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Magnesium in PDB 8a2r: Cryo-Em Structure of F-Actin in the MG2+-Adp-BEF3- Nucleotide State.

Other elements in 8a2r:

The structure of Cryo-Em Structure of F-Actin in the MG2+-Adp-BEF3- Nucleotide State. also contains other interesting chemical elements:

Fluorine (F) 15 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of F-Actin in the MG2+-Adp-BEF3- Nucleotide State. (pdb code 8a2r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Cryo-Em Structure of F-Actin in the MG2+-Adp-BEF3- Nucleotide State., PDB code: 8a2r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 8a2r

Go back to Magnesium Binding Sites List in 8a2r
Magnesium binding site 1 out of 5 in the Cryo-Em Structure of F-Actin in the MG2+-Adp-BEF3- Nucleotide State.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of F-Actin in the MG2+-Adp-BEF3- Nucleotide State. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:25.1
occ:1.00
 F2 C:BEF403 1.9 23.5 1.0
O C:HOH523 1.9 25.8 1.0
O C:HOH543 2.0 25.6 1.0
O C:HOH515 2.0 22.7 1.0
O2B C:ADP401 2.1 22.7 1.0
O C:HOH511 2.6 28.4 1.0
PB C:ADP401 3.2 22.7 1.0
BE C:BEF403 3.3 23.5 1.0
O3B C:ADP401 3.4 22.7 1.0
O3A C:ADP401 3.9 22.7 1.0
O C:HOH551 3.9 26.5 1.0
O2A C:ADP401 4.0 22.7 1.0
O C:HOH501 4.0 24.9 1.0
F3 C:BEF403 4.1 23.5 1.0
OD1 C:ASP154 4.1 24.1 1.0
OE1 C:GLN137 4.1 30.8 1.0
OD2 C:ASP11 4.2 28.7 1.0
F1 C:BEF403 4.4 23.5 1.0
PA C:ADP401 4.4 22.7 1.0
NZ C:LYS18 4.4 25.6 1.0
OD1 C:ASP11 4.4 28.7 1.0
CD C:GLN137 4.5 30.8 1.0
O1B C:ADP401 4.5 22.7 1.0
O C:HOH589 4.5 29.8 1.0
NE2 C:GLN137 4.5 30.8 1.0
CA C:GLY156 4.6 21.9 1.0
CA C:GLY13 4.6 25.1 1.0
OD2 C:ASP154 4.8 24.1 1.0
CG C:ASP11 4.8 28.7 1.0
O1A C:ADP401 4.8 22.7 1.0
CG C:ASP154 4.8 24.1 1.0
CG2 C:VAL339 5.0 26.3 1.0

Magnesium binding site 2 out of 5 in 8a2r

Go back to Magnesium Binding Sites List in 8a2r
Magnesium binding site 2 out of 5 in the Cryo-Em Structure of F-Actin in the MG2+-Adp-BEF3- Nucleotide State.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of F-Actin in the MG2+-Adp-BEF3- Nucleotide State. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:25.1
occ:1.00
 F2 A:BEF403 1.9 23.5 1.0
O A:HOH526 1.9 33.6 1.0
O A:HOH527 1.9 32.9 1.0
O2B A:ADP401 2.1 22.7 1.0
O A:HOH508 2.2 28.9 1.0
O A:HOH538 2.2 33.4 1.0
PB A:ADP401 3.2 22.7 1.0
BE A:BEF403 3.3 23.5 1.0
O3B A:ADP401 3.4 22.7 1.0
O3A A:ADP401 3.9 22.7 1.0
O2A A:ADP401 4.0 22.7 1.0
F3 A:BEF403 4.1 23.5 1.0
OD1 A:ASP154 4.1 24.1 1.0
O A:HOH501 4.1 30.0 1.0
OE1 A:GLN137 4.1 30.8 1.0
O A:HOH511 4.2 32.9 1.0
OD2 A:ASP11 4.2 28.7 1.0
O A:HOH541 4.3 34.5 1.0
F1 A:BEF403 4.4 23.5 1.0
PA A:ADP401 4.4 22.7 1.0
NZ A:LYS18 4.4 25.6 1.0
OD1 A:ASP11 4.4 28.7 1.0
CD A:GLN137 4.5 30.8 1.0
O1B A:ADP401 4.5 22.7 1.0
NE2 A:GLN137 4.5 30.8 1.0
CA A:GLY156 4.6 21.9 1.0
CA A:GLY13 4.6 25.1 1.0
OD2 A:ASP154 4.8 24.1 1.0
CG A:ASP11 4.8 28.7 1.0
O1A A:ADP401 4.8 22.7 1.0
CG A:ASP154 4.8 24.1 1.0
CG2 A:VAL339 5.0 26.3 1.0

Magnesium binding site 3 out of 5 in 8a2r

Go back to Magnesium Binding Sites List in 8a2r
Magnesium binding site 3 out of 5 in the Cryo-Em Structure of F-Actin in the MG2+-Adp-BEF3- Nucleotide State.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of F-Actin in the MG2+-Adp-BEF3- Nucleotide State. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:25.1
occ:1.00
 O B:HOH526 1.9 27.7 1.0
F2 B:BEF403 1.9 23.5 1.0
O B:HOH517 1.9 27.6 1.0
O B:HOH514 2.0 23.9 1.0
O2B B:ADP401 2.1 22.7 1.0
O B:HOH508 2.5 30.1 1.0
PB B:ADP401 3.2 22.7 1.0
BE B:BEF403 3.3 23.5 1.0
O3B B:ADP401 3.4 22.7 1.0
O B:HOH530 3.8 28.0 1.0
O3A B:ADP401 3.9 22.7 1.0
O B:HOH501 3.9 25.4 1.0
O2A B:ADP401 4.0 22.7 1.0
F3 B:BEF403 4.1 23.5 1.0
OD1 B:ASP154 4.1 24.1 1.0
OE1 B:GLN137 4.1 30.8 1.0
OD2 B:ASP11 4.2 28.7 1.0
F1 B:BEF403 4.4 23.5 1.0
PA B:ADP401 4.4 22.7 1.0
NZ B:LYS18 4.4 25.6 1.0
OD1 B:ASP11 4.4 28.7 1.0
CD B:GLN137 4.5 30.8 1.0
O1B B:ADP401 4.5 22.7 1.0
NE2 B:GLN137 4.5 30.8 1.0
CA B:GLY156 4.6 21.9 1.0
CA B:GLY13 4.6 25.1 1.0
O B:HOH593 4.7 31.3 1.0
OD2 B:ASP154 4.8 24.1 1.0
CG B:ASP11 4.8 28.7 1.0
O1A B:ADP401 4.8 22.7 1.0
CG B:ASP154 4.8 24.1 1.0
CG2 B:VAL339 5.0 26.3 1.0

Magnesium binding site 4 out of 5 in 8a2r

Go back to Magnesium Binding Sites List in 8a2r
Magnesium binding site 4 out of 5 in the Cryo-Em Structure of F-Actin in the MG2+-Adp-BEF3- Nucleotide State.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of F-Actin in the MG2+-Adp-BEF3- Nucleotide State. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:25.1
occ:1.00
 F2 D:BEF403 1.9 23.5 1.0
O D:HOH512 2.0 22.6 1.0
O D:HOH547 2.0 27.0 1.0
O D:HOH508 2.0 26.8 1.0
O2B D:ADP401 2.1 22.7 1.0
O D:HOH507 2.6 27.9 1.0
PB D:ADP401 3.2 22.7 1.0
BE D:BEF403 3.3 23.5 1.0
O3B D:ADP401 3.4 22.7 1.0
O D:HOH572 3.8 27.9 1.0
O3A D:ADP401 3.9 22.7 1.0
O2A D:ADP401 4.0 22.7 1.0
O D:HOH504 4.0 25.1 1.0
F3 D:BEF403 4.1 23.5 1.0
OD1 D:ASP154 4.1 24.1 1.0
OE1 D:GLN137 4.1 30.8 1.0
OD2 D:ASP11 4.2 28.7 1.0
F1 D:BEF403 4.4 23.5 1.0
PA D:ADP401 4.4 22.7 1.0
NZ D:LYS18 4.4 25.6 1.0
OD1 D:ASP11 4.4 28.7 1.0
CD D:GLN137 4.5 30.8 1.0
O1B D:ADP401 4.5 22.7 1.0
NE2 D:GLN137 4.5 30.8 1.0
CA D:GLY156 4.6 21.9 1.0
CA D:GLY13 4.6 25.1 1.0
OD2 D:ASP154 4.8 24.1 1.0
CG D:ASP11 4.8 28.7 1.0
O D:HOH590 4.8 31.9 1.0
O1A D:ADP401 4.8 22.7 1.0
CG D:ASP154 4.8 24.1 1.0
CG2 D:VAL339 5.0 26.3 1.0

Magnesium binding site 5 out of 5 in 8a2r

Go back to Magnesium Binding Sites List in 8a2r
Magnesium binding site 5 out of 5 in the Cryo-Em Structure of F-Actin in the MG2+-Adp-BEF3- Nucleotide State.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of F-Actin in the MG2+-Adp-BEF3- Nucleotide State. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:25.1
occ:1.00
 F2 E:BEF403 1.9 23.5 1.0
O E:HOH541 1.9 33.7 1.0
O E:HOH529 2.0 31.2 1.0
O E:HOH504 2.1 34.0 1.0
O2B E:ADP401 2.1 22.7 1.0
O E:HOH505 2.6 35.4 1.0
PB E:ADP401 3.2 22.7 1.0
BE E:BEF403 3.3 23.5 1.0
O3B E:ADP401 3.4 22.7 1.0
O E:HOH545 3.8 35.0 1.0
O3A E:ADP401 3.9 22.7 1.0
O2A E:ADP401 4.0 22.7 1.0
F3 E:BEF403 4.1 23.5 1.0
OD1 E:ASP154 4.1 24.1 1.0
OE1 E:GLN137 4.1 30.8 1.0
O E:HOH506 4.2 32.2 1.0
OD2 E:ASP11 4.2 28.7 1.0
F1 E:BEF403 4.4 23.5 1.0
PA E:ADP401 4.4 22.7 1.0
NZ E:LYS18 4.4 25.6 1.0
OD1 E:ASP11 4.4 28.7 1.0
CD E:GLN137 4.5 30.8 1.0
O1B E:ADP401 4.5 22.7 1.0
NE2 E:GLN137 4.5 30.8 1.0
CA E:GLY156 4.6 21.9 1.0
CA E:GLY13 4.6 25.1 1.0
O E:HOH562 4.7 39.7 1.0
OD2 E:ASP154 4.8 24.1 1.0
CG E:ASP11 4.8 28.7 1.0
O1A E:ADP401 4.8 22.7 1.0
CG E:ASP154 4.8 24.1 1.0
CG2 E:VAL339 5.0 26.3 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: Thu Oct 3 17:11:13 2024

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