Calcium in PDB 6xyr: Structure of the T4LNANO Fusion Protein

All present enzymatic activity of Structure of the T4LNANO Fusion Protein:
3.2.1.17;

The structure of Structure of the T4LNANO Fusion Protein, PDB code: 6xyr was solved by R.M.Benoit, T.Bierig, C.Collu, S.Engilberge, V.Olieric, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.10 / 2.08
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	86.380, 104.260, 63.950, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 23.6

The structure of Structure of the T4LNANO Fusion Protein also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Structure of the T4LNANO Fusion Protein (pdb code 6xyr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structure of the T4LNANO Fusion Protein, PDB code: 6xyr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Structure of the T4LNANO Fusion Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the T4LNANO Fusion Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:41.9 occ:1.00 O A:THR239 2.3 40.0 1.0 OD1 A:ASP233 2.3 38.3 1.0 OE2 A:GLU244 2.4 41.9 1.0 OD1 A:ASP237 2.4 44.0 1.0 O A:HOH533 2.4 41.3 1.0 OD1 A:ASP235 2.5 42.9 1.0 OE1 A:GLU244 2.5 40.5 1.0 CD A:GLU244 2.8 42.8 1.0 HA A:ASP233 3.2 48.0 1.0 CG A:ASP237 3.2 44.1 1.0 H A:THR239 3.3 46.3 1.0 HG1 A:THR239 3.3 55.5 1.0 CG A:ASP235 3.4 44.3 1.0 CG A:ASP233 3.4 39.5 1.0 H A:ASP237 3.4 51.4 1.0 C A:THR239 3.4 37.9 1.0 OD2 A:ASP237 3.6 46.3 1.0 OD2 A:ASP235 3.7 44.2 1.0 H A:ASP235 3.8 49.4 1.0 OG1 A:THR239 3.8 46.2 1.0 HA A:ILE240 3.9 47.2 1.0 HG23 A:THR241 3.9 46.8 1.0 CA A:ASP233 4.0 39.9 1.0 N A:THR239 4.0 38.6 1.0 CB A:ASP233 4.1 39.9 1.0 HB2 A:ASP233 4.2 48.0 1.0 N A:ASP237 4.2 42.8 1.0 CA A:THR239 4.2 38.3 1.0 CG A:GLU244 4.3 41.8 1.0 OD2 A:ASP233 4.3 45.0 1.0 H A:THR241 4.3 40.5 1.0 CB A:ASP237 4.4 37.6 1.0 C A:ASP233 4.4 41.2 1.0 N A:ILE240 4.4 36.4 1.0 H A:GLY236 4.4 49.6 1.0 N A:ASP235 4.5 41.1 1.0 HG3 A:GLU244 4.6 50.2 1.0 HB3 A:ASP237 4.6 45.1 1.0 H A:LYS234 4.6 46.9 1.0 CA A:ILE240 4.6 39.3 1.0 H A:GLY238 4.6 47.9 1.0 CB A:THR239 4.7 41.1 1.0 CA A:ASP237 4.7 36.3 1.0 N A:LYS234 4.7 39.0 1.0 O A:HOH539 4.7 45.0 1.0 HG2 A:GLU244 4.7 50.2 1.0 CB A:ASP235 4.7 41.6 1.0 O A:HOH507 4.7 47.4 1.0 N A:GLY236 4.8 41.3 1.0 CG2 A:THR241 4.8 39.0 1.0 N A:GLY238 4.8 39.9 1.0 N A:THR241 4.9 33.7 1.0 C A:ASP237 4.9 39.8 1.0 HB2 A:GLU244 4.9 49.8 1.0 O A:ASP233 4.9 39.7 1.0 HG21 A:THR241 4.9 46.8 1.0 CA A:ASP235 5.0 44.1 1.0 HB3 A:ASP233 5.0 48.0 1.0

Calcium binding site 2 out of 5 in the Structure of the T4LNANO Fusion Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the T4LNANO Fusion Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:37.8 occ:1.00 OD1 A:ASP269 2.3 38.9 1.0 O A:HOH537 2.3 37.0 1.0 O A:THR275 2.3 39.3 1.0 OD1 A:ASP271 2.4 37.7 1.0 OD1 A:ASN273 2.4 41.9 1.0 OE1 A:GLU280 2.5 37.5 1.0 OE2 A:GLU280 2.5 39.3 1.0 CD A:GLU280 2.8 39.2 1.0 CG A:ASP271 3.3 45.4 1.0 CG A:ASN273 3.4 40.0 1.0 CG A:ASP269 3.4 42.6 1.0 H A:ASN273 3.4 45.7 1.0 HA A:ILE276 3.5 40.6 1.0 C A:THR275 3.6 38.0 1.0 HA A:ASP269 3.6 47.5 1.0 H A:ASP271 3.6 54.3 1.0 OD2 A:ASP271 3.6 44.4 1.0 H A:THR275 3.7 42.3 1.0 H A:ASP277 3.8 42.5 1.0 HD21 A:ASN273 3.9 46.3 1.0 ND2 A:ASN273 4.0 38.5 1.0 O A:HOH581 4.1 43.7 1.0 N A:ASN273 4.2 38.0 1.0 CA A:ASP269 4.2 39.5 1.0 CB A:ASP269 4.2 42.0 1.0 OD2 A:ASP269 4.3 42.6 1.0 N A:THR275 4.3 35.2 1.0 CG A:GLU280 4.3 43.0 1.0 CA A:ILE276 4.3 33.8 1.0 N A:ASP271 4.3 45.2 1.0 HB2 A:ASP269 4.3 50.5 1.0 H A:GLY272 4.4 51.9 1.0 N A:ILE276 4.4 36.5 1.0 CB A:ASN273 4.4 34.9 1.0 H A:GLY274 4.4 53.7 1.0 HB3 A:ASN273 4.4 41.9 1.0 N A:ASP277 4.5 35.4 1.0 C A:ASP269 4.5 46.3 1.0 CB A:ASP271 4.5 41.4 1.0 CA A:THR275 4.6 39.9 1.0 H A:ALA270 4.6 51.5 1.0 HG3 A:GLU280 4.6 51.7 1.0 N A:GLY272 4.6 43.2 1.0 CA A:ASN273 4.7 39.0 1.0 N A:ALA270 4.7 42.9 1.0 OG1 A:THR275 4.7 46.0 1.0 HG13 A:ILE276 4.7 56.1 1.0 HG2 A:GLU280 4.8 51.7 1.0 CA A:ASP271 4.8 40.6 1.0 N A:GLY274 4.8 44.7 1.0 HD22 A:ASN273 4.8 46.3 1.0 HB3 A:ASP277 4.8 45.0 1.0 C A:ASP271 4.8 38.9 1.0 CG A:ASP277 4.9 45.4 1.0 HB3 A:ASP271 4.9 49.8 1.0 C A:ILE276 4.9 37.8 1.0 OD1 A:ASP277 4.9 47.9 1.0 C A:ASN273 4.9 41.0 1.0 HB2 A:GLU280 4.9 50.6 1.0 O A:ASP269 5.0 40.5 1.0 O A:HOH601 5.0 40.9 1.0

Calcium binding site 3 out of 5 in the Structure of the T4LNANO Fusion Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the T4LNANO Fusion Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:45.6 occ:1.00 OD1 A:ASP342 2.3 42.7 1.0 O A:GLN348 2.4 45.6 1.0 OD1 A:ASP344 2.4 46.9 1.0 O A:HOH559 2.4 47.8 1.0 OE1 A:GLU353 2.4 53.5 1.0 OE2 A:GLU353 2.5 48.5 1.0 OD1 A:ASP346 2.5 47.6 1.0 CD A:GLU353 2.8 49.4 1.0 CG A:ASP344 3.1 46.6 1.0 OD2 A:ASP344 3.3 55.5 1.0 CG A:ASP346 3.4 50.0 1.0 H A:GLN348 3.4 55.0 1.0 CG A:ASP342 3.5 47.2 1.0 H A:ASP344 3.5 55.9 1.0 C A:GLN348 3.5 45.1 1.0 H A:ASP346 3.6 55.7 1.0 HA A:ASP342 3.6 51.0 1.0 H A:GLY345 3.6 54.3 1.0 HA A:VAL349 3.7 59.0 1.0 OD2 A:ASP346 3.8 55.5 1.0 H A:ILE343 3.8 51.3 1.0 H A:ASN350 3.9 60.0 1.0 N A:GLN348 4.2 45.8 1.0 N A:ASP344 4.2 46.5 1.0 N A:ASP346 4.2 46.4 1.0 H A:GLY347 4.3 56.6 1.0 OD2 A:ASP342 4.3 38.2 1.0 N A:GLY345 4.3 45.2 1.0 CG A:GLU353 4.3 48.6 1.0 CA A:ASP342 4.3 42.5 1.0 N A:VAL349 4.4 46.5 1.0 N A:ILE343 4.4 42.7 1.0 CA A:GLN348 4.4 42.3 1.0 CB A:ASP342 4.4 38.7 1.0 CA A:VAL349 4.4 49.1 1.0 CB A:ASP344 4.4 47.6 1.0 HB2 A:GLN348 4.5 53.5 1.0 N A:ASN350 4.5 49.9 1.0 CB A:ASP346 4.6 46.9 1.0 N A:GLY347 4.6 47.1 1.0 HG3 A:GLU353 4.7 58.4 1.0 HB2 A:ASP342 4.7 46.5 1.0 CA A:ASP344 4.7 49.8 1.0 HG2 A:GLU353 4.7 58.4 1.0 HB3 A:ASP346 4.8 56.3 1.0 HB3 A:ASP344 4.8 57.2 1.0 CA A:ASP346 4.8 48.5 1.0 ND2 A:ASN350 4.8 55.3 1.0 C A:ASP342 4.8 44.4 1.0 C A:ASP344 4.8 50.4 1.0 HD22 A:ASN350 4.9 66.4 1.0 HD1 A:TYR312 4.9 67.5 1.0 HB3 A:ASN350 4.9 63.9 1.0 HD21 A:ASN350 4.9 66.4 1.0 C A:ASP346 4.9 50.2 1.0 CB A:GLN348 4.9 44.6 1.0 HB2 A:GLU353 5.0 61.8 1.0 C A:VAL349 5.0 53.2 1.0 CG A:ASN350 5.0 49.2 1.0

Calcium binding site 4 out of 5 in the Structure of the T4LNANO Fusion Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the T4LNANO Fusion Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:55.1 occ:1.00 OD1 A:ASP306 2.2 54.6 1.0 O A:HOH605 2.2 59.4 1.0 OE2 A:GLU317 2.3 57.9 1.0 OD1 A:ASN310 2.3 64.3 1.0 O A:TYR312 2.3 55.2 1.0 OE1 A:GLU317 2.5 53.4 1.0 OD1 A:ASP308 2.7 59.7 1.0 CD A:GLU317 2.7 56.5 1.0 CG A:ASN310 3.2 60.9 1.0 CG A:ASP308 3.3 65.9 1.0 H A:ASN310 3.4 71.3 1.0 CG A:ASP306 3.4 55.1 1.0 H A:TYR312 3.4 60.6 1.0 HD21 A:ASN310 3.5 70.9 1.0 OD2 A:ASP308 3.5 64.1 1.0 C A:TYR312 3.5 53.7 1.0 HA A:ASP306 3.6 62.9 1.0 ND2 A:ASN310 3.7 59.0 1.0 H A:ASP308 3.8 74.9 1.0 HA A:ILE313 3.8 54.9 1.0 H A:SER314 3.9 55.3 1.0 HB2 A:TYR312 4.1 63.1 1.0 N A:ASN310 4.1 59.4 1.0 N A:TYR312 4.2 50.4 1.0 OD2 A:ASP306 4.2 53.0 1.0 CG A:GLU317 4.2 49.6 1.0 CA A:ASP306 4.3 52.4 1.0 H A:GLY309 4.3 70.1 1.0 CB A:ASN310 4.3 51.0 1.0 CA A:TYR312 4.3 55.5 1.0 CB A:ASP306 4.3 48.6 1.0 N A:ILE313 4.4 52.6 1.0 HB3 A:ASN310 4.4 61.2 1.0 N A:ASP308 4.4 62.3 1.0 C A:ASP306 4.5 60.0 1.0 HD22 A:ASN310 4.5 70.9 1.0 CA A:ILE313 4.5 45.7 1.0 HG3 A:GLU317 4.5 59.6 1.0 H A:GLY311 4.5 69.1 1.0 N A:SER314 4.5 46.0 1.0 HB3 A:SER314 4.6 61.5 1.0 N A:GLY309 4.6 58.4 1.0 H A:LYS307 4.6 72.0 1.0 CB A:ASP308 4.6 62.7 1.0 HB2 A:ASP306 4.6 58.4 1.0 HG2 A:GLU317 4.7 59.6 1.0 CA A:ASN310 4.7 54.4 1.0 O A:HOH587 4.7 53.1 1.0 N A:LYS307 4.7 60.0 1.0 CB A:TYR312 4.7 52.5 1.0 C A:ASP308 4.8 59.1 1.0 CA A:ASP308 4.8 59.0 1.0 N A:GLY311 4.8 57.5 1.0 HB3 A:ASP308 4.9 75.3 1.0 HB2 A:GLU317 4.9 56.1 1.0 O A:ASP306 4.9 55.7 1.0 C A:ASN310 5.0 56.3 1.0 C A:ILE313 5.0 44.8 1.0

Calcium binding site 5 out of 5 in the Structure of the T4LNANO Fusion Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the T4LNANO Fusion Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:66.1 occ:1.00 H A:SER152 2.6 57.2 1.0 O A:HOH611 2.7 60.3 1.0 HD22 A:ASN167 3.0 74.0 1.0 HA A:PHE149 3.0 56.7 1.0 H12 A:GOL407 3.1 78.0 1.0 OG A:SER152 3.2 49.8 1.0 H A:ASN151 3.2 59.2 1.0 HB2 A:ASN151 3.2 71.7 1.0 HG A:SER152 3.2 59.8 1.0 HB2 A:SER152 3.3 48.7 1.0 HD2 A:PHE149 3.3 52.5 1.0 HD21 A:ASN167 3.3 74.0 1.0 N A:SER152 3.4 47.6 1.0 ND2 A:ASN167 3.5 61.6 1.0 C A:PHE149 3.5 53.8 1.0 HB3 A:PHE149 3.6 62.0 1.0 CA A:PHE149 3.6 47.2 1.0 CB A:SER152 3.7 40.5 1.0 O A:PHE149 3.7 46.1 1.0 O A:HOH577 3.7 62.6 1.0 N A:ASN151 3.8 49.3 1.0 N A:THR150 4.0 53.8 1.0 CD2 A:PHE149 4.0 43.7 1.0 C1 A:GOL407 4.0 65.0 1.0 CB A:PHE149 4.0 51.6 1.0 H A:THR150 4.0 64.6 1.0 H2 A:GOL407 4.0 84.4 1.0 CB A:ASN151 4.1 59.7 1.0 CA A:SER152 4.2 50.3 1.0 HO1 A:GOL407 4.3 87.0 1.0 CA A:ASN151 4.3 49.4 1.0 O1 A:GOL407 4.3 72.5 1.0 C A:ASN151 4.3 51.0 1.0 CG A:PHE149 4.4 46.3 1.0 HB3 A:SER152 4.5 48.7 1.0 C2 A:GOL407 4.6 70.3 1.0 HB3 A:ASN151 4.6 71.7 1.0 C A:THR150 4.7 46.5 1.0 HA A:SER152 4.7 60.4 1.0 CG A:ASN167 4.7 61.4 1.0 H32 A:GOL407 4.8 83.2 1.0 HD23 A:LEU168 4.8 55.6 1.0 HG22 A:THR150 4.8 77.7 1.0 H11 A:GOL407 4.8 78.0 1.0 H A:LEU153 4.8 48.7 1.0 O A:GLY148 4.9 52.7 1.0 HD22 A:ASN151 4.9 78.0 1.0 HB3 A:ASN167 4.9 57.1 1.0 HB2 A:PHE149 4.9 62.0 1.0 HG23 A:THR150 4.9 77.7 1.0 CA A:THR150 4.9 52.8 1.0 N A:PHE149 5.0 45.9 1.0

G.Collu, T.Bierig, A.-S.Krebs, S.Engilberge, N.Varma, R.Guixa-Gonzalez, X.Deupi, V.Olieric, E.Poghosyan, R.M.Benoit. Chimeric Single Alpha-Helical Domains As Rigid Fusion Protein Connections For Protein Nanotechnology and Structural Biology Biorxiv 2020.
DOI: 10.1101/2020.09.29.318410