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Magnesium in PDB 5bq5: Crystal Structure of the Istb Aaa+ Domain Bound to Adp-BEF3

Protein crystallography data

The structure of Crystal Structure of the Istb Aaa+ Domain Bound to Adp-BEF3, PDB code: 5bq5 was solved by E.Arias-Palomo, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.80 / 2.10
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 133.806, 133.806, 70.950, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 20.3

Other elements in 5bq5:

The structure of Crystal Structure of the Istb Aaa+ Domain Bound to Adp-BEF3 also contains other interesting chemical elements:

Fluorine (F) 9 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Istb Aaa+ Domain Bound to Adp-BEF3 (pdb code 5bq5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Istb Aaa+ Domain Bound to Adp-BEF3, PDB code: 5bq5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5bq5

Go back to Magnesium Binding Sites List in 5bq5
Magnesium binding site 1 out of 3 in the Crystal Structure of the Istb Aaa+ Domain Bound to Adp-BEF3


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 the Istb Aaa+ Domain Bound to Adp-BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:23.3
occ:1.00
F3 A:BEF303 1.8 22.7 1.0
O1B A:ADP301 2.0 16.1 1.0
O A:HOH416 2.1 21.3 1.0
O A:HOH457 2.1 16.3 1.0
O A:HOH499 2.1 19.5 1.0
OG1 A:THR112 2.1 17.8 1.0
BE A:BEF303 3.0 22.0 1.0
PB A:ADP301 3.1 19.3 1.0
HB A:THR112 3.2 20.7 1.0
O2B A:ADP301 3.2 20.3 1.0
CB A:THR112 3.2 17.3 1.0
H A:THR112 3.5 21.3 1.0
HG3 A:GLU167 3.7 36.8 1.0
F1 A:BEF303 3.8 22.7 1.0
HH22 A:ARG237 3.8 25.2 1.0
OD1 A:ASP166 4.0 24.7 1.0
HG21 A:THR112 4.0 20.1 1.0
O3A A:ADP301 4.0 23.8 1.0
OD2 A:ASP166 4.1 23.3 1.0
N A:THR112 4.1 17.8 1.0
HB2 A:LYS111 4.1 22.2 1.0
O1A A:ADP301 4.1 19.8 1.0
O A:HOH575 4.2 49.1 1.0
F2 A:BEF303 4.2 23.8 1.0
CG2 A:THR112 4.2 16.8 1.0
CA A:THR112 4.2 17.1 1.0
HE2 A:LYS111 4.2 26.5 1.0
O3B A:ADP301 4.2 20.0 1.0
O A:HOH562 4.3 32.9 1.0
HZ3 A:LYS111 4.4 26.9 1.0
OE2 A:GLU167 4.4 32.0 1.0
OG1 A:THR197 4.4 23.6 1.0
CG A:ASP166 4.5 23.4 1.0
HA A:THR112 4.5 20.5 1.0
PA A:ADP301 4.6 20.8 1.0
HG23 A:THR112 4.6 20.1 1.0
HE2 A:TYR170 4.6 60.4 1.0
NH2 A:ARG237 4.6 21.0 1.0
CG A:GLU167 4.6 30.6 1.0
HZ2 A:LYS111 4.6 26.9 1.0
HH21 A:ARG237 4.8 25.2 1.0
HB A:THR197 4.8 27.1 1.0
HA A:GLU167 4.8 30.8 1.0
O2A A:ADP301 4.8 21.8 1.0
NZ A:LYS111 4.9 22.4 1.0
H A:GLU167 4.9 27.9 1.0

Magnesium binding site 2 out of 3 in 5bq5

Go back to Magnesium Binding Sites List in 5bq5
Magnesium binding site 2 out of 3 in the Crystal Structure of the Istb Aaa+ Domain Bound to Adp-BEF3


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 the Istb Aaa+ Domain Bound to Adp-BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:28.0
occ:1.00
F3 B:BEF303 1.8 32.0 1.0
O B:HOH436 2.1 21.7 1.0
O B:HOH465 2.1 25.4 1.0
OG1 B:THR112 2.1 23.7 1.0
O2B B:ADP301 2.1 23.9 1.0
O B:HOH426 2.1 32.2 1.0
BE B:BEF303 3.0 29.3 1.0
HB B:THR112 3.2 29.0 1.0
PB B:ADP301 3.2 25.0 1.0
CB B:THR112 3.2 24.1 1.0
O3B B:ADP301 3.3 27.4 1.0
H B:THR112 3.5 28.4 1.0
HG3 B:GLU167 3.5 48.0 1.0
HG1 B:THR197 3.7 33.2 1.0
F1 B:BEF303 3.7 29.7 1.0
HH22 B:ARG237 3.9 33.0 1.0
OD1 B:ASP166 4.0 28.8 1.0
OD2 B:ASP166 4.0 30.0 1.0
HB2 B:LYS111 4.0 28.4 1.0
N B:THR112 4.1 23.7 1.0
HG21 B:THR112 4.1 29.1 1.0
O2A B:ADP301 4.1 25.0 1.0
HE2 B:LYS111 4.1 31.9 1.0
O3A B:ADP301 4.1 26.2 1.0
F2 B:BEF303 4.2 31.8 1.0
CA B:THR112 4.2 23.9 1.0
CG2 B:THR112 4.2 24.2 1.0
O1B B:ADP301 4.3 25.4 1.0
CG B:ASP166 4.4 29.1 1.0
OG1 B:THR197 4.4 27.7 1.0
O B:HOH525 4.4 37.8 1.0
CG B:GLU167 4.4 40.0 1.0
HZ3 B:LYS111 4.5 31.1 1.0
HA B:THR112 4.5 28.8 1.0
OE2 B:GLU167 4.5 40.8 1.0
O B:HOH520 4.6 49.8 1.0
HG23 B:THR112 4.6 29.1 1.0
PA B:ADP301 4.6 26.3 1.0
NH2 B:ARG237 4.6 27.5 1.0
HE2 B:TYR170 4.6 72.5 1.0
HZ2 B:LYS111 4.7 31.1 1.0
HG2 B:GLU167 4.7 48.0 1.0
HB B:THR197 4.7 32.0 1.0
HH21 B:ARG237 4.7 33.0 1.0
H B:GLU167 4.8 38.8 1.0
O1A B:ADP301 4.9 26.3 1.0
NZ B:LYS111 4.9 25.9 1.0
HA B:GLU167 4.9 43.7 1.0
CE B:LYS111 4.9 26.6 1.0
CB B:LYS111 5.0 23.7 1.0
HG21 B:THR197 5.0 30.4 1.0

Magnesium binding site 3 out of 3 in 5bq5

Go back to Magnesium Binding Sites List in 5bq5
Magnesium binding site 3 out of 3 in the Crystal Structure of the Istb Aaa+ Domain Bound to Adp-BEF3


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 the Istb Aaa+ Domain Bound to Adp-BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:33.2
occ:1.00
F3 C:BEF303 1.8 34.7 1.0
O3B C:ADP301 2.0 29.9 1.0
O C:HOH430 2.1 26.6 1.0
O C:HOH497 2.1 23.7 1.0
O C:HOH437 2.1 30.3 1.0
OG1 C:THR112 2.1 26.7 1.0
BE C:BEF303 2.9 34.0 1.0
PB C:ADP301 3.1 30.9 1.0
HB C:THR112 3.1 31.9 1.0
CB C:THR112 3.2 26.6 1.0
O2B C:ADP301 3.2 32.2 1.0
H C:THR112 3.5 33.5 1.0
HG3 C:GLU167 3.6 48.9 1.0
F1 C:BEF303 3.7 35.3 1.0
HG1 C:THR197 3.7 35.0 1.0
HH22 B:ARG221 3.8 56.0 1.0
HH22 C:ARG237 3.9 36.4 1.0
OD1 C:ASP166 4.0 34.2 1.0
HB2 C:LYS111 4.0 33.6 1.0
O3A C:ADP301 4.0 32.4 1.0
N C:THR112 4.0 27.9 1.0
HG21 C:THR112 4.1 30.1 1.0
OD2 C:ASP166 4.1 36.3 1.0
O2A C:ADP301 4.1 29.7 1.0
O C:HOH533 4.1 46.5 1.0
HE2 C:LYS111 4.1 38.4 1.0
F2 C:BEF303 4.1 33.9 1.0
CA C:THR112 4.2 27.4 1.0
CG2 C:THR112 4.2 25.1 1.0
HH21 B:ARG221 4.2 56.0 1.0
O1B C:ADP301 4.2 31.5 1.0
NH2 B:ARG221 4.3 46.7 1.0
HE1 C:TYR170 4.3 87.3 1.0
HZ3 C:LYS111 4.4 40.3 1.0
OG1 C:THR197 4.4 29.2 1.0
CG C:ASP166 4.4 35.7 1.0
CG C:GLU167 4.5 40.7 1.0
HA C:THR112 4.5 32.9 1.0
PA C:ADP301 4.5 30.5 1.0
HG23 C:THR112 4.6 30.1 1.0
O C:HOH540 4.6 44.4 1.0
HZ2 C:LYS111 4.6 40.3 1.0
HG2 C:GLU167 4.6 48.9 1.0
OE2 C:GLU167 4.6 44.5 1.0
HB C:THR197 4.6 32.9 1.0
NH2 C:ARG237 4.7 30.3 1.0
O1A C:ADP301 4.8 31.0 1.0
NZ C:LYS111 4.8 33.6 1.0
HH C:TYR170 4.8 0.7 1.0
HH21 C:ARG237 4.8 36.4 1.0
HG21 C:THR197 4.9 30.4 1.0
H C:GLU167 4.9 39.4 1.0
CE C:LYS111 4.9 32.0 1.0
CB C:LYS111 4.9 28.0 1.0
HA C:GLU167 5.0 42.5 1.0
HG22 C:THR112 5.0 30.1 1.0

Reference:

E.Arias-Palomo, J.M.Berger. An Atypical Aaa+ Atpase Assembly Controls Efficient Transposition Through Dna Remodeling and Transposase Recruitment. Cell V. 162 860 2015.
ISSN: ISSN 1097-4172
PubMed: 26276634
DOI: 10.1016/J.CELL.2015.07.037
Page generated: Sun Sep 29 01:14:28 2024

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