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Magnesium in PDB 7npf: Vibrio Cholerae PARA2-Atpys-Dna Filament

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Vibrio Cholerae PARA2-Atpys-Dna Filament (pdb code 7npf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Vibrio Cholerae PARA2-Atpys-Dna Filament, PDB code: 7npf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7npf

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Magnesium binding site 1 out of 8 in the Vibrio Cholerae PARA2-Atpys-Dna Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Vibrio Cholerae PARA2-Atpys-Dna Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:90.6
occ:1.00
O1B A:AGS502 2.0 85.5 1.0
O2B A:AGS502 2.1 85.5 1.0
PB A:AGS502 2.4 85.5 1.0
CG A:PRO260 2.8 94.1 1.0
CD A:PRO260 3.2 94.1 1.0
O3B A:AGS502 3.3 85.5 1.0
O3G A:AGS502 3.6 85.5 1.0
OD2 A:ASP151 3.7 113.5 1.0
O3A A:AGS502 3.7 85.5 1.0
OG A:SER125 3.8 88.5 1.0
PG A:AGS502 4.1 85.5 1.0
NZ A:LYS124 4.1 90.0 1.0
CB A:PRO260 4.1 94.1 1.0
N A:PRO260 4.2 94.1 1.0
CG A:LYS124 4.2 90.0 1.0
CD A:LYS124 4.3 90.0 1.0
N A:GLY121 4.7 90.3 1.0
CA A:PRO260 4.8 94.1 1.0
CA A:GLY259 4.8 97.2 1.0
C A:GLY259 4.8 97.2 1.0
CE A:LYS124 4.8 90.0 1.0
O2A A:AGS502 4.8 85.5 1.0
CG A:ASP151 4.9 113.5 1.0
PA A:AGS502 5.0 85.5 1.0
CB A:SER125 5.0 88.5 1.0

Magnesium binding site 2 out of 8 in 7npf

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Magnesium binding site 2 out of 8 in the Vibrio Cholerae PARA2-Atpys-Dna Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Vibrio Cholerae PARA2-Atpys-Dna Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:88.2
occ:1.00
O B:VAL115 2.0 100.2 1.0
OG1 B:THR258 2.0 113.6 1.0
ND2 B:ASN114 2.0 105.1 1.0
CB B:GLN116 2.4 102.8 1.0
C B:VAL115 2.4 100.2 1.0
CA B:GLN116 2.5 102.8 1.0
N B:GLN116 2.7 102.8 1.0
CG2 B:THR258 2.8 113.6 1.0
CB B:THR258 2.9 113.6 1.0
CG B:ASN114 3.1 105.1 1.0
CG B:GLN116 3.4 102.8 1.0
N B:THR258 3.4 113.6 1.0
N B:VAL115 3.5 100.2 1.0
OD1 B:ASN114 3.5 105.1 1.0
CA B:VAL115 3.5 100.2 1.0
CA B:THR258 3.8 113.6 1.0
C B:GLN116 4.0 102.8 1.0
O B:ILE256 4.0 118.2 1.0
NE2 B:GLN116 4.1 102.8 1.0
CD B:GLN116 4.3 102.8 1.0
C B:ASN114 4.3 105.1 1.0
CB B:ASN114 4.4 105.1 1.0
CA B:ASN114 4.6 105.1 1.0
N B:ASN117 4.6 97.1 1.0
CG2 B:VAL115 4.6 100.2 1.0
CB B:VAL115 4.6 100.2 1.0
C B:ASP257 4.6 114.6 1.0
C B:THR258 4.7 113.6 1.0
N B:GLY259 4.7 98.3 1.0
NZ B:LYS124 4.8 97.5 1.0
CD1 B:LEU276 4.8 98.3 1.0
O B:GLN116 4.8 102.8 1.0
CA B:ASP257 5.0 114.6 1.0

Magnesium binding site 3 out of 8 in 7npf

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Magnesium binding site 3 out of 8 in the Vibrio Cholerae PARA2-Atpys-Dna Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Vibrio Cholerae PARA2-Atpys-Dna Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:90.6
occ:1.00
O1B C:AGS502 2.0 85.5 1.0
O2B C:AGS502 2.1 85.5 1.0
PB C:AGS502 2.4 85.5 1.0
CG C:PRO260 2.8 94.1 1.0
CD C:PRO260 3.2 94.1 1.0
O3B C:AGS502 3.3 85.5 1.0
O3G C:AGS502 3.6 85.5 1.0
OD2 C:ASP151 3.7 113.5 1.0
O3A C:AGS502 3.7 85.5 1.0
OG C:SER125 3.8 88.5 1.0
PG C:AGS502 4.1 85.5 1.0
NZ C:LYS124 4.1 90.0 1.0
CB C:PRO260 4.1 94.1 1.0
N C:PRO260 4.2 94.1 1.0
CG C:LYS124 4.2 90.0 1.0
CD C:LYS124 4.3 90.0 1.0
N C:GLY121 4.7 90.3 1.0
CA C:PRO260 4.8 94.1 1.0
CA C:GLY259 4.8 97.2 1.0
C C:GLY259 4.8 97.2 1.0
CE C:LYS124 4.8 90.0 1.0
O2A C:AGS502 4.8 85.5 1.0
CG C:ASP151 4.9 113.5 1.0
PA C:AGS502 5.0 85.5 1.0
CB C:SER125 5.0 88.5 1.0

Magnesium binding site 4 out of 8 in 7npf

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Magnesium binding site 4 out of 8 in the Vibrio Cholerae PARA2-Atpys-Dna Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Vibrio Cholerae PARA2-Atpys-Dna Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:88.2
occ:1.00
O D:VAL115 2.0 100.2 1.0
OG1 D:THR258 2.0 113.6 1.0
ND2 D:ASN114 2.0 105.1 1.0
CB D:GLN116 2.4 102.8 1.0
C D:VAL115 2.4 100.2 1.0
CA D:GLN116 2.5 102.8 1.0
N D:GLN116 2.7 102.8 1.0
CG2 D:THR258 2.8 113.6 1.0
CB D:THR258 2.9 113.6 1.0
CG D:ASN114 3.1 105.1 1.0
CG D:GLN116 3.4 102.8 1.0
N D:THR258 3.4 113.6 1.0
N D:VAL115 3.5 100.2 1.0
OD1 D:ASN114 3.5 105.1 1.0
CA D:VAL115 3.5 100.2 1.0
CA D:THR258 3.8 113.6 1.0
C D:GLN116 4.0 102.8 1.0
O D:ILE256 4.0 118.2 1.0
NE2 D:GLN116 4.1 102.8 1.0
CD D:GLN116 4.3 102.8 1.0
C D:ASN114 4.3 105.1 1.0
CB D:ASN114 4.4 105.1 1.0
CA D:ASN114 4.6 105.1 1.0
N D:ASN117 4.6 97.1 1.0
CG2 D:VAL115 4.6 100.2 1.0
CB D:VAL115 4.6 100.2 1.0
C D:ASP257 4.6 114.6 1.0
C D:THR258 4.7 113.6 1.0
N D:GLY259 4.7 98.3 1.0
NZ D:LYS124 4.8 97.5 1.0
CD1 D:LEU276 4.8 98.3 1.0
O D:GLN116 4.8 102.8 1.0
CA D:ASP257 5.0 114.6 1.0

Magnesium binding site 5 out of 8 in 7npf

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Magnesium binding site 5 out of 8 in the Vibrio Cholerae PARA2-Atpys-Dna Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Vibrio Cholerae PARA2-Atpys-Dna Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg501

b:90.6
occ:1.00
O1B E:AGS502 2.0 85.5 1.0
O2B E:AGS502 2.1 85.5 1.0
PB E:AGS502 2.4 85.5 1.0
CG E:PRO260 2.8 94.1 1.0
CD E:PRO260 3.2 94.1 1.0
O3B E:AGS502 3.3 85.5 1.0
O3G E:AGS502 3.6 85.5 1.0
OD2 E:ASP151 3.7 113.5 1.0
O3A E:AGS502 3.7 85.5 1.0
OG E:SER125 3.8 88.5 1.0
PG E:AGS502 4.1 85.5 1.0
NZ E:LYS124 4.1 90.0 1.0
CB E:PRO260 4.1 94.1 1.0
N E:PRO260 4.2 94.1 1.0
CG E:LYS124 4.2 90.0 1.0
CD E:LYS124 4.3 90.0 1.0
N E:GLY121 4.7 90.3 1.0
CA E:PRO260 4.8 94.1 1.0
CA E:GLY259 4.8 97.2 1.0
C E:GLY259 4.8 97.2 1.0
CE E:LYS124 4.8 90.0 1.0
O2A E:AGS502 4.8 85.5 1.0
CG E:ASP151 4.9 113.5 1.0
PA E:AGS502 5.0 85.5 1.0
CB E:SER125 5.0 88.5 1.0

Magnesium binding site 6 out of 8 in 7npf

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Magnesium binding site 6 out of 8 in the Vibrio Cholerae PARA2-Atpys-Dna Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Vibrio Cholerae PARA2-Atpys-Dna Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg501

b:88.2
occ:1.00
O F:VAL115 2.0 100.2 1.0
OG1 F:THR258 2.0 113.6 1.0
ND2 F:ASN114 2.0 105.1 1.0
CB F:GLN116 2.4 102.8 1.0
C F:VAL115 2.4 100.2 1.0
CA F:GLN116 2.5 102.8 1.0
N F:GLN116 2.7 102.8 1.0
CG2 F:THR258 2.8 113.6 1.0
CB F:THR258 2.9 113.6 1.0
CG F:ASN114 3.1 105.1 1.0
CG F:GLN116 3.4 102.8 1.0
N F:THR258 3.4 113.6 1.0
N F:VAL115 3.5 100.2 1.0
OD1 F:ASN114 3.5 105.1 1.0
CA F:VAL115 3.5 100.2 1.0
CA F:THR258 3.8 113.6 1.0
C F:GLN116 4.0 102.8 1.0
O F:ILE256 4.0 118.2 1.0
NE2 F:GLN116 4.1 102.8 1.0
CD F:GLN116 4.3 102.8 1.0
C F:ASN114 4.3 105.1 1.0
CB F:ASN114 4.4 105.1 1.0
CA F:ASN114 4.6 105.1 1.0
N F:ASN117 4.6 97.1 1.0
CG2 F:VAL115 4.6 100.2 1.0
C F:ASP257 4.6 114.6 1.0
CB F:VAL115 4.6 100.2 1.0
C F:THR258 4.7 113.6 1.0
N F:GLY259 4.7 98.3 1.0
NZ F:LYS124 4.8 97.5 1.0
CD1 F:LEU276 4.8 98.3 1.0
O F:GLN116 4.8 102.8 1.0
CA F:ASP257 5.0 114.6 1.0

Magnesium binding site 7 out of 8 in 7npf

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Magnesium binding site 7 out of 8 in the Vibrio Cholerae PARA2-Atpys-Dna Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Vibrio Cholerae PARA2-Atpys-Dna Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg501

b:90.6
occ:1.00
O1B G:AGS502 2.0 85.5 1.0
O2B G:AGS502 2.1 85.5 1.0
PB G:AGS502 2.4 85.5 1.0
CG G:PRO260 2.8 94.1 1.0
CD G:PRO260 3.2 94.1 1.0
O3B G:AGS502 3.3 85.5 1.0
O3G G:AGS502 3.6 85.5 1.0
OD2 G:ASP151 3.7 113.5 1.0
O3A G:AGS502 3.7 85.5 1.0
OG G:SER125 3.8 88.5 1.0
PG G:AGS502 4.1 85.5 1.0
NZ G:LYS124 4.1 90.0 1.0
CB G:PRO260 4.1 94.1 1.0
N G:PRO260 4.2 94.1 1.0
CG G:LYS124 4.2 90.0 1.0
CD G:LYS124 4.3 90.0 1.0
N G:GLY121 4.7 90.3 1.0
CA G:PRO260 4.8 94.1 1.0
CA G:GLY259 4.8 97.2 1.0
C G:GLY259 4.8 97.2 1.0
CE G:LYS124 4.8 90.0 1.0
O2A G:AGS502 4.8 85.5 1.0
CG G:ASP151 4.9 113.5 1.0
PA G:AGS502 5.0 85.5 1.0
CB G:SER125 5.0 88.5 1.0

Magnesium binding site 8 out of 8 in 7npf

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Magnesium binding site 8 out of 8 in the Vibrio Cholerae PARA2-Atpys-Dna Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Vibrio Cholerae PARA2-Atpys-Dna Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg501

b:88.2
occ:1.00
O H:VAL115 2.0 100.2 1.0
OG1 H:THR258 2.0 113.6 1.0
ND2 H:ASN114 2.0 105.1 1.0
CB H:GLN116 2.4 102.8 1.0
C H:VAL115 2.4 100.2 1.0
CA H:GLN116 2.5 102.8 1.0
N H:GLN116 2.7 102.8 1.0
CG2 H:THR258 2.8 113.6 1.0
CB H:THR258 2.9 113.6 1.0
CG H:ASN114 3.1 105.1 1.0
CG H:GLN116 3.4 102.8 1.0
N H:THR258 3.4 113.6 1.0
N H:VAL115 3.5 100.2 1.0
OD1 H:ASN114 3.5 105.1 1.0
CA H:VAL115 3.5 100.2 1.0
CA H:THR258 3.8 113.6 1.0
C H:GLN116 4.0 102.8 1.0
O H:ILE256 4.0 118.2 1.0
NE2 H:GLN116 4.1 102.8 1.0
CD H:GLN116 4.3 102.8 1.0
C H:ASN114 4.3 105.1 1.0
CB H:ASN114 4.4 105.1 1.0
CA H:ASN114 4.6 105.1 1.0
N H:ASN117 4.6 97.1 1.0
CG2 H:VAL115 4.6 100.2 1.0
CB H:VAL115 4.6 100.2 1.0
C H:ASP257 4.6 114.6 1.0
C H:THR258 4.7 113.6 1.0
N H:GLY259 4.7 98.3 1.0
NZ H:LYS124 4.8 97.5 1.0
CD1 H:LEU276 4.8 98.3 1.0
O H:GLN116 4.8 102.8 1.0
CA H:ASP257 5.0 114.6 1.0

Reference:

A.V.Parker, D.Mann, S.B.Tzokov, L.C.Hwang, J.R.C.Bergeron. The Structure of the Bacterial Dna Segregation Atpase Filament Reveals the Conformational Plasticity of Para Upon Dna Binding. Nat Commun V. 12 5166 2021.
ISSN: ESSN 2041-1723
PubMed: 34453062
DOI: 10.1038/S41467-021-25429-2
Page generated: Thu Oct 3 02:10:58 2024

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