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Magnesium in PDB 5nwl: Crystal Structure of A Human RAD51-Atp Filament.

Protein crystallography data

The structure of Crystal Structure of A Human RAD51-Atp Filament., PDB code: 5nwl was solved by L.Pellegrini, T.Moschetti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.14 / 3.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 117.700, 128.000, 230.100, 90.00, 90.30, 90.00
R / Rfree (%) 26.8 / 31.7

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of A Human RAD51-Atp Filament. (pdb code 5nwl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Crystal Structure of A Human RAD51-Atp Filament., PDB code: 5nwl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 5nwl

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Magnesium binding site 1 out of 14 in the Crystal Structure of A Human RAD51-Atp Filament.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Human RAD51-Atp Filament. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:0.0
occ:1.00
 O1B A:ATP402 2.0 0.0 1.0
OG1 A:THR134 2.1 0.8 1.0
O1G A:ATP402 2.2 0.7 1.0
CB A:THR134 3.3 0.1 1.0
PG A:ATP402 3.4 0.3 1.0
PB A:ATP402 3.4 0.5 1.0
OG1 A:THR165 3.5 0.4 1.0
OD2 A:ASP222 3.6 0.4 1.0
O3G A:ATP402 3.7 0.7 1.0
O3B A:ATP402 3.9 0.1 1.0
CG2 A:THR165 3.9 0.7 1.0
CG2 A:THR134 4.0 0.9 1.0
CB A:THR165 4.1 0.4 1.0
O1A A:ATP402 4.2 0.8 1.0
OD1 A:ASP222 4.2 0.5 1.0
CG A:GLU163 4.3 0.8 1.0
CG A:ASP222 4.3 0.2 1.0
CA A:THR134 4.4 0.4 1.0
N A:THR134 4.4 0.5 1.0
O3A A:ATP402 4.4 0.2 1.0
CB A:GLU163 4.5 0.8 1.0
O2B A:ATP402 4.5 0.7 1.0
PA A:ATP402 4.6 0.9 1.0
O2G A:ATP402 4.7 0.6 1.0
O2A A:ATP402 4.7 0.5 1.0

Magnesium binding site 2 out of 14 in 5nwl

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Magnesium binding site 2 out of 14 in the Crystal Structure of A Human RAD51-Atp Filament.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Human RAD51-Atp Filament. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:60.4
occ:1.00
 O1B B:ATP402 2.1 76.3 1.0
OG1 B:THR134 2.1 74.4 1.0
O3G B:ATP402 2.1 91.9 1.0
OD2 B:ASP222 3.4 72.1 1.0
PB B:ATP402 3.4 92.1 1.0
CB B:THR134 3.4 93.4 1.0
PG B:ATP402 3.4 0.8 1.0
OG1 B:THR165 3.5 91.7 1.0
OD1 B:ASP222 3.7 92.5 1.0
O3B B:ATP402 3.9 0.8 1.0
CG B:ASP222 4.0 80.5 1.0
O1G B:ATP402 4.0 0.8 1.0
CG2 B:THR134 4.1 96.7 1.0
O2B B:ATP402 4.2 94.3 1.0
CG B:GLU163 4.2 1.0 1.0
CB B:THR165 4.4 0.5 1.0
O1A B:ATP402 4.4 0.7 1.0
CG2 B:THR165 4.4 1.0 1.0
N B:THR134 4.4 87.7 1.0
CA B:THR134 4.4 87.4 1.0
O3A B:ATP402 4.6 0.5 1.0
CB B:GLU163 4.6 0.1 1.0
O2G B:ATP402 4.6 0.6 1.0
PA B:ATP402 4.8 78.5 1.0
NE2 B:GLN268 4.9 0.8 1.0
O2A B:ATP402 4.9 54.1 1.0

Magnesium binding site 3 out of 14 in 5nwl

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Magnesium binding site 3 out of 14 in the Crystal Structure of A Human RAD51-Atp Filament.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Human RAD51-Atp Filament. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:77.0
occ:1.00
 O3G C:ATP402 1.9 99.4 1.0
OG1 C:THR134 2.1 93.6 1.0
O1B C:ATP402 2.2 0.4 1.0
OD2 C:ASP222 3.0 0.9 1.0
OG1 C:THR165 3.3 86.1 1.0
CB C:THR134 3.4 93.1 1.0
PB C:ATP402 3.4 1.0 1.0
PG C:ATP402 3.4 0.6 1.0
OD1 C:ASP222 3.5 0.1 1.0
CG C:ASP222 3.7 0.7 1.0
CG C:GLU163 3.8 0.5 1.0
CG2 C:THR165 3.9 0.8 1.0
O3B C:ATP402 3.9 0.9 1.0
CG2 C:THR134 4.0 97.5 1.0
O2B C:ATP402 4.0 93.2 1.0
CB C:THR165 4.1 0.1 1.0
CB C:GLU163 4.1 0.8 1.0
O2G C:ATP402 4.2 0.1 1.0
O1G C:ATP402 4.4 0.1 1.0
CA C:THR134 4.5 88.8 1.0
N C:THR134 4.5 89.6 1.0
CD C:GLU163 4.7 0.8 1.0
O1A C:ATP402 4.7 0.3 1.0
O3A C:ATP402 4.7 0.1 1.0
OE2 C:GLU163 5.0 0.2 1.0

Magnesium binding site 4 out of 14 in 5nwl

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Magnesium binding site 4 out of 14 in the Crystal Structure of A Human RAD51-Atp Filament.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Human RAD51-Atp Filament. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:72.6
occ:1.00
 O2G D:ATP402 1.9 0.9 1.0
OG1 D:THR134 2.1 72.7 1.0
O2B D:ATP402 2.2 93.4 1.0
OD1 D:ASP222 3.1 0.0 1.0
PB D:ATP402 3.2 88.0 1.0
OD2 D:ASP222 3.3 0.6 1.0
PG D:ATP402 3.3 0.5 1.0
CB D:THR134 3.4 83.1 1.0
CG D:ASP222 3.6 0.7 1.0
N D:THR134 3.6 77.4 1.0
O1B D:ATP402 3.7 79.5 1.0
O3B D:ATP402 3.7 90.7 1.0
CA D:THR134 3.9 81.5 1.0
O1G D:ATP402 4.0 0.6 1.0
CB D:LYS133 4.1 99.4 1.0
CE D:LYS133 4.2 0.8 1.0
NZ D:LYS133 4.4 0.3 1.0
C D:LYS133 4.4 89.1 1.0
CG2 D:THR134 4.4 83.1 1.0
O3G D:ATP402 4.5 0.3 1.0
O3A D:ATP402 4.6 0.6 1.0
OG1 D:THR165 4.7 89.6 1.0
CA D:LYS133 4.8 92.9 1.0
OG1 D:THR266 4.8 90.2 1.0
O2A D:ATP402 4.9 60.5 1.0
CG D:GLU163 5.0 0.5 1.0
O1A D:ATP402 5.0 0.6 1.0

Magnesium binding site 5 out of 14 in 5nwl

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Magnesium binding site 5 out of 14 in the Crystal Structure of A Human RAD51-Atp Filament.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of A Human RAD51-Atp Filament. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:64.0
occ:1.00
 O2B E:ATP402 2.0 87.3 1.0
OG1 E:THR134 2.1 70.4 1.0
O2G E:ATP402 2.2 0.2 1.0
CB E:THR134 3.2 95.4 1.0
PG E:ATP402 3.3 0.1 1.0
OG1 E:THR165 3.4 87.2 1.0
PB E:ATP402 3.4 95.9 1.0
O3G E:ATP402 3.5 0.9 1.0
OD2 E:ASP222 3.7 97.5 1.0
CG2 E:THR134 3.8 86.8 1.0
O3B E:ATP402 3.8 95.0 1.0
CG2 E:THR165 3.8 0.8 1.0
O2A E:ATP402 3.9 0.4 1.0
CB E:THR165 4.0 0.5 1.0
OD1 E:ASP222 4.3 0.1 1.0
O3A E:ATP402 4.4 0.7 1.0
CA E:THR134 4.4 0.1 1.0
PA E:ATP402 4.5 0.8 1.0
CG E:ASP222 4.5 0.6 1.0
CG E:GLU163 4.5 0.0 1.0
O1B E:ATP402 4.5 99.5 1.0
N E:THR134 4.6 95.9 1.0
O1G E:ATP402 4.6 0.8 1.0
CB E:GLU163 4.6 0.2 1.0
O1A E:ATP402 4.6 86.4 1.0

Magnesium binding site 6 out of 14 in 5nwl

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Magnesium binding site 6 out of 14 in the Crystal Structure of A Human RAD51-Atp Filament.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of A Human RAD51-Atp Filament. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:0.5
occ:1.00
 OG1 F:THR134 2.1 0.5 1.0
O1G F:ATP402 2.1 0.6 1.0
O2B F:ATP402 2.1 0.5 1.0
CB F:THR134 3.4 0.8 1.0
PG F:ATP402 3.4 0.4 1.0
OD2 F:ASP222 3.5 91.3 1.0
PB F:ATP402 3.5 0.4 1.0
OG1 F:THR165 3.6 95.2 1.0
O3G F:ATP402 3.9 0.9 1.0
OD1 F:ASP222 3.9 0.7 1.0
O3B F:ATP402 4.0 0.6 1.0
CG2 F:THR134 4.1 88.5 1.0
CG F:ASP222 4.1 0.5 1.0
CG2 F:THR165 4.2 0.7 1.0
CB F:THR165 4.3 1.0 1.0
O2A F:ATP402 4.4 0.8 1.0
CG F:GLU163 4.4 0.1 1.0
O1B F:ATP402 4.4 0.8 1.0
CA F:THR134 4.4 97.2 1.0
N F:THR134 4.5 0.4 1.0
O2G F:ATP402 4.6 0.2 1.0
O3A F:ATP402 4.6 0.2 1.0
CB F:GLU163 4.7 0.1 1.0
PA F:ATP402 4.9 0.3 1.0

Magnesium binding site 7 out of 14 in 5nwl

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Magnesium binding site 7 out of 14 in the Crystal Structure of A Human RAD51-Atp Filament.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of A Human RAD51-Atp Filament. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg401

b:0.7
occ:1.00
 OG1 G:THR134 2.1 0.4 1.0
O2B G:ATP402 2.1 0.3 1.0
O1G G:ATP402 2.1 1.0 1.0
CB G:THR134 3.4 0.4 1.0
OD2 G:ASP222 3.4 0.8 1.0
PG G:ATP402 3.4 0.8 1.0
OG1 G:THR165 3.5 1.0 1.0
PB G:ATP402 3.5 0.3 1.0
O3G G:ATP402 3.9 0.5 1.0
OD1 G:ASP222 3.9 0.8 1.0
O3B G:ATP402 4.0 0.7 1.0
CG2 G:THR134 4.0 0.6 1.0
CG G:ASP222 4.1 0.5 1.0
CG2 G:THR165 4.1 0.6 1.0
CB G:THR165 4.2 0.2 1.0
CG G:GLU163 4.3 0.1 1.0
O2A G:ATP402 4.3 0.6 1.0
O1B G:ATP402 4.4 0.0 1.0
CA G:THR134 4.5 0.4 1.0
CB G:GLU163 4.5 0.5 1.0
N G:THR134 4.5 0.6 1.0
O3A G:ATP402 4.6 0.2 1.0
O2G G:ATP402 4.6 0.8 1.0
PA G:ATP402 4.8 0.3 1.0
O1A G:ATP402 4.9 0.5 1.0
NE2 G:GLN268 5.0 0.1 1.0

Magnesium binding site 8 out of 14 in 5nwl

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Magnesium binding site 8 out of 14 in the Crystal Structure of A Human RAD51-Atp Filament.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of A Human RAD51-Atp Filament. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg401

b:0.4
occ:1.00
 O1B H:ATP402 2.0 0.2 1.0
OG1 H:THR134 2.1 0.9 1.0
O3G H:ATP402 2.2 0.8 1.0
CB H:THR134 3.2 0.6 1.0
PG H:ATP402 3.3 0.6 1.0
PB H:ATP402 3.4 0.2 1.0
O1G H:ATP402 3.5 0.3 1.0
OG1 H:THR165 3.7 0.4 1.0
O3B H:ATP402 3.8 0.6 1.0
O1A H:ATP402 3.9 0.8 1.0
CG2 H:THR134 3.9 0.6 1.0
CG2 H:THR165 4.0 0.5 1.0
OD2 H:ASP222 4.0 0.6 1.0
O3A H:ATP402 4.2 0.5 1.0
CB H:THR165 4.2 1.0 1.0
PA H:ATP402 4.4 0.8 1.0
CA H:THR134 4.4 0.2 1.0
N H:THR134 4.4 0.2 1.0
O2A H:ATP402 4.5 0.3 1.0
O2B H:ATP402 4.5 0.3 1.0
CG H:GLU163 4.6 0.1 1.0
O2G H:ATP402 4.7 0.5 1.0
OD1 H:ASP222 4.7 0.8 1.0
CB H:GLU163 4.8 1.0 1.0
CG H:ASP222 4.8 0.8 1.0

Magnesium binding site 9 out of 14 in 5nwl

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Magnesium binding site 9 out of 14 in the Crystal Structure of A Human RAD51-Atp Filament.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of A Human RAD51-Atp Filament. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg401

b:0.4
occ:1.00
 O3G I:ATP402 1.9 0.8 1.0
OG1 I:THR134 2.0 0.9 1.0
O2B I:ATP402 2.3 0.4 1.0
OD2 I:ASP222 2.9 0.1 1.0
OG1 I:THR165 3.1 0.6 1.0
CB I:THR134 3.3 0.6 1.0
PG I:ATP402 3.4 0.7 1.0
PB I:ATP402 3.6 0.1 1.0
OD1 I:ASP222 3.7 0.6 1.0
CG I:ASP222 3.7 0.4 1.0
CG2 I:THR134 3.9 1.0 1.0
O3B I:ATP402 4.0 0.1 1.0
CB I:THR165 4.0 0.7 1.0
O2G I:ATP402 4.1 0.8 1.0
CG I:GLU163 4.2 0.7 1.0
CG2 I:THR165 4.2 0.5 1.0
O1G I:ATP402 4.3 0.6 1.0
CA I:THR134 4.4 0.2 1.0
CB I:GLU163 4.5 0.9 1.0
O1B I:ATP402 4.5 0.8 1.0
O1A I:ATP402 4.6 0.8 1.0
N I:THR134 4.6 0.8 1.0
O3A I:ATP402 4.8 0.6 1.0

Magnesium binding site 10 out of 14 in 5nwl

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Magnesium binding site 10 out of 14 in the Crystal Structure of A Human RAD51-Atp Filament.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of A Human RAD51-Atp Filament. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg401

b:0.4
occ:1.00
 O2B J:ATP402 2.1 0.1 1.0
OG1 J:THR134 2.1 0.2 1.0
O2G J:ATP402 2.2 0.8 1.0
CB J:THR134 3.1 0.6 1.0
PG J:ATP402 3.2 0.1 1.0
O3G J:ATP402 3.3 0.1 1.0
PB J:ATP402 3.4 0.1 1.0
OG1 J:THR165 3.4 0.4 1.0
CG2 J:THR165 3.6 0.5 1.0
O2A J:ATP402 3.7 0.7 1.0
O3B J:ATP402 3.7 0.6 1.0
CB J:THR165 3.8 0.7 1.0
CG2 J:THR134 3.8 0.7 1.0
OD2 J:ASP222 3.9 0.5 1.0
O3A J:ATP402 4.2 0.3 1.0
PA J:ATP402 4.3 0.3 1.0
CA J:THR134 4.4 0.1 1.0
N J:THR134 4.4 0.9 1.0
O1A J:ATP402 4.5 0.6 1.0
O1G J:ATP402 4.5 0.0 1.0
O1B J:ATP402 4.6 0.9 1.0
OD1 J:ASP222 4.6 98.6 1.0
CG J:GLU163 4.7 0.4 1.0
CB J:GLU163 4.7 0.8 1.0
CG J:ASP222 4.7 0.4 1.0

Reference:

I.Brouwer, T.Moschetti, A.Candelli, E.B.Garcin, M.Modesti, L.Pellegrini, G.J.Wuite, E.J.Peterman. Two Distinct Conformational States Define the Interaction of Human RAD51-Atp with Single-Stranded Dna. Embo J. V. 37 2018.
ISSN: ESSN 1460-2075
PubMed: 29507080
DOI: 10.15252/EMBJ.201798162
Page generated: Sun Sep 29 23:40:00 2024

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