Calcium in PDB 8a2u: Cryo-Em Structure of F-Actin in the CA2+-Adp-BEF3- Nucleotide State.

Other elements in 8a2u:

The structure of Cryo-Em Structure of F-Actin in the CA2+-Adp-BEF3- Nucleotide State. also contains other interesting chemical elements:

Fluorine (F) 15 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of F-Actin in the CA2+-Adp-BEF3- Nucleotide State. (pdb code 8a2u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Cryo-Em Structure of F-Actin in the CA2+-Adp-BEF3- Nucleotide State., PDB code: 8a2u:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 8a2u

Go back to Calcium Binding Sites List in 8a2u
Calcium binding site 1 out of 5 in the Cryo-Em Structure of F-Actin in the CA2+-Adp-BEF3- Nucleotide State.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of F-Actin in the CA2+-Adp-BEF3- Nucleotide State. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:21.2
occ:1.00
 F2 C:BEF403 2.2 16.6 1.0
O C:HOH508 2.2 15.1 1.0
O2B C:ADP401 2.3 15.9 1.0
O C:HOH503 2.3 19.0 1.0
O C:HOH560 2.4 21.3 1.0
O C:HOH504 2.8 20.4 1.0
PB C:ADP401 3.4 15.9 1.0
BE C:BEF403 3.5 16.6 1.0
O3B C:ADP401 3.5 15.9 1.0
O2A C:ADP401 4.1 15.9 1.0
O C:HOH527 4.1 19.4 1.0
O C:HOH558 4.1 17.4 1.0
O3A C:ADP401 4.1 15.9 1.0
OE1 C:GLN137 4.1 22.9 1.0
F3 C:BEF403 4.2 16.6 1.0
OD2 C:ASP11 4.3 22.2 1.0
OD1 C:ASP11 4.3 22.2 1.0
O C:HOH617 4.4 22.6 1.0
NE2 C:GLN137 4.4 22.9 1.0
NZ C:LYS18 4.4 19.8 1.0
CD C:GLN137 4.5 22.9 1.0
PA C:ADP401 4.6 15.9 1.0
CA C:GLY13 4.6 18.4 1.0
F1 C:BEF403 4.6 16.6 1.0
O1B C:ADP401 4.6 15.9 1.0
OD1 C:ASP154 4.7 16.9 1.0
CG C:ASP11 4.8 22.2 1.0
CA C:GLY156 4.9 14.8 1.0
O1A C:ADP401 5.0 15.9 1.0
CG2 C:VAL339 5.0 19.9 1.0

Calcium binding site 2 out of 5 in 8a2u

Go back to Calcium Binding Sites List in 8a2u
Calcium binding site 2 out of 5 in the Cryo-Em Structure of F-Actin in the CA2+-Adp-BEF3- Nucleotide State.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of F-Actin in the CA2+-Adp-BEF3- Nucleotide State. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:21.2
occ:1.00
 F2 A:BEF403 2.2 16.6 1.0
O A:HOH550 2.2 21.3 1.0
O A:HOH505 2.3 15.1 1.0
O2B A:ADP401 2.3 15.9 1.0
O A:HOH503 2.3 19.0 1.0
O A:HOH501 2.9 20.4 1.0
PB A:ADP401 3.4 15.9 1.0
BE A:BEF403 3.5 16.6 1.0
O3B A:ADP401 3.5 15.9 1.0
O2A A:ADP401 4.1 15.9 1.0
O A:HOH523 4.1 19.4 1.0
O3A A:ADP401 4.1 15.9 1.0
OE1 A:GLN137 4.1 22.9 1.0
O A:HOH535 4.2 17.4 1.0
F3 A:BEF403 4.2 16.6 1.0
OD2 A:ASP11 4.3 22.2 1.0
OD1 A:ASP11 4.3 22.2 1.0
NE2 A:GLN137 4.4 22.9 1.0
NZ A:LYS18 4.4 19.8 1.0
CD A:GLN137 4.5 22.9 1.0
PA A:ADP401 4.6 15.9 1.0
CA A:GLY13 4.6 18.4 1.0
F1 A:BEF403 4.6 16.6 1.0
O1B A:ADP401 4.6 15.9 1.0
O A:HOH574 4.7 22.6 1.0
OD1 A:ASP154 4.7 16.9 1.0
CG A:ASP11 4.8 22.2 1.0
CA A:GLY156 4.9 14.8 1.0
O1A A:ADP401 5.0 15.9 1.0
CG2 A:VAL339 5.0 19.9 1.0

Calcium binding site 3 out of 5 in 8a2u

Go back to Calcium Binding Sites List in 8a2u
Calcium binding site 3 out of 5 in the Cryo-Em Structure of F-Actin in the CA2+-Adp-BEF3- Nucleotide State.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of F-Actin in the CA2+-Adp-BEF3- Nucleotide State. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:21.2
occ:1.00
 F2 B:BEF403 2.2 16.6 1.0
O2B B:ADP401 2.3 15.9 1.0
O B:HOH564 2.3 21.3 1.0
O B:HOH503 2.3 15.1 1.0
O B:HOH502 2.4 19.0 1.0
O B:HOH501 2.8 20.4 1.0
PB B:ADP401 3.4 15.9 1.0
BE B:BEF403 3.5 16.6 1.0
O3B B:ADP401 3.5 15.9 1.0
O2A B:ADP401 4.1 15.9 1.0
O B:HOH557 4.1 17.4 1.0
O B:HOH523 4.1 19.4 1.0
O3A B:ADP401 4.1 15.9 1.0
OE1 B:GLN137 4.1 22.9 1.0
F3 B:BEF403 4.2 16.6 1.0
OD2 B:ASP11 4.3 22.2 1.0
OD1 B:ASP11 4.3 22.2 1.0
NE2 B:GLN137 4.4 22.9 1.0
NZ B:LYS18 4.4 19.8 1.0
O B:HOH608 4.4 22.6 1.0
CD B:GLN137 4.5 22.9 1.0
PA B:ADP401 4.6 15.9 1.0
CA B:GLY13 4.6 18.4 1.0
F1 B:BEF403 4.6 16.6 1.0
O1B B:ADP401 4.6 15.9 1.0
OD1 B:ASP154 4.7 16.9 1.0
CG B:ASP11 4.8 22.2 1.0
CA B:GLY156 4.9 14.8 1.0
O1A B:ADP401 5.0 15.9 1.0
CG2 B:VAL339 5.0 19.9 1.0

Calcium binding site 4 out of 5 in 8a2u

Go back to Calcium Binding Sites List in 8a2u
Calcium binding site 4 out of 5 in the Cryo-Em Structure of F-Actin in the CA2+-Adp-BEF3- Nucleotide State.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of F-Actin in the CA2+-Adp-BEF3- Nucleotide State. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:21.2
occ:1.00
 F2 D:BEF403 2.2 16.6 1.0
O D:HOH534 2.3 21.3 1.0
O2B D:ADP401 2.3 15.9 1.0
O D:HOH504 2.3 15.1 1.0
O D:HOH502 2.5 19.0 1.0
O D:HOH503 2.8 20.4 1.0
PB D:ADP401 3.4 15.9 1.0
BE D:BEF403 3.5 16.6 1.0
O3B D:ADP401 3.5 15.9 1.0
O2A D:ADP401 4.1 15.9 1.0
O3A D:ADP401 4.1 15.9 1.0
O D:HOH522 4.1 19.4 1.0
OE1 D:GLN137 4.1 22.9 1.0
O D:HOH526 4.2 17.4 1.0
F3 D:BEF403 4.2 16.6 1.0
OD2 D:ASP11 4.3 22.2 1.0
OD1 D:ASP11 4.3 22.2 1.0
NE2 D:GLN137 4.4 22.9 1.0
NZ D:LYS18 4.4 19.8 1.0
CD D:GLN137 4.5 22.9 1.0
O D:HOH597 4.5 22.6 1.0
PA D:ADP401 4.6 15.9 1.0
CA D:GLY13 4.6 18.4 1.0
F1 D:BEF403 4.6 16.6 1.0
O1B D:ADP401 4.6 15.9 1.0
OD1 D:ASP154 4.7 16.9 1.0
CG D:ASP11 4.8 22.2 1.0
CA D:GLY156 4.9 14.8 1.0
O1A D:ADP401 5.0 15.9 1.0
CG2 D:VAL339 5.0 19.9 1.0

Calcium binding site 5 out of 5 in 8a2u

Go back to Calcium Binding Sites List in 8a2u
Calcium binding site 5 out of 5 in the Cryo-Em Structure of F-Actin in the CA2+-Adp-BEF3- Nucleotide State.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structure of F-Actin in the CA2+-Adp-BEF3- Nucleotide State. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:21.2
occ:1.00
 F2 E:BEF403 2.2 16.6 1.0
O2B E:ADP401 2.3 15.9 1.0
O E:HOH501 2.3 19.0 1.0
O E:HOH506 2.4 15.1 1.0
O E:HOH539 2.4 21.3 1.0
O E:HOH502 2.8 20.4 1.0
PB E:ADP401 3.4 15.9 1.0
BE E:BEF403 3.5 16.6 1.0
O3B E:ADP401 3.5 15.9 1.0
O E:HOH518 4.0 19.4 1.0
O2A E:ADP401 4.1 15.9 1.0
O3A E:ADP401 4.1 15.9 1.0
OE1 E:GLN137 4.1 22.9 1.0
F3 E:BEF403 4.2 16.6 1.0
O E:HOH528 4.3 17.4 1.0
OD2 E:ASP11 4.3 22.2 1.0
OD1 E:ASP11 4.3 22.2 1.0
NE2 E:GLN137 4.4 22.9 1.0
O E:HOH575 4.4 22.6 1.0
NZ E:LYS18 4.4 19.8 1.0
CD E:GLN137 4.5 22.9 1.0
PA E:ADP401 4.6 15.9 1.0
CA E:GLY13 4.6 18.4 1.0
F1 E:BEF403 4.6 16.6 1.0
O1B E:ADP401 4.6 15.9 1.0
OD1 E:ASP154 4.7 16.9 1.0
CG E:ASP11 4.8 22.2 1.0
CA E:GLY156 4.9 14.8 1.0
O1A E:ADP401 5.0 15.9 1.0
CG2 E:VAL339 5.0 19.9 1.0

Reference:

W.Oosterheert, B.U.Klink, A.Belyy, S.Pospich, S.Raunser. Structural Basis of Actin Filament Assembly and Aging. Nature V. 611 374 2022.
ISSN: ESSN 1476-4687
PubMed: 36289337
DOI: 10.1038/S41586-022-05241-8
Page generated: Tue Apr 4 19:23:33 2023

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