein, PDB code: 7op2 was solved by P.J.Rizkallah, A.T.Baker, A.L.Parker, A.Teijeira Crespo, M.Lipka-Lloyd, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.04 / 1.59
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	98.427, 112.26, 98.605, 90, 92.61, 90
R / Rfree (%)	22.4 / 24.4

The binding sites of Calcium atom in the CHADOX1/ Chimpanzee Adenovirus Y25 Fiber Knob Protein (pdb code 7op2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the CHADOX1/ Chimpanzee Adenovirus Y25 Fiber Knob Protein, PDB code: 7op2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the CHADOX1/ Chimpanzee Adenovirus Y25 Fiber Knob Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of CHADOX1/ Chimpanzee Adenovirus Y25 Fiber Knob Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:18.5 occ:1.00 O A:HOH598 2.1 22.1 1.0 OE2 A:GLU331 2.3 26.0 1.0 OD1 A:ASP333 2.5 29.1 1.0 OD2 A:ASP333 2.5 30.5 1.0 CG A:ASP333 2.8 30.9 1.0 CD A:GLU331 3.4 26.4 1.0 O A:HOH501 4.1 26.2 1.0 OE1 A:GLU331 4.1 25.2 1.0 CB A:GLU331 4.2 27.5 1.0 CG A:GLU331 4.3 26.2 1.0 CB A:ASP333 4.3 32.7 1.0 O A:HOH504 4.8 28.4 1.0

Calcium binding site 2 out of 4 in the CHADOX1/ Chimpanzee Adenovirus Y25 Fiber Knob Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of CHADOX1/ Chimpanzee Adenovirus Y25 Fiber Knob Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:25.0 occ:1.00 O D:LYS353 2.2 28.9 1.0 O D:HOH583 2.3 21.6 1.0 O D:LYS355 2.4 30.7 1.0 C D:LYS353 3.3 29.2 1.0 C D:LYS355 3.6 30.9 1.0 C D:ASP354 4.0 31.6 1.0 N D:LYS355 4.0 31.0 1.0 N D:ASP354 4.2 30.0 1.0 CA D:LYS353 4.3 28.3 1.0 CA D:ASP354 4.3 31.6 1.0 O D:ASP354 4.4 32.4 1.0 CA D:LYS355 4.4 31.2 1.0 N D:ASN356 4.5 30.7 1.0 CA D:ASN356 4.6 30.8 1.0 O D:TYR352 4.7 26.5 1.0 OD1 D:ASN356 4.8 33.5 1.0 O D:HOH503 4.9 19.9 1.0 CB D:ASN356 4.9 32.4 1.0

Calcium binding site 3 out of 4 in the CHADOX1/ Chimpanzee Adenovirus Y25 Fiber Knob Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of CHADOX1/ Chimpanzee Adenovirus Y25 Fiber Knob Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca402 b:28.0 occ:1.00 O D:HOH575 2.3 26.7 1.0 OE2 D:GLU331 2.4 31.2 1.0 OD1 D:ASP333 2.4 36.3 1.0 OD2 D:ASP333 2.7 37.3 1.0 CG D:ASP333 2.9 37.8 1.0 CD D:GLU331 3.4 31.8 1.0 CB D:GLU331 4.0 32.6 1.0 OE1 D:GLU331 4.2 31.6 1.0 CG D:GLU331 4.2 31.7 1.0 CB D:ASP333 4.4 39.6 1.0

Calcium binding site 4 out of 4 in the CHADOX1/ Chimpanzee Adenovirus Y25 Fiber Knob Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of CHADOX1/ Chimpanzee Adenovirus Y25 Fiber Knob Protein within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca401 b:32.0 occ:1.00 O G:HOH595 2.4 28.6 1.0 OD1 G:ASP333 2.4 36.1 1.0 OE1 G:GLU331 2.4 31.9 1.0 OD2 G:ASP333 2.6 36.8 1.0 CG G:ASP333 2.9 37.4 1.0 CD G:GLU331 3.5 33.6 1.0 CB G:GLU331 3.9 34.5 1.0 CG G:GLU331 4.1 33.3 1.0 O G:HOH598 4.2 36.8 1.0 OE2 G:GLU331 4.3 31.5 1.0 CB G:ASP333 4.4 38.2 1.0 O G:HOH506 4.4 29.6 1.0 O G:HOH600 4.4 53.6 1.0

A.T.Baker, R.J.Boyd, D.Sarkar, J.Vant, A.T.Crespo, C.D.Truong, E.Bates, E.Wilson, C.K.Chan, M.Lipka-Lloyd, P.Fromme, M.B.Nagalo, M.Heurich, D.Williams, P.L.Chiu, P.J.Rizkallah, A.L.Parker, A.Singharoy, M.J.Borad. The Structure of CHADOX1/Azd-1222 Reveals Interactions with Car and PF4 with Implications For Vaccine-Induced Immune Thrombotic Thrombocytopenia Biorxiv 2021.
DOI: 10.1101/2021.05.19.444882