Magnesium in PDB 9fjy: Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2).

Enzymatic activity of Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2).

All present enzymatic activity of Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2).:
3.1.21.1;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2). (pdb code 9fjy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2)., PDB code: 9fjy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 9fjy

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Magnesium binding site 1 out of 8 in the Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:86.8
occ:1.00
 O2 A:PO4403 2.0 91.9 1.0
O1B A:ADP401 2.0 87.7 1.0
O2B A:ADP401 2.3 87.7 1.0
PB A:ADP401 2.4 87.7 1.0
O3B A:ADP401 3.2 87.7 1.0
P A:PO4403 3.3 91.9 1.0
O1 A:PO4403 3.6 91.9 1.0
O2A A:ADP401 3.7 87.7 1.0
O3A A:ADP401 3.8 87.7 1.0
O4 A:PO4403 3.9 91.9 1.0
OE1 A:GLN137 3.9 102.6 1.0
CA A:GLY156 4.1 86.9 1.0
PA A:ADP401 4.5 87.7 1.0
OD2 A:ASP11 4.5 98.9 1.0
O3 A:PO4403 4.5 91.9 1.0
OD1 A:ASP154 4.5 96.3 1.0
CA A:GLY13 4.7 90.5 1.0
N A:ASP157 4.8 88.0 1.0
OD2 A:ASP154 4.8 96.3 1.0
NZ A:LYS18 4.9 91.7 1.0
CD A:GLN137 4.9 102.6 1.0

Magnesium binding site 2 out of 8 in 9fjy

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Magnesium binding site 2 out of 8 in the Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:74.5
occ:1.00
 O2B B:ADP401 1.9 61.5 1.0
O4 B:PO4403 1.9 62.3 1.0
PB B:ADP401 2.5 61.5 1.0
O3B B:ADP401 2.5 61.5 1.0
P B:PO4403 2.6 62.3 1.0
O3 B:PO4403 2.8 62.3 1.0
O2 B:PO4403 2.9 62.3 1.0
O1B B:ADP401 3.3 61.5 1.0
OE1 B:GLN137 3.4 58.4 1.0
O3A B:ADP401 3.9 61.5 1.0
CA B:GLY156 3.9 55.3 1.0
O1 B:PO4403 4.1 62.3 1.0
CD B:GLN137 4.3 58.4 1.0
NE2 B:GLN137 4.4 58.4 1.0
N B:ASP157 4.6 58.6 1.0
OD2 B:ASP154 4.7 55.7 1.0
C B:GLY156 4.8 55.3 1.0
O B:SER14 4.9 59.7 1.0
N B:GLY156 4.9 55.3 1.0

Magnesium binding site 3 out of 8 in 9fjy

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Magnesium binding site 3 out of 8 in the Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:57.6
occ:1.00
 O2 C:PO4403 2.0 58.2 1.0
O3 C:PO4403 2.0 58.2 1.0
P C:PO4403 2.5 58.2 1.0
NE2 C:GLN137 2.6 50.1 1.0
O1B C:ADP401 2.9 56.3 1.0
O1 C:PO4403 3.5 58.2 1.0
PB C:ADP401 3.5 56.3 1.0
O2B C:ADP401 3.6 56.3 1.0
O4 C:PO4403 3.7 58.2 1.0
CD C:GLN137 3.8 50.1 1.0
CA C:GLY156 3.9 45.9 1.0
OD1 C:ASP154 4.0 45.9 1.0
O3B C:ADP401 4.0 56.3 1.0
OD2 C:ASP154 4.3 45.9 1.0
OE1 C:GLN137 4.4 50.1 1.0
CG C:ASP154 4.6 45.9 1.0
N C:GLY156 4.7 45.9 1.0
N C:ASP157 4.8 52.7 1.0
OD2 C:ASP11 4.8 55.2 1.0
O2A C:ADP401 4.9 56.3 1.0
CG C:GLN137 4.9 50.1 1.0
C C:GLY156 4.9 45.9 1.0
OD1 C:ASP11 5.0 55.2 1.0

Magnesium binding site 4 out of 8 in 9fjy

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Magnesium binding site 4 out of 8 in the Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:64.4
occ:1.00
 O3 D:PO4403 2.0 65.1 1.0
O2B D:ADP401 2.0 66.8 1.0
OE1 D:GLN137 2.5 55.4 1.0
P D:PO4403 2.6 65.1 1.0
O4 D:PO4403 2.9 65.1 1.0
O2 D:PO4403 2.9 65.1 1.0
PB D:ADP401 3.5 66.8 1.0
CD D:GLN137 3.5 55.4 1.0
OD2 D:ASP154 3.6 57.6 1.0
CA D:GLY156 3.9 56.0 1.0
NE2 D:GLN137 3.9 55.4 1.0
OD1 D:ASP154 4.0 57.6 1.0
CG D:ASP154 4.1 57.6 1.0
O1 D:PO4403 4.1 65.1 1.0
O1B D:ADP401 4.2 66.8 1.0
O3B D:ADP401 4.3 66.8 1.0
O3A D:ADP401 4.4 66.8 1.0
N D:GLY156 4.6 56.0 1.0
N D:ASP157 4.8 64.0 1.0
CG1 D:VAL159 4.9 50.9 1.0
CG D:GLN137 4.9 55.4 1.0
C D:GLY156 4.9 56.0 1.0
O D:ASP154 5.0 57.6 1.0

Magnesium binding site 5 out of 8 in 9fjy

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Magnesium binding site 5 out of 8 in the Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2). within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:107.5
occ:1.00
 OD2 E:ASP251 2.3 131.5 1.0
CG E:ARG9 3.1 123.2 1.0
CG E:ASP251 3.3 131.5 1.0
CB E:ARG9 3.7 123.2 1.0
OD1 E:ASP251 3.7 131.5 1.0
CA E:ARG9 4.1 123.2 1.0
CD E:ARG9 4.2 123.2 1.0
NE2 E:HIS252 4.4 129.5 1.0
CB E:ASP251 4.5 131.5 1.0
NE E:ARG9 4.5 123.2 1.0
N E:THR10 4.9 116.8 1.0
C E:ARG9 5.0 123.2 1.0

Magnesium binding site 6 out of 8 in 9fjy

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Magnesium binding site 6 out of 8 in the Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2). within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:129.8
occ:1.00
 O E:ASP198 2.7 140.4 1.0
OD2 E:ASP172 2.9 151.7 1.0
CG E:ASP172 3.0 151.7 1.0
OD1 E:ASP172 3.3 151.7 1.0
C E:ASP198 3.7 140.4 1.0
CB E:ASP172 3.7 151.7 1.0
N E:ALA210 4.0 139.6 1.0
CB E:ASP198 4.0 140.4 1.0
CA E:ASP198 4.1 140.4 1.0
ND2 E:ASN208 4.1 144.6 1.0
CB E:ALA210 4.2 139.6 1.0
OD1 E:ASN208 4.5 144.6 1.0
CG E:ASN208 4.5 144.6 1.0
CA E:CYS209 4.7 144.1 1.0
CA E:ALA210 4.7 139.6 1.0
SG E:CYS173 4.8 159.5 1.0
O E:ASN208 4.8 144.6 1.0
N E:SER199 4.8 141.2 1.0
C E:CYS209 4.8 144.1 1.0
O E:ALA200 4.9 141.2 1.0

Magnesium binding site 7 out of 8 in 9fjy

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Magnesium binding site 7 out of 8 in the Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2). within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg301

b:157.0
occ:1.00
 OD2 F:ASP251 2.2 163.9 1.0
OD1 F:ASP251 2.7 163.9 1.0
CG F:ASP251 2.7 163.9 1.0
CB F:ARG9 2.8 156.9 1.0
CG F:ARG9 2.8 156.9 1.0
CD F:ARG9 3.1 156.9 1.0
CA F:ARG9 3.2 156.9 1.0
OE2 F:GLU39 4.1 150.2 1.0
CE1 F:HIS252 4.1 164.5 1.0
CB F:ASP251 4.2 163.9 1.0
NE F:ARG9 4.2 156.9 1.0
C F:ARG9 4.2 156.9 1.0
N F:ARG9 4.2 156.9 1.0
NE2 F:HIS252 4.5 164.5 1.0
N F:THR10 4.5 153.6 1.0
CD F:GLU39 4.6 150.2 1.0
ND1 F:HIS252 4.7 164.5 1.0
N F:ASP251 4.8 163.9 1.0
CG2 F:THR10 4.9 153.6 1.0
CG F:GLU39 5.0 150.2 1.0

Magnesium binding site 8 out of 8 in 9fjy

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Magnesium binding site 8 out of 8 in the Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 2). within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:176.3
occ:1.00
 O F:ASP198 2.1 186.9 1.0
OD2 F:ASP172 2.6 184.7 1.0
CG F:ASP172 2.9 184.7 1.0
C F:ASP198 3.0 186.9 1.0
OD1 F:ASP172 3.2 184.7 1.0
CB F:ASP198 3.6 186.9 1.0
CA F:ASP198 3.6 186.9 1.0
CB F:ASP172 3.7 184.7 1.0
O F:ASN208 3.8 180.5 1.0
N F:SER199 4.0 187.3 1.0
CA F:SER199 4.4 187.3 1.0
N F:ALA210 4.5 178.6 1.0
CA F:CYS209 4.5 180.2 1.0
C F:ASN208 4.6 180.5 1.0
C F:SER199 4.8 187.3 1.0
O F:ALA200 4.9 187.1 1.0
CG F:ASP198 4.9 186.9 1.0
N F:CYS209 4.9 180.2 1.0
C F:CYS209 4.9 180.2 1.0
N F:ASP198 5.0 186.9 1.0

Reference:

M.Boiero Sanders, W.Oosterheert, O.Hofnagel, P.Bieling, S.Raunser. Phalloidin and Dnase I-Bound F-Actin Pointed End Structures Reveal Principles of Filament Stabilization and Disassembly Nat Commun 2024.
ISSN: ESSN 2041-1723
Page generated: Sat Oct 5 09:34:04 2024

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