Calcium in PDB 6ep0: Enterococcus Faecalis Fic Protein in Complex with Amp and Calcium Ion.

The structure of Enterococcus Faecalis Fic Protein in Complex with Amp and Calcium Ion., PDB code: 6ep0 was solved by S.Veyron, J.Cherfils, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.82 / 2.35
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	64.975, 64.975, 246.239, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 26.4

The structure of Enterococcus Faecalis Fic Protein in Complex with Amp and Calcium Ion. also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Enterococcus Faecalis Fic Protein in Complex with Amp and Calcium Ion. (pdb code 6ep0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Enterococcus Faecalis Fic Protein in Complex with Amp and Calcium Ion., PDB code: 6ep0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Enterococcus Faecalis Fic Protein in Complex with Amp and Calcium Ion.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Enterococcus Faecalis Fic Protein in Complex with Amp and Calcium Ion. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:79.7 occ:1.00 O A:HOH415 2.1 0.7 1.0 OE1 A:GLU122 2.1 58.4 1.0 O A:HOH419 2.1 56.1 1.0 O2P A:AMP301 2.4 53.1 1.0 O B:HOH454 2.5 69.7 1.0 O A:HOH418 2.9 75.1 1.0 CD A:GLU122 3.2 83.8 1.0 OE2 A:GLU122 3.7 87.1 1.0 P A:AMP301 3.7 48.6 1.0 CL A:CL307 4.1 61.4 1.0 OE1 A:GLU197 4.2 57.6 1.0 O3P A:AMP301 4.3 44.2 1.0 CG A:GLU122 4.4 62.3 1.0 O5' A:AMP301 4.6 48.6 1.0 O1P A:AMP301 4.7 55.1 1.0 NH2 A:ARG126 4.7 47.6 1.0 NZ A:LYS78 4.7 0.6 1.0 C5' A:AMP301 4.7 48.4 1.0 N A:GLY123 4.8 46.2 1.0 CD A:GLU197 4.9 67.6 1.0 CB A:GLU197 4.9 48.1 1.0

Calcium binding site 2 out of 6 in the Enterococcus Faecalis Fic Protein in Complex with Amp and Calcium Ion.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Enterococcus Faecalis Fic Protein in Complex with Amp and Calcium Ion. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:74.9 occ:1.00 O A:HOH401 1.7 30.0 1.0 O A:HOH434 1.8 30.0 1.0 OE2 A:GLU201 2.3 70.0 1.0 O B:HOH407 2.3 54.6 1.0 O A:GLU201 2.4 63.4 1.0 OE1 B:GLU201 2.4 68.5 1.0 CD B:GLU201 3.2 96.1 1.0 OE2 B:GLU201 3.3 0.3 1.0 CD A:GLU201 3.4 81.1 1.0 C A:GLU201 3.6 62.1 1.0 O B:HOH402 3.6 40.0 1.0 OE1 A:GLU201 4.2 77.5 1.0 CA A:GLU201 4.4 55.0 1.0 CG A:GLU201 4.4 61.9 1.0 N A:TYR202 4.5 58.9 1.0 CZ B:ARG23 4.5 85.4 1.0 NH2 B:ARG23 4.6 69.3 1.0 CA A:TYR202 4.6 57.9 1.0 CG B:GLU201 4.7 73.6 1.0 O A:HOH446 4.7 57.5 1.0 NH1 B:ARG23 4.7 81.9 1.0 NE B:ARG23 4.9 68.3 1.0 CA A:CA304 5.0 0.9 1.0 CB A:GLU201 5.0 56.8 1.0

Calcium binding site 3 out of 6 in the Enterococcus Faecalis Fic Protein in Complex with Amp and Calcium Ion.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Enterococcus Faecalis Fic Protein in Complex with Amp and Calcium Ion. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:0.9 occ:1.00 O B:HOH402 2.0 40.0 1.0 OE1 A:GLU201 2.2 77.5 1.0 O B:HOH457 2.3 1.0 1.0 O A:HOH460 2.6 30.0 1.0 O B:GLU201 3.1 75.6 1.0 CD A:GLU201 3.2 81.1 1.0 OE2 A:GLU201 3.5 70.0 1.0 NH2 A:ARG23 3.6 71.0 1.0 O B:HOH458 3.8 61.0 1.0 C B:GLU201 4.3 73.8 1.0 OE1 B:GLU201 4.4 68.5 1.0 CG A:GLU201 4.4 61.9 1.0 CZ A:ARG23 4.5 94.5 1.0 NH1 A:ARG23 4.8 80.2 1.0 CA A:CA303 5.0 74.9 1.0

Calcium binding site 4 out of 6 in the Enterococcus Faecalis Fic Protein in Complex with Amp and Calcium Ion.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Enterococcus Faecalis Fic Protein in Complex with Amp and Calcium Ion. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:64.3 occ:1.00 OD2 A:ASP63 2.4 76.8 1.0 OD1 A:ASN32 2.5 63.4 1.0 O A:HOH455 2.7 51.6 1.0 NH1 A:ARG35 3.3 0.8 1.0 CG A:ASP63 3.3 70.2 1.0 CG A:ASN32 3.5 64.1 1.0 OD1 A:ASP63 3.5 71.9 1.0 ND2 A:ASN32 3.7 53.3 1.0 CZ A:ARG35 4.3 0.7 1.0 NH2 A:ARG35 4.4 99.7 1.0 OE1 A:GLU31 4.6 94.5 1.0 CA A:CA306 4.7 90.2 1.0 CB A:ASP63 4.7 64.2 1.0 O A:VAL28 4.8 57.4 1.0 CB A:ASN32 4.9 51.4 1.0

Calcium binding site 5 out of 6 in the Enterococcus Faecalis Fic Protein in Complex with Amp and Calcium Ion.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Enterococcus Faecalis Fic Protein in Complex with Amp and Calcium Ion. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca306 b:90.2 occ:1.00 OD1 A:ASP63 2.7 71.9 1.0 CG A:ASP63 3.9 70.2 1.0 OD2 A:ASP63 4.6 76.8 1.0 CA A:CA305 4.7 64.3 1.0 CB A:ASP63 4.9 64.2 1.0

Calcium binding site 6 out of 6 in the Enterococcus Faecalis Fic Protein in Complex with Amp and Calcium Ion.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Enterococcus Faecalis Fic Protein in Complex with Amp and Calcium Ion. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:59.1 occ:1.00 O B:HOH403 2.1 49.6 1.0 O2P B:AMP301 2.3 62.1 1.0 OE2 B:GLU122 2.4 50.0 1.0 O B:HOH449 2.4 67.2 1.0 OE1 B:GLU122 2.6 92.6 1.0 CD B:GLU122 2.8 83.0 1.0 O B:HOH411 2.9 64.2 1.0 CL B:CL303 3.3 72.2 1.0 P B:AMP301 3.7 54.8 1.0 NZ B:LYS78 4.0 58.4 1.0 O3P B:AMP301 4.2 54.2 1.0 OE2 B:GLU197 4.2 58.4 1.0 CG B:GLU122 4.3 65.9 1.0 NH2 B:ARG126 4.4 54.2 1.0 O5' B:AMP301 4.5 50.8 1.0 O1P B:AMP301 4.6 58.1 1.0 N B:GLY123 4.6 48.9 1.0 CB B:GLU197 4.7 49.9 1.0 OH B:TYR199 4.8 60.7 1.0 C5' B:AMP301 4.8 50.7 1.0 CD B:GLU197 4.9 68.7 1.0

S.Veyron, G.Oliva, M.Rolando, C.Buchrieser, G.Peyroche, J.Cherfils. A CA2+-Regulated Deampylation Switch in Human and Bacterial Fic Proteins. Nat Commun V. 10 1142 2019.
ISSN: ESSN 2041-1723
PubMed: 30850593
DOI: 10.1038/S41467-019-09023-1