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Magnesium in PDB 7nbb: Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3

Protein crystallography data

The structure of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3, PDB code: 7nbb was solved by S.M.Lange, Y.Kulathu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.95 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.389, 97.615, 74.967, 90, 109.96, 90
R / Rfree (%) 17.5 / 21.2

Other elements in 7nbb:

The structure of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Chlorine (Cl) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 (pdb code 7nbb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3, PDB code: 7nbb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 7nbb

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Magnesium binding site 1 out of 7 in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:25.8
occ:1.00
 O A:HOH234 2.0 20.8 1.0
O B:HOH371 2.1 25.4 1.0
O A:HOH274 2.2 26.5 1.0
O B:HOH305 2.2 25.7 1.0
O B:HOH314 4.0 18.8 1.0
O B:HOH337 4.0 30.7 1.0
OE2 B:GLU34 4.2 31.8 1.0
OE1 B:GLU34 4.2 25.8 1.0
O A:GLY53 4.3 19.9 1.0
O B:HOH374 4.3 19.9 1.0
CA A:GLY53 4.4 19.3 1.0
O A:HOH271 4.5 42.3 1.0
O A:HOH262 4.5 30.8 1.0
CD B:GLU34 4.7 33.7 1.0
O A:HOH250 4.8 25.1 1.0
C A:GLY53 4.8 18.0 1.0

Magnesium binding site 2 out of 7 in 7nbb

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Magnesium binding site 2 out of 7 in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:25.0
occ:0.43
 O A:HOH223 1.9 30.3 1.0
OD1 A:ASP32 2.0 30.9 1.0
O A:HOH277 2.0 39.7 1.0
O A:HOH220 2.2 26.0 1.0
O A:HOH247 2.3 36.3 1.0
CG A:ASP32 3.1 27.3 1.0
OD2 A:ASP32 3.6 30.8 1.0
OE1 A:GLN31 4.1 23.7 1.0
O A:HOH270 4.1 37.1 1.0
O A:HOH287 4.2 43.0 1.0
CB A:ASP32 4.4 21.2 1.0
O A:ALA28 4.4 16.6 1.0
O A:HOH242 4.5 22.6 1.0
CA A:ASP32 4.6 19.5 1.0
CD A:GLN31 4.6 24.3 1.0
N A:ASP32 4.6 17.1 1.0
O A:HOH286 4.8 40.3 1.0
CG A:GLN31 4.8 18.3 1.0

Magnesium binding site 3 out of 7 in 7nbb

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Magnesium binding site 3 out of 7 in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg103

b:22.9
occ:1.00
 O3 B:GOL201 2.7 18.9 1.0
ND1 C:HIS68 2.8 18.1 1.0
ND1 B:HIS68 2.8 17.9 1.0
O1 B:GOL201 2.8 18.8 1.0
C1 B:GOL201 3.1 20.6 1.0
C3 B:GOL201 3.3 21.7 1.0
CG2 C:ILE44 3.5 17.6 1.0
CG B:HIS68 3.6 15.6 1.0
CG2 B:ILE44 3.6 18.9 1.0
CB B:HIS68 3.6 17.3 1.0
CG C:HIS68 3.6 20.4 1.0
CB C:HIS68 3.7 19.4 1.0
CE1 C:HIS68 3.8 17.4 1.0
CE1 B:HIS68 3.8 19.0 1.0
C2 B:GOL201 3.9 25.0 1.0
CB C:ILE44 3.9 16.9 1.0
CB B:ILE44 4.2 14.9 1.0
CD1 C:ILE44 4.5 19.7 1.0
O C:ILE44 4.6 20.2 1.0
CD2 B:HIS68 4.8 14.6 1.0
CD2 C:HIS68 4.8 16.6 1.0
C C:ILE44 4.9 20.4 1.0
CG1 C:ILE44 4.9 17.2 1.0
O2 B:GOL201 4.9 30.7 1.0
NE2 B:HIS68 4.9 15.6 1.0
O B:ILE44 4.9 19.2 1.0
NE2 C:HIS68 4.9 16.4 1.0
CD1 B:ILE44 4.9 17.9 1.0

Magnesium binding site 4 out of 7 in 7nbb

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Magnesium binding site 4 out of 7 in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:50.3
occ:1.00
 O D:HOH424 2.2 44.0 1.0
O E:HOH271 2.4 36.2 1.0
O H:HOH395 2.6 42.8 1.0
O E:HOH211 2.6 42.4 1.0
OE2 D:GLU88 3.7 41.5 1.0
OE1 E:GLU18 3.9 41.9 1.0
O H:ASP102 4.0 29.7 1.0
O E:HOH243 4.0 22.4 1.0
O H:HOH386 4.3 19.2 1.0
CD D:GLU88 4.7 33.4 1.0
CD E:GLU18 4.7 32.7 1.0
O D:HOH451 4.9 27.4 1.0

Magnesium binding site 5 out of 7 in 7nbb

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Magnesium binding site 5 out of 7 in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg101

b:28.1
occ:1.00
 O F:HOH373 2.1 25.9 1.0
O E:HOH232 2.1 25.1 1.0
O F:HOH309 2.1 25.3 1.0
O E:HOH279 2.2 26.8 1.0
O F:HOH372 2.3 24.0 1.0
O F:HOH323 4.0 20.2 1.0
O F:HOH347 4.0 28.4 1.0
OE2 F:GLU34 4.1 31.2 1.0
O E:GLY53 4.3 18.9 1.0
OE1 F:GLU34 4.3 27.9 1.0
O F:HOH377 4.3 26.3 1.0
CA E:GLY53 4.4 19.0 1.0
O E:HOH275 4.6 32.1 1.0
CD F:GLU34 4.6 35.3 1.0
O E:HOH252 4.7 24.3 1.0
C E:GLY53 4.9 19.5 1.0
O E:HOH222 5.0 18.9 1.0

Magnesium binding site 6 out of 7 in 7nbb

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Magnesium binding site 6 out of 7 in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg203

b:18.2
occ:1.00
 O1 F:GOL201 2.8 9.2 0.8
O3 F:GOL201 2.8 10.8 0.8
ND1 F:HIS68 2.8 13.0 1.0
ND1 G:HIS68 2.9 11.5 1.0
C1 F:GOL201 3.3 13.8 0.8
C3 F:GOL201 3.3 13.8 0.8
CG2 F:ILE44 3.4 12.4 1.0
CG2 G:ILE44 3.5 17.1 1.0
CB F:HIS68 3.6 13.2 1.0
CG F:HIS68 3.6 11.4 1.0
CG G:HIS68 3.7 11.2 1.0
CB G:HIS68 3.7 13.0 1.0
CE1 F:HIS68 3.9 14.7 1.0
CE1 G:HIS68 3.9 15.7 1.0
CB G:ILE44 4.0 10.4 1.0
C2 F:GOL201 4.0 14.2 0.8
CB F:ILE44 4.2 14.0 1.0
O G:ILE44 4.6 10.4 1.0
CD1 G:ILE44 4.7 16.2 1.0
C G:ILE44 4.8 10.8 1.0
O F:ILE44 4.8 13.3 1.0
CD2 F:HIS68 4.8 10.5 1.0
CD1 F:ILE44 4.8 12.6 1.0
CD2 G:HIS68 4.9 11.6 1.0
NE2 F:HIS68 4.9 11.5 1.0
CG1 G:ILE44 4.9 13.6 1.0
NE2 G:HIS68 4.9 13.7 1.0
C F:ILE44 5.0 14.3 1.0

Magnesium binding site 7 out of 7 in 7nbb

Go back to Magnesium Binding Sites List in 7nbb
Magnesium binding site 7 out of 7 in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg202

b:49.2
occ:1.00
 O D:HOH421 2.2 41.5 1.0
O H:HOH407 2.3 47.6 1.0
O H:HOH310 2.3 41.6 1.0
O D:HOH307 2.4 35.6 1.0
O A:HOH261 2.4 38.3 1.0
OE2 H:GLU88 3.9 35.5 1.0
OE1 A:GLU18 4.1 35.8 1.0
O A:HOH241 4.3 26.8 1.0
O D:ASP102 4.4 30.6 0.5
O D:ASP102 4.4 30.6 0.5
O H:HOH399 4.5 38.9 1.0
O D:HOH406 4.6 20.7 1.0
CD H:GLU88 4.7 36.6 1.0
CD A:GLU18 4.7 32.8 1.0
OE1 H:GLU88 4.9 33.0 1.0

Reference:

S.M.Lange, Y.Kulathu. Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 To Be Published.
Page generated: Thu Oct 3 01:23:05 2024

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