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Calcium in PDB 8a2z: Cryo-Em Structure of F-Actin in the CA2+-Adp Nucleotide State.

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of F-Actin in the CA2+-Adp Nucleotide State. (pdb code 8a2z). 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 Nucleotide State., PDB code: 8a2z:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 8a2z

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

b:26.3
occ:1.00
 O2B C:ADP401 2.2 20.3 1.0
O2A C:ADP401 2.2 20.3 1.0
O C:HOH528 2.2 24.2 1.0
O C:HOH582 2.3 23.3 1.0
O C:HOH535 2.3 23.6 1.0
O C:HOH578 2.4 22.5 1.0
PA C:ADP401 3.4 20.3 1.0
PB C:ADP401 3.5 20.3 1.0
O3A C:ADP401 3.6 20.3 1.0
O C:HOH586 4.0 23.6 1.0
NZ C:LYS18 4.2 23.8 1.0
OD2 C:ASP11 4.3 25.7 1.0
O3B C:ADP401 4.3 20.3 1.0
CA C:GLY156 4.3 19.0 1.0
O1A C:ADP401 4.4 20.3 1.0
O C:HOH602 4.4 21.6 1.0
CA C:GLY301 4.4 19.1 1.0
OD1 C:ASP154 4.5 19.7 1.0
OD2 C:ASP154 4.5 19.7 1.0
O5' C:ADP401 4.6 20.3 1.0
O1B C:ADP401 4.6 20.3 1.0
OD1 C:ASP11 4.7 25.7 1.0
O C:HOH619 4.8 25.6 1.0
N C:GLY156 4.8 19.0 1.0
CG2 C:VAL339 4.9 21.8 1.0
CG C:ASP154 4.9 19.7 1.0
CG C:ASP11 4.9 25.7 1.0
O C:HOH537 4.9 21.8 1.0
CA C:GLY13 5.0 25.6 1.0
N C:GLY302 5.0 19.2 1.0

Calcium binding site 2 out of 5 in 8a2z

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

b:26.3
occ:1.00
 O A:HOH556 2.2 29.3 1.0
O2B A:ADP401 2.2 20.3 1.0
O2A A:ADP401 2.2 20.3 1.0
O A:HOH544 2.3 31.9 1.0
O A:HOH567 2.3 29.9 1.0
O A:HOH512 2.4 31.2 1.0
PA A:ADP401 3.4 20.3 1.0
PB A:ADP401 3.5 20.3 1.0
O3A A:ADP401 3.6 20.3 1.0
O A:HOH569 4.0 31.3 1.0
NZ A:LYS18 4.2 23.8 1.0
OD2 A:ASP11 4.3 25.7 1.0
O3B A:ADP401 4.3 20.3 1.0
CA A:GLY156 4.3 19.0 1.0
O A:HOH574 4.3 30.0 1.0
O1A A:ADP401 4.4 20.3 1.0
CA A:GLY301 4.4 19.1 1.0
OD1 A:ASP154 4.5 19.7 1.0
OD2 A:ASP154 4.5 19.7 1.0
O5' A:ADP401 4.6 20.3 1.0
O1B A:ADP401 4.6 20.3 1.0
O A:HOH583 4.6 30.0 1.0
OD1 A:ASP11 4.7 25.7 1.0
O A:HOH528 4.8 30.4 1.0
N A:GLY156 4.8 19.0 1.0
CG2 A:VAL339 4.9 21.8 1.0
CG A:ASP154 4.9 19.7 1.0
CG A:ASP11 4.9 25.7 1.0
CA A:GLY13 5.0 25.6 1.0
N A:GLY302 5.0 19.2 1.0

Calcium binding site 3 out of 5 in 8a2z

Go back to Calcium Binding Sites List in 8a2z
Calcium binding site 3 out of 5 in the Cryo-Em Structure of F-Actin in the CA2+-Adp 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 Nucleotide State. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:26.3
occ:1.00
 O B:HOH578 2.2 24.1 1.0
O2B B:ADP401 2.2 20.3 1.0
O2A B:ADP401 2.2 20.3 1.0
O B:HOH585 2.4 23.1 1.0
O B:HOH516 2.4 25.4 1.0
O B:HOH546 2.6 26.3 1.0
PA B:ADP401 3.4 20.3 1.0
PB B:ADP401 3.5 20.3 1.0
O3A B:ADP401 3.6 20.3 1.0
O B:HOH583 4.1 25.0 1.0
NZ B:LYS18 4.2 23.8 1.0
OD2 B:ASP11 4.3 25.7 1.0
O3B B:ADP401 4.3 20.3 1.0
CA B:GLY156 4.3 19.0 1.0
O B:HOH594 4.4 22.6 1.0
O1A B:ADP401 4.4 20.3 1.0
CA B:GLY301 4.4 19.1 1.0
OD1 B:ASP154 4.5 19.7 1.0
OD2 B:ASP154 4.5 19.7 1.0
O5' B:ADP401 4.6 20.3 1.0
O1B B:ADP401 4.6 20.3 1.0
O B:HOH600 4.7 25.0 1.0
OD1 B:ASP11 4.7 25.7 1.0
N B:GLY156 4.8 19.0 1.0
O B:HOH515 4.8 23.0 1.0
CG2 B:VAL339 4.9 21.8 1.0
CG B:ASP154 4.9 19.7 1.0
CG B:ASP11 4.9 25.7 1.0
CA B:GLY13 5.0 25.6 1.0
N B:GLY302 5.0 19.2 1.0

Calcium binding site 4 out of 5 in 8a2z

Go back to Calcium Binding Sites List in 8a2z
Calcium binding site 4 out of 5 in the Cryo-Em Structure of F-Actin in the CA2+-Adp 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 Nucleotide State. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:26.3
occ:1.00
 O2B D:ADP401 2.2 20.3 1.0
O D:HOH570 2.2 24.5 1.0
O2A D:ADP401 2.2 20.3 1.0
O D:HOH536 2.2 26.3 1.0
O D:HOH517 2.4 25.2 1.0
O D:HOH513 2.5 24.9 1.0
PA D:ADP401 3.4 20.3 1.0
PB D:ADP401 3.5 20.3 1.0
O3A D:ADP401 3.6 20.3 1.0
O D:HOH584 4.1 24.4 1.0
NZ D:LYS18 4.2 23.8 1.0
OD2 D:ASP11 4.3 25.7 1.0
O3B D:ADP401 4.3 20.3 1.0
CA D:GLY156 4.3 19.0 1.0
O D:HOH595 4.3 23.7 1.0
O1A D:ADP401 4.4 20.3 1.0
CA D:GLY301 4.4 19.1 1.0
OD1 D:ASP154 4.5 19.7 1.0
OD2 D:ASP154 4.5 19.7 1.0
O5' D:ADP401 4.6 20.3 1.0
O1B D:ADP401 4.6 20.3 1.0
OD1 D:ASP11 4.7 25.7 1.0
O D:HOH602 4.8 25.2 1.0
N D:GLY156 4.8 19.0 1.0
CG2 D:VAL339 4.9 21.8 1.0
CG D:ASP154 4.9 19.7 1.0
CG D:ASP11 4.9 25.7 1.0
CA D:GLY13 5.0 25.6 1.0
N D:GLY302 5.0 19.2 1.0

Calcium binding site 5 out of 5 in 8a2z

Go back to Calcium Binding Sites List in 8a2z
Calcium binding site 5 out of 5 in the Cryo-Em Structure of F-Actin in the CA2+-Adp 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 Nucleotide State. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:26.3
occ:1.00
 O2B E:ADP401 2.2 20.3 1.0
O E:HOH524 2.2 32.0 1.0
O2A E:ADP401 2.2 20.3 1.0
O E:HOH552 2.3 32.2 1.0
O E:HOH514 2.3 31.1 1.0
O E:HOH515 2.3 31.6 1.0
PA E:ADP401 3.4 20.3 1.0
PB E:ADP401 3.5 20.3 1.0
O3A E:ADP401 3.6 20.3 1.0
O E:HOH562 4.0 29.5 1.0
O E:HOH572 4.2 30.6 1.0
NZ E:LYS18 4.2 23.8 1.0
OD2 E:ASP11 4.3 25.7 1.0
O3B E:ADP401 4.3 20.3 1.0
CA E:GLY156 4.3 19.0 1.0
O1A E:ADP401 4.4 20.3 1.0
CA E:GLY301 4.4 19.1 1.0
OD1 E:ASP154 4.5 19.7 1.0
OD2 E:ASP154 4.5 19.7 1.0
O5' E:ADP401 4.6 20.3 1.0
O1B E:ADP401 4.6 20.3 1.0
OD1 E:ASP11 4.7 25.7 1.0
O E:HOH578 4.8 30.2 1.0
N E:GLY156 4.8 19.0 1.0
CG2 E:VAL339 4.9 21.8 1.0
CG E:ASP154 4.9 19.7 1.0
CG E:ASP11 4.9 25.7 1.0
CA E:GLY13 5.0 25.6 1.0
N E:GLY302 5.0 19.2 1.0
O E:HOH529 5.0 30.8 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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