Atomistry » Magnesium » PDB 9b2d-9bm0 » 9b2d
Atomistry »
  Magnesium »
    PDB 9b2d-9bm0 »
      9b2d »

Magnesium in PDB 9b2d: Yeast RAD51-Ssdna Filament

Other elements in 9b2d:

The structure of Yeast RAD51-Ssdna Filament also contains other interesting chemical elements:

Aluminium (Al) 6 atoms
Fluorine (F) 18 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast RAD51-Ssdna Filament (pdb code 9b2d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Yeast RAD51-Ssdna Filament, PDB code: 9b2d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 9b2d

Go back to Magnesium Binding Sites List in 9b2d
Magnesium binding site 1 out of 6 in the Yeast RAD51-Ssdna Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast RAD51-Ssdna Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:6.9
occ:1.00
O1B C:ADP501 2.1 20.7 1.0
PB C:ADP501 3.5 0.0 1.0
O2B C:ADP501 3.9 6.0 1.0
F3 C:AF3502 3.9 13.8 1.0
CD2 D:HIS352 3.9 9.9 1.0
F2 C:AF3502 4.0 17.7 1.0
AL C:AF3502 4.2 21.0 1.0
NZ C:LYS191 4.2 1.4 1.0
N C:ARG188 4.4 2.2 1.0
O3B C:ADP501 4.4 0.0 1.0
CA C:PHE187 4.4 10.4 1.0
O3A C:ADP501 4.5 11.7 1.0
NE2 D:HIS352 4.6 0.0 1.0
F1 C:AF3502 4.7 18.0 1.0
CB C:PHE187 4.7 2.2 1.0
OE1 C:GLU221 4.7 14.5 1.0
CE C:LYS191 4.8 10.7 1.0
C C:PHE187 5.0 7.4 1.0

Magnesium binding site 2 out of 6 in 9b2d

Go back to Magnesium Binding Sites List in 9b2d
Magnesium binding site 2 out of 6 in the Yeast RAD51-Ssdna Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast RAD51-Ssdna Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:11.0
occ:1.00
O3B D:ADP501 2.0 24.8 1.0
PB D:ADP501 3.4 4.7 1.0
O2B D:ADP501 3.9 9.5 1.0
F1 D:AF3502 4.0 23.1 1.0
F2 D:AF3502 4.0 25.2 1.0
CD2 E:HIS352 4.0 3.8 1.0
AL D:AF3502 4.2 35.5 1.0
N D:ARG188 4.2 6.8 1.0
NZ D:LYS191 4.3 6.2 1.0
O3A D:ADP501 4.3 8.0 1.0
O1B D:ADP501 4.4 6.4 1.0
CA D:PHE187 4.4 10.6 1.0
F3 D:AF3502 4.6 29.8 1.0
CB D:PHE187 4.7 0.0 1.0
NE2 E:HIS352 4.7 0.0 1.0
OE1 D:GLU221 4.8 28.0 1.0
C D:PHE187 4.9 7.7 1.0
CE D:LYS191 5.0 12.3 1.0

Magnesium binding site 3 out of 6 in 9b2d

Go back to Magnesium Binding Sites List in 9b2d
Magnesium binding site 3 out of 6 in the Yeast RAD51-Ssdna Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Yeast RAD51-Ssdna Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg503

b:1.8
occ:1.00
O1B E:ADP501 2.0 26.5 1.0
PB E:ADP501 3.4 0.0 1.0
O2B E:ADP501 3.8 10.1 1.0
CD2 F:HIS352 3.9 4.2 1.0
F1 E:AF3502 4.0 20.2 1.0
F2 E:AF3502 4.0 20.8 1.0
AL E:AF3502 4.2 26.8 1.0
NZ E:LYS191 4.3 1.9 1.0
O3B E:ADP501 4.3 3.4 1.0
N E:ARG188 4.4 1.4 1.0
O3A E:ADP501 4.4 10.3 1.0
CA E:PHE187 4.4 10.7 1.0
NE2 F:HIS352 4.6 0.0 1.0
CB E:PHE187 4.7 0.0 1.0
F3 E:AF3502 4.7 20.4 1.0
OE1 E:GLU221 4.8 28.1 1.0
CE E:LYS191 5.0 14.7 1.0
C E:PHE187 5.0 3.8 1.0

Magnesium binding site 4 out of 6 in 9b2d

Go back to Magnesium Binding Sites List in 9b2d
Magnesium binding site 4 out of 6 in the Yeast RAD51-Ssdna Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Yeast RAD51-Ssdna Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg503

b:16.4
occ:1.00
O3B F:ADP501 2.1 31.0 1.0
PB F:ADP501 3.5 8.8 1.0
AL F:AF3502 3.7 29.8 1.0
F1 F:AF3502 3.9 24.5 1.0
O2B F:ADP501 4.0 15.3 1.0
F2 F:AF3502 4.0 37.0 1.0
NZ F:LYS191 4.4 10.1 1.0
N F:ARG188 4.4 17.1 1.0
O1B F:ADP501 4.4 16.2 1.0
CA F:PHE187 4.4 18.1 1.0
F3 F:AF3502 4.4 28.5 1.0
O3A F:ADP501 4.5 17.1 1.0
OE1 F:GLU221 4.5 27.3 1.0
CB F:PHE187 4.7 11.7 1.0
CE F:LYS191 5.0 17.0 1.0

Magnesium binding site 5 out of 6 in 9b2d

Go back to Magnesium Binding Sites List in 9b2d
Magnesium binding site 5 out of 6 in the Yeast RAD51-Ssdna Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Yeast RAD51-Ssdna Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:15.3
occ:1.00
O1B A:ADP501 2.3 34.2 1.0
PB A:ADP501 3.6 0.0 1.0
AL A:AF3502 3.8 31.9 1.0
F1 A:AF3502 3.8 16.3 1.0
CD2 B:HIS352 3.9 11.4 1.0
F2 A:AF3502 3.9 21.6 1.0
O2B A:ADP501 3.9 16.1 1.0
F3 A:AF3502 4.5 19.4 1.0
NZ A:LYS191 4.5 1.2 1.0
O3B A:ADP501 4.5 9.5 1.0
CA A:PHE187 4.5 10.1 1.0
N A:ARG188 4.5 9.2 1.0
NE2 B:HIS352 4.6 12.2 1.0
OE1 A:GLU221 4.6 20.9 1.0
O3A A:ADP501 4.6 24.0 1.0
CB A:PHE187 4.8 3.4 1.0
O B:HIS352 4.9 17.8 1.0
CG B:HIS352 5.0 18.9 1.0

Magnesium binding site 6 out of 6 in 9b2d

Go back to Magnesium Binding Sites List in 9b2d
Magnesium binding site 6 out of 6 in the Yeast RAD51-Ssdna Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Yeast RAD51-Ssdna Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:3.7
occ:1.00
O1B B:ADP501 2.0 25.7 1.0
PB B:ADP501 3.3 0.0 1.0
O2B B:ADP501 3.8 16.4 1.0
CD2 C:HIS352 4.0 4.1 1.0
F2 B:AF3502 4.0 33.3 1.0
F1 B:AF3502 4.0 26.6 1.0
O3B B:ADP501 4.2 8.2 1.0
AL B:AF3502 4.2 44.7 1.0
N B:ARG188 4.3 4.5 1.0
NZ B:LYS191 4.3 2.1 1.0
CA B:PHE187 4.3 12.0 1.0
O3A B:ADP501 4.4 15.7 1.0
CB B:PHE187 4.6 5.7 1.0
NE2 C:HIS352 4.7 0.9 1.0
OE1 B:GLU221 4.8 30.4 1.0
F3 B:AF3502 4.8 27.7 1.0
C B:PHE187 4.9 2.9 1.0
CE B:LYS191 4.9 9.7 1.0

Reference:

J.Liu, S.Gore, W.-D.Heyer. Yeast RAD51-Ssdna Filament To Be Published.
Page generated: Fri Aug 15 23:13:52 2025

Last articles

Mn in 2QF2
Mn in 2QGI
Mn in 2QEY
Mn in 2QF1
Mn in 2QCS
Mn in 2PYO
Mn in 2QEW
Mn in 2QB0
Mn in 2QB5
Mn in 2QB6
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy