Magnesium in PDB 9fju: Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 1)

Enzymatic activity of Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 1)

All present enzymatic activity of Structure of the Dnase I- and Phalloidin-Bound Pointed End of F-Actin (Conformer 1):
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 1) (pdb code 9fju). 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 1), PDB code: 9fju:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 9fju

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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 1)


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 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:103.6
occ:1.00
 O1 A:PO4403 2.0 106.9 1.0
O1B A:ADP401 2.0 103.8 1.0
O4 A:PO4403 2.3 106.9 1.0
P A:PO4403 2.6 106.9 1.0
PB A:ADP401 2.7 103.8 1.0
O2B A:ADP401 2.9 103.8 1.0
OE1 A:GLN137 3.1 105.4 1.0
O3B A:ADP401 3.4 103.8 1.0
O2 A:PO4403 3.4 106.9 1.0
CA A:GLY156 3.8 101.5 1.0
O3 A:PO4403 3.9 106.9 1.0
CD A:GLN137 4.1 105.4 1.0
O2A A:ADP401 4.1 103.8 1.0
O3A A:ADP401 4.2 103.8 1.0
NE2 A:GLN137 4.4 105.4 1.0
OD2 A:ASP154 4.4 107.9 1.0
CA A:GLY13 4.5 106.8 1.0
N A:ASP157 4.5 101.5 1.0
N A:GLY156 4.7 101.5 1.0
C A:GLY156 4.7 101.5 1.0
OD2 A:ASP11 4.8 112.0 1.0
PA A:ADP401 4.8 103.8 1.0
OD1 A:ASP154 4.8 107.9 1.0
OD1 A:ASP11 4.9 112.0 1.0

Magnesium binding site 2 out of 8 in 9fju

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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 1)


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 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:69.3
occ:1.00
 O2B B:ADP401 2.0 73.9 1.0
O3 B:PO4403 2.3 77.3 1.0
NE2 B:GLN137 2.9 73.2 1.0
PB B:ADP401 3.0 73.9 1.0
O3B B:ADP401 3.2 73.9 1.0
O4 B:PO4403 3.4 77.3 1.0
P B:PO4403 3.4 77.3 1.0
O1B B:ADP401 3.8 73.9 1.0
CA B:GLY156 4.1 67.9 1.0
OD1 B:ASP154 4.1 71.0 1.0
O2 B:PO4403 4.2 77.3 1.0
CD B:GLN137 4.2 73.2 1.0
O3A B:ADP401 4.3 73.9 1.0
O2A B:ADP401 4.5 73.9 1.0
O1 B:PO4403 4.7 77.3 1.0
OE1 B:GLN137 4.7 73.2 1.0
N B:GLY156 4.9 67.9 1.0
CG B:ASP154 4.9 71.0 1.0
N B:ASP157 4.9 72.4 1.0

Magnesium binding site 3 out of 8 in 9fju

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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 1)


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 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:72.7
occ:1.00
 O2B C:ADP401 2.0 71.8 1.0
O3 C:PO4403 2.0 72.2 1.0
O1 C:PO4403 2.0 72.2 1.0
P C:PO4403 2.5 72.2 1.0
PB C:ADP401 2.9 71.8 1.0
OE1 C:GLN137 3.1 64.1 1.0
O1B C:ADP401 3.3 71.8 1.0
O3B C:ADP401 3.4 71.8 1.0
O4 C:PO4403 3.5 72.2 1.0
O2 C:PO4403 3.7 72.2 1.0
CD C:GLN137 3.7 64.1 1.0
NE2 C:GLN137 3.8 64.1 1.0
CA C:GLY156 4.1 62.0 1.0
O3A C:ADP401 4.3 71.8 1.0
OD1 C:ASP154 4.5 61.5 1.0
CA C:GLY13 4.7 68.5 1.0
OD2 C:ASP154 4.7 61.5 1.0
OD2 C:ASP11 4.7 63.2 1.0
NZ C:LYS18 4.8 60.3 1.0
N C:ASP157 4.8 67.8 1.0
OD1 C:ASP11 4.9 63.2 1.0
CG C:GLN137 4.9 64.1 1.0
N C:GLY156 5.0 62.0 1.0

Magnesium binding site 4 out of 8 in 9fju

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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 1)


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 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:75.4
occ:1.00
 O2 D:PO4403 2.0 78.2 1.0
O2B D:ADP401 2.1 80.5 1.0
O1B D:ADP401 2.2 80.5 1.0
P D:PO4403 2.4 78.2 1.0
PB D:ADP401 2.5 80.5 1.0
O3 D:PO4403 2.5 78.2 1.0
O4 D:PO4403 2.7 78.2 1.0
O3B D:ADP401 3.5 80.5 1.0
CA D:GLY156 3.6 69.6 1.0
O3A D:ADP401 3.9 80.5 1.0
O1 D:PO4403 3.9 78.2 1.0
N D:ASP157 4.1 77.9 1.0
OD2 D:ASP154 4.4 64.9 1.0
C D:GLY156 4.4 69.6 1.0
OG D:SER14 4.5 76.0 1.0
N D:GLY156 4.6 69.6 1.0
OD2 D:ASP11 4.8 72.4 1.0
O2A D:ADP401 4.9 80.5 1.0
O D:SER14 4.9 76.0 1.0
N D:SER14 4.9 76.0 1.0

Magnesium binding site 5 out of 8 in 9fju

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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 1)


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 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:137.5
occ:1.00
 OD2 E:ASP251 2.0 136.2 1.0
OD1 E:ASP251 2.4 136.2 1.0
CD E:ARG9 2.5 124.8 1.0
CG E:ASP251 2.5 136.2 1.0
NH1 E:ARG9 3.2 124.8 1.0
CG E:ARG9 3.3 124.8 1.0
NE E:ARG9 3.3 124.8 1.0
CB E:ARG9 3.6 124.8 1.0
CZ E:ARG9 3.6 124.8 1.0
CB E:ASP251 4.0 136.2 1.0
OE1 E:GLU39 4.1 121.6 1.0
CA E:ARG9 4.3 124.8 1.0
ND2 E:ASN7 4.7 116.4 1.0
OE2 E:GLU39 4.7 121.6 1.0
N E:ASP251 4.8 136.2 1.0
ND1 E:HIS252 4.8 133.6 1.0
CD E:GLU39 4.8 121.6 1.0
NH2 E:ARG9 4.9 124.8 1.0
CA E:ASP251 4.9 136.2 1.0

Magnesium binding site 6 out of 8 in 9fju

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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 1)


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 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:154.7
occ:1.00
 O E:ASP198 2.0 157.1 1.0
OD2 E:ASP172 2.5 155.7 1.0
C E:ASP198 2.8 157.1 1.0
CG E:ASP172 2.9 155.7 1.0
CB E:ASP198 2.9 157.1 1.0
CA E:ASP198 3.1 157.1 1.0
OD1 E:ASP172 3.3 155.7 1.0
OD2 E:ASP198 3.5 157.1 1.0
CG E:ASP198 3.5 157.1 1.0
CB E:ASP172 3.8 155.7 1.0
CB E:ALA210 3.8 145.8 1.0
ND2 E:ASN208 3.9 151.6 1.0
N E:SER199 4.0 158.3 1.0
N E:ALA210 4.2 145.8 1.0
OD1 E:ASN208 4.4 151.6 1.0
CG E:ASN208 4.5 151.6 1.0
N E:ASP198 4.5 157.1 1.0
OD1 E:ASP198 4.6 157.1 1.0
CA E:SER199 4.6 158.3 1.0
CA E:ALA210 4.7 145.8 1.0
O E:ALA200 4.8 154.0 1.0
NH2 E:ARG213 4.8 142.8 1.0
C E:SER199 5.0 158.3 1.0

Magnesium binding site 7 out of 8 in 9fju

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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 1)


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 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg301

b:180.0
occ:1.00
 CA F:ARG9 3.9 184.4 1.0
OD2 F:ASP251 4.0 191.8 1.0
CD F:GLU39 4.0 174.4 1.0
CG F:GLU39 4.0 174.4 1.0
CB F:ARG9 4.0 184.4 1.0
CG F:ARG9 4.1 184.4 1.0
OE2 F:GLU39 4.2 174.4 1.0
OE1 F:GLU39 4.3 174.4 1.0
N F:THR10 4.3 177.6 1.0
OD1 F:ASP251 4.3 191.8 1.0
NE F:ARG9 4.5 184.4 1.0
CG F:ASP251 4.5 191.8 1.0
C F:ARG9 4.6 184.4 1.0
CG2 F:THR10 4.7 177.6 1.0
N F:ARG9 4.9 184.4 1.0
CD F:ARG9 4.9 184.4 1.0
CB F:GLU39 5.0 174.4 1.0

Magnesium binding site 8 out of 8 in 9fju

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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 1)


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 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:205.2
occ:1.00
 O F:ASN208 3.2 204.1 1.0
CG F:ASP172 3.2 206.1 1.0
OD1 F:ASP172 3.3 206.1 1.0
O F:ASP198 3.4 200.3 1.0
OD2 F:ASP172 3.6 206.1 1.0
CB F:ASP172 3.6 206.1 1.0
N F:ALA210 3.9 199.3 1.0
C F:ASN208 4.2 204.1 1.0
CA F:CYS209 4.2 202.9 1.0
SG F:CYS173 4.2 209.5 1.0
C F:ASP198 4.3 200.3 1.0
CB F:ALA210 4.5 199.3 1.0
C F:CYS209 4.5 202.9 1.0
N F:CYS173 4.5 209.5 1.0
N F:CYS209 4.6 202.9 1.0
CB F:ASP198 4.6 200.3 1.0
CA F:ASP198 4.8 200.3 1.0
CA F:ALA210 4.8 199.3 1.0
CA F:ASP172 5.0 206.1 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 09:34:09 2024

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