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Magnesium in PDB 3jbx: Cryo-Electron Microscopy Structure of Rag Signal End Complex (C2 Symmetry)

Other elements in 3jbx:

The structure of Cryo-Electron Microscopy Structure of Rag Signal End Complex (C2 Symmetry) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Electron Microscopy Structure of Rag Signal End Complex (C2 Symmetry) (pdb code 3jbx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryo-Electron Microscopy Structure of Rag Signal End Complex (C2 Symmetry), PDB code: 3jbx:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3jbx

Go back to Magnesium Binding Sites List in 3jbx
Magnesium binding site 1 out of 4 in the Cryo-Electron Microscopy Structure of Rag Signal End Complex (C2 Symmetry)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Electron Microscopy Structure of Rag Signal End Complex (C2 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:30.0
occ:1.00
OD1 A:ASP620 2.3 29.4 1.0
OE2 A:GLU984 2.4 22.4 1.0
O3' G:DG15 2.5 21.6 1.0
O3' J:DC14 2.6 52.1 1.0
CG A:ASP620 3.3 29.3 1.0
O A:GLY621 3.4 50.5 1.0
CD A:GLU984 3.5 22.3 1.0
OD2 A:ASP620 3.6 38.0 1.0
MG A:MG1103 3.8 30.0 1.0
C3' G:DG15 3.9 66.4 1.0
C3' J:DC14 3.9 46.8 1.0
OE1 A:GLU984 3.9 22.5 1.0
OD2 A:ASP730 3.9 25.6 1.0
CG A:ASP730 4.1 60.3 1.0
C2' J:DC14 4.3 52.9 1.0
NE2 A:HIS817 4.3 34.6 1.0
OD1 A:ASP730 4.4 89.8 1.0
C2' G:DG15 4.5 58.6 1.0
C4' G:DG15 4.5 51.8 1.0
C A:GLY621 4.6 44.0 1.0
CB A:ASP730 4.7 45.6 1.0
CB A:ASP620 4.7 29.9 1.0
N A:GLY621 4.7 51.9 1.0
CG A:GLU984 4.7 31.2 1.0
CE1 A:HIS817 4.7 23.5 1.0

Magnesium binding site 2 out of 4 in 3jbx

Go back to Magnesium Binding Sites List in 3jbx
Magnesium binding site 2 out of 4 in the Cryo-Electron Microscopy Structure of Rag Signal End Complex (C2 Symmetry)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Electron Microscopy Structure of Rag Signal End Complex (C2 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:30.0
occ:1.00
OE2 A:GLU684 3.2 71.7 1.0
O3' J:DC14 3.4 52.1 1.0
OD2 A:ASP730 3.7 25.6 1.0
O A:GLY621 3.7 50.5 1.0
C2' J:DC14 3.8 52.9 1.0
MG A:MG1102 3.8 30.0 1.0
CD A:GLU684 4.0 66.9 1.0
C3' J:DC14 4.0 46.8 1.0
C A:GLY621 4.1 44.0 1.0
CA A:GLY621 4.1 56.6 1.0
C4' J:DC14 4.3 46.2 1.0
N A:GLY621 4.4 51.9 1.0
CG A:GLU684 4.5 68.6 1.0
C1' J:DC14 4.5 43.0 1.0
CE A:MET733 4.7 65.6 1.0
OE1 A:GLU684 4.8 58.6 1.0
CG A:ASP730 4.8 60.3 1.0
OD1 A:ASP620 4.9 29.4 1.0
O4' J:DC14 4.9 41.0 1.0

Magnesium binding site 3 out of 4 in 3jbx

Go back to Magnesium Binding Sites List in 3jbx
Magnesium binding site 3 out of 4 in the Cryo-Electron Microscopy Structure of Rag Signal End Complex (C2 Symmetry)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Electron Microscopy Structure of Rag Signal End Complex (C2 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1102

b:30.0
occ:1.00
O3' F:DG15 2.2 21.3 1.0
OD1 C:ASP620 2.4 47.5 1.0
OE2 C:GLU984 2.7 24.7 1.0
OD2 C:ASP620 3.0 43.8 1.0
CG C:ASP620 3.1 39.7 1.0
O3' L:DC14 3.1 49.2 1.0
O C:GLY621 3.5 50.1 1.0
OD2 C:ASP730 3.6 63.5 1.0
CD C:GLU984 3.6 24.4 1.0
C3' F:DG15 3.6 49.3 1.0
MG C:MG1103 3.8 30.0 1.0
OE1 C:GLU984 3.8 24.6 1.0
C3' L:DC14 4.0 53.8 1.0
NE2 C:HIS817 4.2 26.2 1.0
CG C:ASP730 4.2 68.5 1.0
C2' F:DG15 4.3 44.7 1.0
C4' F:DG15 4.4 43.1 1.0
C2' L:DC14 4.4 57.2 1.0
CB C:ASP620 4.5 35.1 1.0
C C:GLY621 4.7 46.0 1.0
CE1 C:HIS817 4.7 26.6 1.0
N C:GLY621 4.8 49.8 1.0
CB C:ASP730 4.8 33.3 1.0
OD1 C:ASP730 4.9 76.4 1.0
CG C:GLU984 4.9 24.5 1.0

Magnesium binding site 4 out of 4 in 3jbx

Go back to Magnesium Binding Sites List in 3jbx
Magnesium binding site 4 out of 4 in the Cryo-Electron Microscopy Structure of Rag Signal End Complex (C2 Symmetry)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Electron Microscopy Structure of Rag Signal End Complex (C2 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1103

b:30.0
occ:1.00
O3' L:DC14 2.6 49.2 1.0
OE2 C:GLU684 3.3 75.3 1.0
O C:GLY621 3.6 50.1 1.0
OD2 C:ASP730 3.7 63.5 1.0
MG C:MG1102 3.8 30.0 1.0
C3' L:DC14 4.0 53.8 1.0
CD C:GLU684 4.0 65.4 1.0
C C:GLY621 4.1 46.0 1.0
CA C:GLY621 4.3 54.1 1.0
C4' L:DC14 4.5 60.8 1.0
N C:GLY621 4.5 49.8 1.0
OD1 C:ASP620 4.5 47.5 1.0
C2' L:DC14 4.6 57.2 1.0
CG C:GLU684 4.6 66.3 1.0
C1' L:DC14 4.6 50.5 1.0
OE1 C:GLU684 4.7 53.8 1.0
CE C:MET733 4.8 99.1 1.0
O4' L:DC14 4.9 50.7 1.0
CG C:ASP730 4.9 68.5 1.0

Reference:

H.Ru, M.G.Chambers, T.M.Fu, A.B.Tong, M.Liao, H.Wu. Molecular Mechanism of V(D)J Recombination From Synaptic RAG1-RAG2 Complex Structures. Cell(Cambridge,Mass.) V. 163 1138 2015.
ISSN: ISSN 0092-8674
PubMed: 26548953
DOI: 10.1016/J.CELL.2015.10.055
Page generated: Mon Dec 14 08:20:01 2020

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