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Magnesium in PDB 6izr: Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum

Magnesium Binding Sites:

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30;

Binding sites:

The binding sites of Magnesium atom in the Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum (pdb code 6izr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 30 binding sites of Magnesium where determined in the Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum, PDB code: 6izr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 30 in 6izr

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Magnesium binding site 1 out of 30 in the Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum


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A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg402

b:1.0
occ:1.00
 NE2 1:GLN168 2.1 0.3 1.0
O2B 1:ADP401 2.3 0.9 1.0
OD2 1:ASP195 2.8 0.4 1.0
CD 1:GLN168 2.9 0.3 1.0
ND2 1:ASN338 3.1 0.6 1.0
PB 1:ADP401 3.3 0.9 1.0
OE1 1:GLN168 3.4 0.3 1.0
O3A 1:ADP401 3.5 0.9 1.0
O3B 1:ADP401 3.6 0.9 1.0
CG 1:ASP195 3.7 0.4 1.0
CG 1:GLN168 4.1 0.3 1.0
OD2 1:ASP9 4.1 0.4 1.0
OD1 1:ASP195 4.1 0.4 1.0
NZ 1:LYS16 4.3 0.2 1.0
CG 1:ASN338 4.4 0.6 1.0
CE 1:LYS16 4.5 0.2 1.0
O2A 1:ADP401 4.6 0.9 1.0
PA 1:ADP401 4.7 0.9 1.0
OD2 1:ASP202 4.7 0.4 1.0
O1B 1:ADP401 4.7 0.9 1.0
CG 1:ASP9 4.9 0.4 1.0
CB 1:ASP195 4.9 0.4 1.0
OD1 1:ASP9 4.9 0.4 1.0
CA 1:GLY11 5.0 0.1 1.0

Magnesium binding site 2 out of 30 in 6izr

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Magnesium binding site 2 out of 30 in the Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg402

b:0.5
occ:1.00
 NE2 2:GLN168 2.1 0.6 1.0
O2B 2:ADP401 2.3 0.5 1.0
OD2 2:ASP195 2.8 0.0 1.0
CD 2:GLN168 2.9 0.6 1.0
ND2 2:ASN338 3.1 0.3 1.0
PB 2:ADP401 3.3 0.5 1.0
OE1 2:GLN168 3.4 0.6 1.0
O3A 2:ADP401 3.5 0.5 1.0
O3B 2:ADP401 3.6 0.5 1.0
CG 2:ASP195 3.7 0.0 1.0
CG 2:GLN168 4.1 0.6 1.0
OD2 2:ASP9 4.1 0.2 1.0
OD1 2:ASP195 4.1 0.0 1.0
NZ 2:LYS16 4.3 0.5 1.0
CG 2:ASN338 4.4 0.3 1.0
CE 2:LYS16 4.5 0.5 1.0
O2A 2:ADP401 4.6 0.5 1.0
PA 2:ADP401 4.7 0.5 1.0
OD2 2:ASP202 4.7 0.7 1.0
O1B 2:ADP401 4.7 0.5 1.0
CG 2:ASP9 4.9 0.2 1.0
CB 2:ASP195 4.9 0.0 1.0
OD1 2:ASP9 4.9 0.2 1.0
CA 2:GLY11 5.0 0.4 1.0

Magnesium binding site 3 out of 30 in 6izr

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Magnesium binding site 3 out of 30 in the Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:0.8
occ:1.00
 NE2 A:GLN168 2.1 0.0 1.0
O1B A:ADP401 2.3 1.0 1.0
OD2 A:ASP195 2.8 1.0 1.0
CD A:GLN168 3.1 0.0 1.0
PB A:ADP401 3.3 1.0 1.0
ND2 A:ASN338 3.3 0.4 1.0
O3A A:ADP401 3.5 1.0 1.0
O3B A:ADP401 3.7 1.0 1.0
CG A:GLN168 3.7 0.0 1.0
CG A:ASP195 3.9 1.0 1.0
OE1 A:GLN168 4.0 0.0 1.0
NZ A:LYS16 4.2 0.0 1.0
OD2 A:ASP9 4.3 0.3 1.0
OD1 A:ASP195 4.3 1.0 1.0
CE A:LYS16 4.5 0.0 1.0
O1A A:ADP401 4.6 1.0 1.0
CA A:GLY197 4.7 0.6 1.0
PA A:ADP401 4.7 1.0 1.0
CG A:ASN338 4.7 0.4 1.0
OD1 A:ASP9 4.7 0.3 1.0
O2B A:ADP401 4.7 1.0 1.0
CG A:ASP9 4.9 0.3 1.0

Magnesium binding site 4 out of 30 in 6izr

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Magnesium binding site 4 out of 30 in the Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:0.4
occ:1.00
 NE2 B:GLN168 2.1 0.4 1.0
O2B B:ADP401 2.3 0.5 1.0
OD2 B:ASP195 3.0 0.2 1.0
CD B:GLN168 3.1 0.4 1.0
ND2 B:ASN338 3.2 0.3 1.0
PB B:ADP401 3.3 0.5 1.0
O3A B:ADP401 3.5 0.5 1.0
OD1 B:ASP195 3.6 0.2 1.0
CG B:ASP195 3.6 0.2 1.0
O1B B:ADP401 3.7 0.5 1.0
OD2 B:ASP9 3.7 0.4 1.0
CG B:GLN168 3.8 0.4 1.0
OE1 B:GLN168 3.9 0.4 1.0
NZ B:LYS16 4.2 0.6 1.0
CG B:ASN338 4.5 0.3 1.0
CE B:LYS16 4.6 0.6 1.0
O1A B:ADP401 4.6 0.5 1.0
PA B:ADP401 4.7 0.5 1.0
O3B B:ADP401 4.7 0.5 1.0
CG B:ASP9 4.8 0.4 1.0
CA B:GLY197 4.8 0.2 1.0
OD1 B:ASP9 5.0 0.4 1.0

Magnesium binding site 5 out of 30 in 6izr

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Magnesium binding site 5 out of 30 in the Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:0.9
occ:1.00
 NE2 D:GLN168 2.1 0.3 1.0
O2B D:ADP401 2.3 0.9 1.0
OD2 D:ASP195 3.0 0.0 1.0
CD D:GLN168 3.1 0.3 1.0
ND2 D:ASN338 3.2 0.5 1.0
PB D:ADP401 3.3 0.9 1.0
O3A D:ADP401 3.5 0.9 1.0
OD1 D:ASP195 3.6 0.0 1.0
CG D:ASP195 3.6 0.0 1.0
O1B D:ADP401 3.6 0.9 1.0
OD2 D:ASP9 3.7 0.1 1.0
CG D:GLN168 3.8 0.3 1.0
OE1 D:GLN168 3.9 0.3 1.0
NZ D:LYS16 4.2 0.5 1.0
CG D:ASN338 4.5 0.5 1.0
CE D:LYS16 4.6 0.5 1.0
O1A D:ADP401 4.6 0.9 1.0
PA D:ADP401 4.7 0.9 1.0
O3B D:ADP401 4.7 0.9 1.0
CG D:ASP9 4.8 0.1 1.0
CA D:GLY197 4.8 0.3 1.0
OD1 D:ASP9 5.0 0.1 1.0

Magnesium binding site 6 out of 30 in 6izr

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Magnesium binding site 6 out of 30 in the Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:0.6
occ:1.00
 NE2 E:GLN168 2.1 0.0 1.0
O2B E:ADP401 2.3 0.3 1.0
OD2 E:ASP195 3.0 0.8 1.0
ND2 E:ASN338 3.1 0.8 1.0
PB E:ADP401 3.3 0.3 1.0
CD E:GLN168 3.4 0.0 1.0
O3A E:ADP401 3.5 0.3 1.0
O1B E:ADP401 3.7 0.3 1.0
OD2 E:ASP9 3.8 0.6 1.0
CG E:ASP195 4.0 0.8 1.0
OE1 E:GLN168 4.2 0.0 1.0
OD1 E:ASP195 4.3 0.8 1.0
OD1 E:ASP9 4.3 0.6 1.0
CG E:GLN168 4.3 0.0 1.0
CG E:ASN338 4.3 0.8 1.0
CG E:ASP9 4.5 0.6 1.0
CA E:GLY197 4.5 0.5 1.0
O1A E:ADP401 4.6 0.3 1.0
PA E:ADP401 4.7 0.3 1.0
NZ E:LYS16 4.7 0.5 1.0
O3B E:ADP401 4.7 0.3 1.0
CE E:LYS16 4.9 0.5 1.0

Magnesium binding site 7 out of 30 in 6izr

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Magnesium binding site 7 out of 30 in the Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg402

b:0.1
occ:1.00
 NE2 G:GLN168 2.1 0.3 1.0
O2B G:ADP401 2.3 0.8 1.0
OD2 G:ASP195 3.0 0.7 1.0
ND2 G:ASN338 3.1 0.4 1.0
PB G:ADP401 3.3 0.8 1.0
CD G:GLN168 3.4 0.3 1.0
O3A G:ADP401 3.5 0.8 1.0
O1B G:ADP401 3.6 0.8 1.0
OD2 G:ASP9 3.8 0.1 1.0
CG G:ASP195 4.0 0.7 1.0
OE1 G:GLN168 4.2 0.3 1.0
OD1 G:ASP195 4.3 0.7 1.0
OD1 G:ASP9 4.3 0.1 1.0
CG G:GLN168 4.3 0.3 1.0
CG G:ASN338 4.3 0.4 1.0
CG G:ASP9 4.5 0.1 1.0
CA G:GLY197 4.5 0.5 1.0
O1A G:ADP401 4.6 0.8 1.0
PA G:ADP401 4.7 0.8 1.0
NZ G:LYS16 4.7 0.2 1.0
O3B G:ADP401 4.7 0.8 1.0
CE G:LYS16 4.9 0.2 1.0

Magnesium binding site 8 out of 30 in 6izr

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Magnesium binding site 8 out of 30 in the Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg402

b:0.6
occ:1.00
 NE2 H:GLN168 2.1 0.4 1.0
O1B H:ADP401 2.3 0.1 1.0
OD2 H:ASP195 2.7 0.1 1.0
ND2 H:ASN338 3.2 0.7 1.0
CD H:GLN168 3.3 0.4 1.0
PB H:ADP401 3.3 0.1 1.0
O3A H:ADP401 3.5 0.1 1.0
O3B H:ADP401 3.7 0.1 1.0
CG H:ASP195 3.7 0.1 1.0
OD2 H:ASP9 4.1 0.1 1.0
OE1 H:GLN168 4.1 0.4 1.0
OD1 H:ASP195 4.1 0.1 1.0
CG H:GLN168 4.2 0.4 1.0
NZ H:LYS16 4.4 0.8 1.0
CG H:ASN338 4.5 0.7 1.0
CA H:GLY197 4.5 0.2 1.0
CE H:LYS16 4.6 0.8 1.0
O1A H:ADP401 4.6 0.1 1.0
PA H:ADP401 4.7 0.1 1.0
O2B H:ADP401 4.7 0.1 1.0
CG H:ASP9 4.8 0.1 1.0
OD1 H:ASP9 4.9 0.1 1.0

Magnesium binding site 9 out of 30 in 6izr

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Magnesium binding site 9 out of 30 in the Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg402

b:0.8
occ:1.00
 NE2 J:GLN168 2.1 0.5 1.0
O1B J:ADP401 2.3 0.7 1.0
OD2 J:ASP195 2.7 0.0 1.0
ND2 J:ASN338 3.2 0.1 1.0
CD J:GLN168 3.3 0.5 1.0
PB J:ADP401 3.3 0.7 1.0
O3A J:ADP401 3.5 0.7 1.0
O3B J:ADP401 3.7 0.7 1.0
CG J:ASP195 3.7 0.0 1.0
OD2 J:ASP9 4.1 0.2 1.0
OE1 J:GLN168 4.1 0.5 1.0
OD1 J:ASP195 4.1 0.0 1.0
CG J:GLN168 4.2 0.5 1.0
NZ J:LYS16 4.4 0.0 1.0
CG J:ASN338 4.5 0.1 1.0
CA J:GLY197 4.5 0.5 1.0
CE J:LYS16 4.6 0.0 1.0
O1A J:ADP401 4.6 0.7 1.0
PA J:ADP401 4.7 0.7 1.0
O2B J:ADP401 4.7 0.7 1.0
CG J:ASP9 4.8 0.2 1.0
OD1 J:ASP9 4.9 0.2 1.0

Magnesium binding site 10 out of 30 in 6izr

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Magnesium binding site 10 out of 30 in the Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Whole Structure of A 15-Stranded Parm Filament From Clostridium Botulinum within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg402

b:0.6
occ:1.00
 NE2 K:GLN168 2.1 0.5 1.0
O1B K:ADP401 2.3 0.4 1.0
OD2 K:ASP195 2.7 0.9 1.0
CD K:GLN168 3.3 0.5 1.0
PB K:ADP401 3.3 0.4 1.0
CG K:ASP195 3.4 0.9 1.0
ND2 K:ASN338 3.5 0.3 1.0
O3A K:ADP401 3.5 0.4 1.0
OD1 K:ASP195 3.5 0.9 1.0
O3B K:ADP401 3.6 0.4 1.0
CG K:GLN168 3.9 0.5 1.0
OE1 K:GLN168 4.2 0.5 1.0
OD2 K:ASP9 4.2 0.5 1.0
OD1 K:ASP9 4.3 0.5 1.0
O1A K:ADP401 4.6 0.4 1.0
CG K:ASN338 4.6 0.3 1.0
CA K:GLY197 4.6 0.4 1.0
PA K:ADP401 4.7 0.4 1.0
CG K:ASP9 4.7 0.5 1.0
NZ K:LYS16 4.7 0.7 1.0
O2B K:ADP401 4.7 0.4 1.0
CB K:ASP195 4.8 0.9 1.0

Reference:

F.Koh, A.Narita, L.J.Lee, K.Tanaka, Y.Z.Tan, V.P.Dandey, D.Popp, R.C.Robinson. The Structure of A 15-Stranded Actin-Like Filament From Clostridium Botulinum. Nat Commun V. 10 2856 2019.
ISSN: ESSN 2041-1723
PubMed: 31253774
DOI: 10.1038/S41467-019-10779-9
Page generated: Tue Oct 1 04:31:42 2024

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