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Calcium in PDB 6ep2: Enterococcus Faecalis Fic Protein in Complex with Adp and Calcium Ion.

Protein crystallography data

The structure of Enterococcus Faecalis Fic Protein in Complex with Adp and Calcium Ion., PDB code: 6ep2 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) 56.04 / 2.15
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 125.311, 125.311, 362.879, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.8

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Calcium atom in the Enterococcus Faecalis Fic Protein in Complex with Adp and Calcium Ion. (pdb code 6ep2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 24 binding sites of Calcium where determined in the Enterococcus Faecalis Fic Protein in Complex with Adp and Calcium Ion., PDB code: 6ep2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 24 in 6ep2

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Calcium binding site 1 out of 24 in the Enterococcus Faecalis Fic Protein in Complex with Adp 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 Adp and Calcium Ion. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:37.3
occ:1.00
 O A:HOH404 2.2 44.1 1.0
O3B A:ADP301 2.3 29.0 1.0
O A:HOH523 2.4 29.5 1.0
O2A A:ADP301 2.5 26.1 1.0
OE1 A:GLU197 2.6 22.8 1.0
O A:HOH521 2.7 31.7 1.0
CD A:GLU197 3.5 24.9 1.0
PB A:ADP301 3.6 26.1 1.0
PA A:ADP301 3.7 26.6 1.0
CB A:GLU197 3.8 24.6 1.0
C5' A:ADP301 3.8 24.3 1.0
O A:HOH449 3.9 32.7 1.0
O3A A:ADP301 3.9 26.4 1.0
CG A:GLU197 4.1 23.6 1.0
O2B A:ADP301 4.2 28.8 1.0
NZ A:LYS78 4.2 36.3 1.0
O5' A:ADP301 4.3 25.3 1.0
CA A:GLU197 4.4 24.1 1.0
OE2 A:GLU197 4.4 25.8 1.0
O A:GLU197 4.4 25.9 1.0
O D:HOH529 4.5 47.4 1.0
O1B A:ADP301 4.8 26.8 1.0
CE A:LYS78 4.8 28.0 1.0
C A:GLU197 4.9 26.2 1.0

Calcium binding site 2 out of 24 in 6ep2

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Calcium binding site 2 out of 24 in the Enterococcus Faecalis Fic Protein in Complex with Adp 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 Adp and Calcium Ion. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:43.1
occ:1.00
 O D:GLU201 2.3 26.5 1.0
OE2 D:GLU201 2.5 30.6 1.0
OE2 A:GLU201 2.5 32.9 1.0
O D:HOH544 2.5 37.2 1.0
O D:HOH548 2.6 33.5 1.0
OE1 A:GLU201 2.8 34.2 1.0
O D:HOH499 2.8 40.1 1.0
CD A:GLU201 3.0 29.0 1.0
C D:GLU201 3.5 27.3 1.0
CD D:GLU201 3.5 27.0 1.0
CA D:CA303 3.7 40.2 1.0
CG D:GLU201 4.2 25.8 1.0
CA D:GLU201 4.2 24.8 1.0
O D:HOH556 4.3 58.0 1.0
OE1 D:GLU201 4.4 29.7 1.0
N D:TYR202 4.5 24.9 1.0
CG A:GLU201 4.5 29.5 1.0
CA D:TYR202 4.6 27.9 1.0
O D:HOH403 4.7 30.0 1.0
O A:HOH540 4.8 43.3 1.0
CB D:GLU201 4.8 27.8 1.0

Calcium binding site 3 out of 24 in 6ep2

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Calcium binding site 3 out of 24 in the Enterococcus Faecalis Fic Protein in Complex with Adp 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 Adp and Calcium Ion. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:36.1
occ:1.00
 O B:HOH415 2.2 42.5 1.0
O1B B:ADP301 2.4 24.5 1.0
OE1 B:GLU197 2.5 25.3 1.0
O B:HOH530 2.5 34.2 1.0
O B:HOH542 2.6 38.9 1.0
O1A B:ADP301 2.6 25.2 1.0
O B:HOH504 2.6 38.4 1.0
O B:HOH550 2.8 42.5 1.0
CD B:GLU197 3.5 27.7 1.0
PB B:ADP301 3.6 25.7 1.0
C5' B:ADP301 3.7 22.6 1.0
PA B:ADP301 3.8 25.6 1.0
CB B:GLU197 3.9 24.7 1.0
O3A B:ADP301 4.0 24.4 1.0
O B:HOH451 4.0 35.5 1.0
CG B:GLU197 4.2 24.9 1.0
O3B B:ADP301 4.2 26.7 1.0
NZ B:LYS78 4.2 37.7 1.0
O5' B:ADP301 4.2 24.0 1.0
CA B:GLU197 4.4 25.9 1.0
O B:GLU197 4.4 28.8 1.0
OE2 B:GLU197 4.5 28.8 1.0
O C:HOH517 4.7 39.9 1.0
O B:HOH469 4.8 44.2 1.0
O2B B:ADP301 4.8 25.7 1.0
CE B:LYS78 4.8 34.2 1.0
C B:GLU197 4.9 26.4 1.0

Calcium binding site 4 out of 24 in 6ep2

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Calcium binding site 4 out of 24 in the Enterococcus Faecalis Fic Protein in Complex with Adp 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 Adp and Calcium Ion. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:44.3
occ:1.00
 O C:HOH519 2.4 51.1 1.0
OE2 B:GLU201 2.4 33.5 1.0
O C:GLU201 2.4 31.5 1.0
OE2 C:GLU201 2.5 36.1 1.0
O B:HOH522 2.7 40.0 1.0
O C:HOH533 2.7 38.0 1.0
OE1 B:GLU201 2.7 35.3 1.0
CD B:GLU201 2.9 30.0 1.0
C C:GLU201 3.6 34.5 1.0
CD C:GLU201 3.6 35.3 1.0
CA C:CA303 3.7 45.6 1.0
CG C:GLU201 4.2 33.8 1.0
CA C:GLU201 4.3 30.8 1.0
CG B:GLU201 4.4 29.1 1.0
O B:HOH516 4.5 47.4 1.0
OE1 C:GLU201 4.5 34.5 1.0
N C:TYR202 4.6 30.0 1.0
O C:HOH542 4.6 41.5 1.0
CA C:TYR202 4.7 32.3 1.0
O C:HOH518 4.7 33.8 1.0
CD1 C:TYR202 4.9 35.1 1.0
CB C:GLU201 4.9 30.0 1.0

Calcium binding site 5 out of 24 in 6ep2

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Calcium binding site 5 out of 24 in the Enterococcus Faecalis Fic Protein in Complex with Adp 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 Adp and Calcium Ion. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:40.1
occ:1.00
 O3B C:ADP301 2.3 27.2 1.0
O C:HOH499 2.3 30.0 1.0
O C:HOH425 2.3 55.8 1.0
O C:HOH501 2.5 35.5 1.0
O B:HOH483 2.5 33.5 1.0
O C:HOH535 2.6 39.9 1.0
OE1 C:GLU197 2.6 23.6 1.0
O2A C:ADP301 2.6 25.5 1.0
CD C:GLU197 3.5 26.7 1.0
PB C:ADP301 3.5 25.8 1.0
PA C:ADP301 3.8 25.2 1.0
C5' C:ADP301 3.8 25.4 1.0
O3A C:ADP301 3.9 26.0 1.0
O C:HOH457 3.9 36.1 1.0
CB C:GLU197 3.9 23.4 1.0
O C:HOH527 4.0 46.4 1.0
O2B C:ADP301 4.0 27.6 1.0
CG C:GLU197 4.2 24.8 1.0
NZ C:LYS78 4.2 34.5 1.0
O5' C:ADP301 4.3 28.5 1.0
OE2 C:GLU197 4.4 27.4 1.0
O B:HOH448 4.5 37.8 1.0
CA C:GLU197 4.5 20.8 1.0
O C:GLU197 4.6 23.5 1.0
O1B C:ADP301 4.8 24.9 1.0
CE C:LYS78 4.9 33.4 1.0
O C:HOH446 4.9 40.0 1.0

Calcium binding site 6 out of 24 in 6ep2

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Calcium binding site 6 out of 24 in the Enterococcus Faecalis Fic Protein in Complex with Adp 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 Adp and Calcium Ion. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:45.6
occ:1.00
 OE2 C:GLU201 2.4 36.1 1.0
O B:GLU201 2.4 27.1 1.0
O B:HOH516 2.4 47.4 1.0
OE2 B:GLU201 2.5 33.5 1.0
O C:HOH542 2.6 41.5 1.0
O B:HOH549 2.8 44.1 1.0
OE1 C:GLU201 2.8 34.5 1.0
O B:HOH522 2.9 40.0 1.0
CD C:GLU201 2.9 35.3 1.0
O C:HOH545 3.1 48.3 1.0
C B:GLU201 3.6 27.7 1.0
CD B:GLU201 3.6 30.0 1.0
CA B:CA303 3.7 44.3 1.0
CG B:GLU201 4.2 29.1 1.0
CA B:GLU201 4.3 27.2 1.0
O C:HOH519 4.4 51.1 1.0
CG C:GLU201 4.4 33.8 1.0
OE1 B:GLU201 4.5 35.3 1.0
N B:TYR202 4.6 26.4 1.0
CA B:TYR202 4.8 29.1 1.0
O B:HOH472 4.8 34.0 1.0
CB B:GLU201 4.9 28.4 1.0

Calcium binding site 7 out of 24 in 6ep2

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Calcium binding site 7 out of 24 in the Enterococcus Faecalis Fic Protein in Complex with Adp and Calcium Ion.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Enterococcus Faecalis Fic Protein in Complex with Adp and Calcium Ion. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:34.2
occ:1.00
 O1B D:ADP301 2.3 25.6 1.0
O D:HOH522 2.4 32.0 1.0
O D:HOH539 2.4 40.6 1.0
O1A D:ADP301 2.4 24.9 1.0
O D:HOH512 2.5 36.8 1.0
O A:HOH515 2.5 31.1 1.0
OE1 D:GLU197 2.6 29.1 1.0
CD D:GLU197 3.6 29.4 1.0
PB D:ADP301 3.6 27.4 1.0
PA D:ADP301 3.7 25.7 1.0
C5' D:ADP301 3.9 24.9 1.0
O3A D:ADP301 3.9 25.3 1.0
CB D:GLU197 4.0 24.7 1.0
NZ D:LYS78 4.0 37.0 1.0
O D:HOH441 4.0 31.0 1.0
O3B D:ADP301 4.2 27.0 1.0
CG D:GLU197 4.3 29.2 1.0
O5' D:ADP301 4.3 27.8 1.0
CA D:GLU197 4.5 25.0 1.0
OE2 D:GLU197 4.5 30.0 1.0
O D:GLU197 4.5 27.5 1.0
O2B D:ADP301 4.8 25.9 1.0
CE D:LYS78 4.8 31.6 1.0

Calcium binding site 8 out of 24 in 6ep2

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Calcium binding site 8 out of 24 in the Enterococcus Faecalis Fic Protein in Complex with Adp and Calcium Ion.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Enterococcus Faecalis Fic Protein in Complex with Adp and Calcium Ion. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca303

b:40.2
occ:1.00
 OE2 D:GLU201 2.4 30.6 1.0
O A:GLU201 2.4 27.7 1.0
O A:HOH540 2.5 43.3 1.0
OE2 A:GLU201 2.5 32.9 1.0
OE1 D:GLU201 2.7 29.7 1.0
O D:HOH499 2.7 40.1 1.0
O A:HOH548 2.7 41.0 1.0
CD D:GLU201 2.9 27.0 1.0
CD A:GLU201 3.6 29.0 1.0
C A:GLU201 3.6 26.9 1.0
CA A:CA303 3.7 43.1 1.0
CG A:GLU201 4.3 29.5 1.0
CA A:GLU201 4.3 28.6 1.0
CG D:GLU201 4.4 25.8 1.0
OE1 A:GLU201 4.5 34.2 1.0
N A:TYR202 4.6 27.6 1.0
O A:HOH446 4.7 37.1 1.0
CA A:TYR202 4.7 29.7 1.0
O D:HOH544 4.8 37.2 1.0
CB A:GLU201 4.9 25.7 1.0
O D:GLU201 5.0 26.5 1.0

Calcium binding site 9 out of 24 in 6ep2

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Calcium binding site 9 out of 24 in the Enterococcus Faecalis Fic Protein in Complex with Adp and Calcium Ion.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Enterococcus Faecalis Fic Protein in Complex with Adp and Calcium Ion. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca302

b:37.8
occ:1.00
 O2B E:ADP301 2.3 26.7 1.0
O E:HOH487 2.4 29.7 1.0
O L:HOH457 2.5 30.8 1.0
O2A E:ADP301 2.5 29.8 1.0
O E:HOH505 2.5 33.2 1.0
O E:HOH516 2.6 44.5 1.0
OE2 E:GLU197 2.6 30.1 1.0
PB E:ADP301 3.6 27.9 1.0
CD E:GLU197 3.6 27.4 1.0
PA E:ADP301 3.7 26.8 1.0
C5' E:ADP301 3.8 26.4 1.0
CB E:GLU197 3.9 29.6 1.0
O3A E:ADP301 3.9 27.9 1.0
O E:HOH444 4.0 35.6 1.0
CG E:GLU197 4.2 26.8 1.0
O1B E:ADP301 4.2 30.1 1.0
NZ E:LYS78 4.2 32.5 1.0
O5' E:ADP301 4.2 27.8 1.0
CA E:GLU197 4.4 25.1 1.0
O E:GLU197 4.5 25.9 1.0
OE1 E:GLU197 4.5 40.2 1.0
O3B E:ADP301 4.8 27.2 1.0
CE E:LYS78 4.9 31.1 1.0
OE2 L:GLU152 4.9 42.6 1.0
C E:GLU197 5.0 25.0 1.0

Calcium binding site 10 out of 24 in 6ep2

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Calcium binding site 10 out of 24 in the Enterococcus Faecalis Fic Protein in Complex with Adp and Calcium Ion.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Enterococcus Faecalis Fic Protein in Complex with Adp and Calcium Ion. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca303

b:43.5
occ:1.00
 O L:GLU201 2.4 34.0 1.0
OE2 L:GLU201 2.4 37.3 1.0
OE2 E:GLU201 2.5 36.2 1.0
O L:HOH491 2.6 38.3 1.0
OE1 E:GLU201 2.7 34.0 1.0
O L:HOH531 2.7 48.0 1.0
O E:HOH522 2.8 30.0 1.0
CD E:GLU201 3.0 35.6 1.0
CD L:GLU201 3.5 32.9 1.0
C L:GLU201 3.5 33.4 1.0
CA L:CA303 3.7 49.3 1.0
CG L:GLU201 4.2 30.1 1.0
CA L:GLU201 4.2 31.7 1.0
OE1 L:GLU201 4.4 36.5 1.0
CG E:GLU201 4.5 33.8 1.0
N L:TYR202 4.6 31.9 1.0
O E:HOH506 4.7 47.4 1.0
CA L:TYR202 4.7 34.0 1.0
O L:HOH480 4.8 30.0 1.0
CB L:GLU201 4.8 29.1 1.0
O E:GLU201 4.9 34.4 1.0
CD1 L:TYR202 4.9 35.4 1.0

Reference:

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
Page generated: Mon Jul 15 18:27:22 2024

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