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Calcium in PDB 8a2y: Cryo-Em Structure of F-Actin in the CA2+-Adp-Pi Nucleotide State.

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of F-Actin in the CA2+-Adp-Pi Nucleotide State. (pdb code 8a2y). 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-Pi Nucleotide State., PDB code: 8a2y:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 8a2y

Go back to Calcium Binding Sites List in 8a2y
Calcium binding site 1 out of 5 in the Cryo-Em Structure of F-Actin in the CA2+-Adp-Pi 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-Pi Nucleotide State. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:18.2
occ:1.00
 O4 C:PO4403 2.2 16.3 1.0
O C:HOH570 2.3 16.1 1.0
O C:HOH507 2.3 19.0 1.0
O2B C:ADP401 2.4 15.7 1.0
O C:HOH501 2.5 18.5 1.0
OE1 C:GLN137 3.0 17.2 1.0
PB C:ADP401 3.5 15.7 1.0
P C:PO4403 3.6 16.3 1.0
CD C:GLN137 3.7 17.2 1.0
O3B C:ADP401 3.7 15.7 1.0
O3A C:ADP401 3.9 15.7 1.0
OD2 C:ASP11 4.2 19.1 1.0
NE2 C:GLN137 4.2 17.2 1.0
O3 C:PO4403 4.2 16.3 1.0
OD2 C:ASP154 4.3 15.2 1.0
OD1 C:ASP11 4.3 19.1 1.0
NZ C:LYS18 4.3 17.5 1.0
CA C:GLY13 4.4 16.9 1.0
O2 C:PO4403 4.5 16.3 1.0
O1 C:PO4403 4.5 16.3 1.0
O2A C:ADP401 4.6 15.7 1.0
O C:HOH503 4.6 17.0 1.0
CG C:ASP11 4.7 19.1 1.0
CA C:GLY156 4.7 14.4 1.0
PA C:ADP401 4.7 15.7 1.0
CG C:GLN137 4.8 17.2 1.0
O1B C:ADP401 4.8 15.7 1.0
CG2 C:VAL339 4.9 15.7 1.0
OD1 C:ASP154 4.9 15.2 1.0
O C:HOH508 5.0 20.2 1.0

Calcium binding site 2 out of 5 in 8a2y

Go back to Calcium Binding Sites List in 8a2y
Calcium binding site 2 out of 5 in the Cryo-Em Structure of F-Actin in the CA2+-Adp-Pi 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-Pi Nucleotide State. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:18.2
occ:1.00
 O4 A:PO4403 2.2 16.3 1.0
O A:HOH551 2.3 21.8 1.0
O2B A:ADP401 2.4 15.7 1.0
O A:HOH505 2.4 25.4 1.0
O A:HOH506 2.5 25.1 1.0
OE1 A:GLN137 3.0 17.2 1.0
PB A:ADP401 3.5 15.7 1.0
P A:PO4403 3.6 16.3 1.0
CD A:GLN137 3.7 17.2 1.0
O3B A:ADP401 3.7 15.7 1.0
O3A A:ADP401 3.9 15.7 1.0
OD2 A:ASP11 4.2 19.1 1.0
NE2 A:GLN137 4.2 17.2 1.0
O3 A:PO4403 4.2 16.3 1.0
OD2 A:ASP154 4.3 15.2 1.0
OD1 A:ASP11 4.3 19.1 1.0
NZ A:LYS18 4.3 17.5 1.0
CA A:GLY13 4.4 16.9 1.0
O2 A:PO4403 4.5 16.3 1.0
O1 A:PO4403 4.5 16.3 1.0
O2A A:ADP401 4.6 15.7 1.0
O A:HOH507 4.7 19.3 1.0
CG A:ASP11 4.7 19.1 1.0
CA A:GLY156 4.7 14.4 1.0
PA A:ADP401 4.7 15.7 1.0
CG A:GLN137 4.8 17.2 1.0
O1B A:ADP401 4.8 15.7 1.0
CG2 A:VAL339 4.9 15.7 1.0
OD1 A:ASP154 4.9 15.2 1.0
O A:HOH517 4.9 25.3 1.0

Calcium binding site 3 out of 5 in 8a2y

Go back to Calcium Binding Sites List in 8a2y
Calcium binding site 3 out of 5 in the Cryo-Em Structure of F-Actin in the CA2+-Adp-Pi 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-Pi Nucleotide State. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:18.2
occ:1.00
 O4 B:PO4403 2.2 16.3 1.0
O B:HOH570 2.3 16.7 1.0
O B:HOH504 2.3 18.7 1.0
O2B B:ADP401 2.4 15.7 1.0
O B:HOH501 2.4 19.5 1.0
OE1 B:GLN137 3.0 17.2 1.0
PB B:ADP401 3.5 15.7 1.0
P B:PO4403 3.6 16.3 1.0
CD B:GLN137 3.7 17.2 1.0
O3B B:ADP401 3.7 15.7 1.0
O3A B:ADP401 3.9 15.7 1.0
OD2 B:ASP11 4.2 19.1 1.0
O3 B:PO4403 4.2 16.3 1.0
NE2 B:GLN137 4.2 17.2 1.0
OD2 B:ASP154 4.3 15.2 1.0
OD1 B:ASP11 4.3 19.1 1.0
NZ B:LYS18 4.3 17.5 1.0
CA B:GLY13 4.4 16.9 1.0
O2 B:PO4403 4.5 16.3 1.0
O1 B:PO4403 4.5 16.3 1.0
O B:HOH514 4.5 16.7 1.0
O2A B:ADP401 4.6 15.7 1.0
CG B:ASP11 4.7 19.1 1.0
CA B:GLY156 4.7 14.4 1.0
PA B:ADP401 4.7 15.7 1.0
CG B:GLN137 4.8 17.2 1.0
O1B B:ADP401 4.8 15.7 1.0
O B:HOH530 4.8 21.4 1.0
CG2 B:VAL339 4.9 15.7 1.0
OD1 B:ASP154 4.9 15.2 1.0

Calcium binding site 4 out of 5 in 8a2y

Go back to Calcium Binding Sites List in 8a2y
Calcium binding site 4 out of 5 in the Cryo-Em Structure of F-Actin in the CA2+-Adp-Pi 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-Pi Nucleotide State. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:18.2
occ:1.00
 O4 D:PO4403 2.2 16.3 1.0
O D:HOH503 2.3 19.8 1.0
O D:HOH564 2.3 17.3 1.0
O2B D:ADP401 2.4 15.7 1.0
O D:HOH506 2.6 19.4 1.0
OE1 D:GLN137 3.0 17.2 1.0
PB D:ADP401 3.5 15.7 1.0
P D:PO4403 3.6 16.3 1.0
CD D:GLN137 3.7 17.2 1.0
O3B D:ADP401 3.7 15.7 1.0
O3A D:ADP401 3.9 15.7 1.0
OD2 D:ASP11 4.2 19.1 1.0
NE2 D:GLN137 4.2 17.2 1.0
O3 D:PO4403 4.2 16.3 1.0
OD2 D:ASP154 4.3 15.2 1.0
OD1 D:ASP11 4.3 19.1 1.0
NZ D:LYS18 4.3 17.5 1.0
CA D:GLY13 4.4 16.9 1.0
O2 D:PO4403 4.5 16.3 1.0
O D:HOH516 4.5 18.3 1.0
O1 D:PO4403 4.5 16.3 1.0
O2A D:ADP401 4.6 15.7 1.0
CG D:ASP11 4.7 19.1 1.0
CA D:GLY156 4.7 14.4 1.0
PA D:ADP401 4.7 15.7 1.0
CG D:GLN137 4.8 17.2 1.0
O1B D:ADP401 4.8 15.7 1.0
CG2 D:VAL339 4.9 15.7 1.0
OD1 D:ASP154 4.9 15.2 1.0
O D:HOH507 4.9 21.3 1.0

Calcium binding site 5 out of 5 in 8a2y

Go back to Calcium Binding Sites List in 8a2y
Calcium binding site 5 out of 5 in the Cryo-Em Structure of F-Actin in the CA2+-Adp-Pi 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-Pi Nucleotide State. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:18.2
occ:1.00
 O4 E:PO4403 2.2 16.3 1.0
O E:HOH512 2.3 26.2 1.0
O2B E:ADP401 2.4 15.7 1.0
O E:HOH504 2.4 24.5 1.0
O E:HOH545 2.4 22.4 1.0
OE1 E:GLN137 3.0 17.2 1.0
PB E:ADP401 3.5 15.7 1.0
P E:PO4403 3.6 16.3 1.0
CD E:GLN137 3.7 17.2 1.0
O3B E:ADP401 3.7 15.7 1.0
O3A E:ADP401 3.9 15.7 1.0
OD2 E:ASP11 4.2 19.1 1.0
NE2 E:GLN137 4.2 17.2 1.0
O3 E:PO4403 4.2 16.3 1.0
OD2 E:ASP154 4.3 15.2 1.0
OD1 E:ASP11 4.3 19.1 1.0
NZ E:LYS18 4.3 17.5 1.0
CA E:GLY13 4.4 16.9 1.0
O2 E:PO4403 4.5 16.3 1.0
O1 E:PO4403 4.5 16.3 1.0
O2A E:ADP401 4.6 15.7 1.0
CG E:ASP11 4.7 19.1 1.0
CA E:GLY156 4.7 14.4 1.0
PA E:ADP401 4.7 15.7 1.0
O E:HOH501 4.7 22.8 1.0
CG E:GLN137 4.8 17.2 1.0
O1B E:ADP401 4.8 15.7 1.0
CG2 E:VAL339 4.9 15.7 1.0
OD1 E:ASP154 4.9 15.2 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: Fri Jul 19 06:44:43 2024

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