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Magnesium in PDB 7qnq: Structure of the AUX2 Relaxosome Protein of Plasmid PLS20

Protein crystallography data

The structure of Structure of the AUX2 Relaxosome Protein of Plasmid PLS20, PDB code: 7qnq was solved by D.R.Boer, I.Crespo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.65 / 1.89
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 137.854, 137.854, 121.709, 90, 90, 90
R / Rfree (%) 18 / 20.1

Other elements in 7qnq:

The structure of Structure of the AUX2 Relaxosome Protein of Plasmid PLS20 also contains other interesting chemical elements:

Chlorine (Cl) 24 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the AUX2 Relaxosome Protein of Plasmid PLS20 (pdb code 7qnq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Structure of the AUX2 Relaxosome Protein of Plasmid PLS20, PDB code: 7qnq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 7qnq

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Magnesium binding site 1 out of 10 in the Structure of the AUX2 Relaxosome Protein of Plasmid PLS20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the AUX2 Relaxosome Protein of Plasmid PLS20 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:49.2
occ:1.00
 O A:HOH332 2.0 50.0 1.0
O H:HOH330 2.4 41.5 1.0
OD1 A:ASN99 2.4 28.1 1.0
O A:HOH329 2.5 32.4 1.0
O H:HOH344 2.5 30.9 1.0
OD1 G:ASN99 2.6 26.5 1.0
CG G:ASN99 3.4 31.9 1.0
CG A:ASN99 3.4 29.3 1.0
ND2 G:ASN99 3.5 26.1 1.0
CB A:ASN99 3.7 24.0 1.0
O G:HOH342 3.8 49.5 1.0
O H:HOH345 3.9 40.6 1.0
O G:HOH325 3.9 48.9 1.0
O A:HOH322 4.0 38.7 1.0
CA A:ASN99 4.1 23.1 1.0
MG G:MG205 4.1 48.0 1.0
O A:ALA98 4.4 23.1 1.0
O H:PRO100 4.6 27.7 1.0
ND2 A:ASN99 4.6 24.9 1.0
MG H:MG203 4.7 50.7 1.0
O H:ASN99 4.8 25.7 1.0
O G:HOH314 4.8 30.6 1.0
CB H:ASN99 4.8 28.4 1.0
CB G:ASN99 4.8 26.2 1.0
O A:HOH362 4.9 46.3 1.0

Magnesium binding site 2 out of 10 in 7qnq

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Magnesium binding site 2 out of 10 in the Structure of the AUX2 Relaxosome Protein of Plasmid PLS20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the AUX2 Relaxosome Protein of Plasmid PLS20 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:35.9
occ:1.00
 O B:HOH338 2.4 38.2 1.0
OD1 D:ASN88 2.5 27.6 1.0
OD1 B:ASN88 2.5 28.5 1.0
OD1 A:ASN88 2.5 29.0 1.0
OD1 C:ASN88 2.7 28.3 1.0
O B:HOH342 2.8 29.0 1.0
CG B:ASN88 3.2 33.9 1.0
CG D:ASN88 3.3 30.3 1.0
CG A:ASN88 3.3 27.1 1.0
CG C:ASN88 3.4 26.4 1.0
ND2 B:ASN88 3.4 28.2 1.0
ND2 A:ASN88 3.5 25.8 1.0
ND2 D:ASN88 3.5 28.4 1.0
ND2 C:ASN88 3.5 27.4 1.0
NE1 A:TRP92 4.0 30.9 1.0
NE1 C:TRP92 4.0 30.0 1.0
NE1 B:TRP92 4.1 27.6 1.0
NE1 D:TRP92 4.1 24.8 1.0
CB B:ASN88 4.6 25.7 1.0
CB D:ASN88 4.6 25.5 1.0
CB A:ASN88 4.7 27.2 1.0
CD1 A:TRP92 4.7 26.3 1.0
CB C:ASN88 4.7 27.1 1.0
CD1 C:TRP92 4.8 27.0 1.0
CD1 B:TRP92 4.8 28.5 1.0
CD1 D:TRP92 4.8 29.3 1.0
CE2 A:TRP92 5.0 30.8 1.0

Magnesium binding site 3 out of 10 in 7qnq

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Magnesium binding site 3 out of 10 in the Structure of the AUX2 Relaxosome Protein of Plasmid PLS20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the AUX2 Relaxosome Protein of Plasmid PLS20 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg203

b:52.4
occ:1.00
 O D:HOH339 2.3 41.6 1.0
O E:HOH329 2.3 44.9 1.0
O D:HOH325 2.4 38.2 1.0
OD1 D:ASN99 2.5 30.9 1.0
O E:HOH336 2.6 29.5 1.0
OD1 H:ASN99 2.8 31.1 1.0
CG D:ASN99 3.4 32.8 1.0
CG H:ASN99 3.6 32.2 1.0
O E:HOH351 3.6 45.2 1.0
CB D:ASN99 3.7 25.9 1.0
ND2 H:ASN99 3.7 26.6 1.0
O E:HOH334 3.8 43.8 1.0
O D:HOH316 3.9 43.2 1.0
CA D:ASN99 3.9 27.6 1.0
O D:ALA98 4.2 25.1 1.0
O H:HOH345 4.2 40.6 1.0
MG H:MG203 4.2 50.7 1.0
O E:PRO100 4.4 28.0 1.0
ND2 D:ASN99 4.6 25.9 1.0
O E:ASN99 4.7 28.9 1.0
MG E:MG205 4.7 53.2 1.0
CB E:ASN99 4.8 24.1 1.0
O C:HOH348 4.9 46.9 1.0
N D:ASN99 4.9 23.8 1.0
C D:ASN99 4.9 25.5 1.0
C D:ALA98 5.0 28.2 1.0

Magnesium binding site 4 out of 10 in 7qnq

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Magnesium binding site 4 out of 10 in the Structure of the AUX2 Relaxosome Protein of Plasmid PLS20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the AUX2 Relaxosome Protein of Plasmid PLS20 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg204

b:48.5
occ:1.00
 O C:HOH335 2.2 39.0 1.0
O C:HOH321 2.4 33.4 1.0
O F:HOH336 2.5 30.4 1.0
O F:HOH320 2.5 42.5 1.0
OD1 C:ASN99 2.6 27.9 1.0
OD1 E:ASN99 2.6 27.8 1.0
CG E:ASN99 3.4 31.9 1.0
O E:HOH349 3.5 45.5 1.0
CG C:ASN99 3.5 34.3 1.0
ND2 E:ASN99 3.6 24.3 1.0
CB C:ASN99 3.9 24.9 1.0
O F:HOH334 3.9 43.4 1.0
O C:HOH311 4.1 39.9 1.0
CA C:ASN99 4.1 28.3 1.0
MG E:MG205 4.1 53.2 1.0
O E:HOH334 4.2 43.8 1.0
O C:ALA98 4.3 25.2 1.0
O F:PRO100 4.4 28.0 1.0
O F:ASN99 4.7 26.7 1.0
ND2 C:ASN99 4.8 23.6 1.0
O E:HOH312 4.8 33.0 1.0
CB F:ASN99 4.8 30.5 1.0
MG F:MG206 4.8 50.8 1.0
CB E:ASN99 4.9 24.1 1.0
CD2 F:LEU101 5.0 21.8 1.0

Magnesium binding site 5 out of 10 in 7qnq

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Magnesium binding site 5 out of 10 in the Structure of the AUX2 Relaxosome Protein of Plasmid PLS20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the AUX2 Relaxosome Protein of Plasmid PLS20 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg205

b:53.2
occ:1.00
 O E:HOH334 2.2 43.8 1.0
O E:HOH312 2.4 33.0 1.0
O D:HOH316 2.4 43.2 1.0
O D:HOH344 2.5 29.2 1.0
OD1 E:ASN99 2.5 27.8 1.0
OD1 C:ASN99 2.7 27.9 1.0
CG E:ASN99 3.5 31.9 1.0
CG C:ASN99 3.5 34.3 1.0
O C:HOH348 3.6 46.9 1.0
ND2 C:ASN99 3.7 23.6 1.0
CB E:ASN99 3.8 24.1 1.0
O E:HOH329 3.9 44.9 1.0
CA E:ASN99 4.0 23.3 1.0
O D:HOH339 4.0 41.6 1.0
MG E:MG204 4.1 48.5 1.0
O C:HOH335 4.2 39.0 1.0
O E:ALA98 4.2 25.2 1.0
O D:PRO100 4.4 25.6 1.0
ND2 E:ASN99 4.7 24.3 1.0
MG D:MG203 4.7 52.4 1.0
O D:ASN99 4.7 27.8 1.0
O C:HOH321 4.8 33.4 1.0
CB D:ASN99 4.8 25.9 1.0
CB C:ASN99 5.0 24.9 1.0
N E:ASN99 5.0 23.9 1.0
O E:HOH351 5.0 45.2 1.0

Magnesium binding site 6 out of 10 in 7qnq

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Magnesium binding site 6 out of 10 in the Structure of the AUX2 Relaxosome Protein of Plasmid PLS20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the AUX2 Relaxosome Protein of Plasmid PLS20 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg205

b:50.3
occ:1.00
 O B:HOH330 2.2 44.7 1.0
O B:HOH310 2.3 34.7 1.0
O G:HOH327 2.4 27.4 1.0
OD1 B:ASN99 2.6 30.0 1.0
OD1 F:ASN99 2.7 29.9 1.0
O B:HOH341 3.0 40.4 1.0
CG F:ASN99 3.5 33.9 1.0
ND2 F:ASN99 3.5 24.4 1.0
CG B:ASN99 3.6 34.2 1.0
O F:HOH353 3.7 46.8 1.0
CB B:ASN99 3.9 26.6 1.0
CA B:ASN99 4.0 27.4 1.0
O G:HOH325 4.1 48.9 1.0
O F:HOH334 4.3 43.4 1.0
O B:ALA98 4.3 24.9 1.0
MG F:MG206 4.3 50.8 1.0
O G:PRO100 4.4 30.1 1.0
O G:ASN99 4.6 24.0 1.0
MG G:MG205 4.7 48.0 1.0
CB G:ASN99 4.7 26.2 1.0
ND2 B:ASN99 4.8 27.1 1.0
CD2 G:LEU101 4.9 25.3 1.0
O F:HOH323 4.9 34.0 1.0
CB F:ASN99 5.0 30.5 1.0
C G:ASN99 5.0 27.4 1.0

Magnesium binding site 7 out of 10 in 7qnq

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Magnesium binding site 7 out of 10 in the Structure of the AUX2 Relaxosome Protein of Plasmid PLS20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the AUX2 Relaxosome Protein of Plasmid PLS20 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg206

b:50.8
occ:1.00
 O F:HOH323 2.2 34.0 1.0
O C:HOH311 2.3 39.9 1.0
O F:HOH334 2.3 43.4 1.0
OD1 F:ASN99 2.5 29.9 1.0
O B:HOH336 2.5 31.7 1.0
OD1 B:ASN99 2.7 30.0 1.0
CG F:ASN99 3.4 33.9 1.0
CG B:ASN99 3.5 34.2 1.0
ND2 B:ASN99 3.6 27.1 1.0
CB F:ASN99 3.7 30.5 1.0
O F:HOH320 3.7 42.5 1.0
O B:HOH350 3.8 45.4 1.0
CA F:ASN99 3.9 29.5 1.0
O C:HOH335 3.9 39.0 1.0
O F:ALA98 4.1 23.9 1.0
O B:HOH330 4.2 44.7 1.0
MG F:MG205 4.3 50.3 1.0
O C:PRO100 4.4 31.9 1.0
ND2 F:ASN99 4.6 24.4 1.0
O C:ASN99 4.7 27.4 1.0
O B:HOH310 4.8 34.7 1.0
MG E:MG204 4.8 48.5 1.0
N F:ASN99 4.8 22.3 1.0
C F:ALA98 4.9 28.6 1.0
C F:ASN99 4.9 25.9 1.0
CB C:ASN99 4.9 24.9 1.0
CB B:ASN99 5.0 26.6 1.0

Magnesium binding site 8 out of 10 in 7qnq

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Magnesium binding site 8 out of 10 in the Structure of the AUX2 Relaxosome Protein of Plasmid PLS20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the AUX2 Relaxosome Protein of Plasmid PLS20 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg207

b:35.8
occ:1.00
 O F:HOH342 2.4 37.7 1.0
OD1 F:ASN88 2.5 28.4 1.0
OD1 H:ASN88 2.5 26.6 1.0
OD1 G:ASN88 2.6 27.3 1.0
OD1 E:ASN88 2.6 26.9 1.0
O F:HOH345 2.7 29.3 1.0
CG H:ASN88 3.2 26.3 1.0
CG F:ASN88 3.2 29.9 1.0
CG E:ASN88 3.3 26.6 1.0
CG G:ASN88 3.3 30.1 1.0
ND2 H:ASN88 3.4 28.0 1.0
ND2 F:ASN88 3.5 32.2 1.0
ND2 E:ASN88 3.5 26.6 1.0
ND2 G:ASN88 3.5 24.6 1.0
NE1 G:TRP92 4.0 28.4 1.0
NE1 E:TRP92 4.1 27.6 1.0
NE1 H:TRP92 4.1 25.7 1.0
NE1 F:TRP92 4.2 27.5 1.0
CB F:ASN88 4.6 25.7 1.0
CB H:ASN88 4.6 27.1 1.0
CB E:ASN88 4.7 29.8 1.0
CB G:ASN88 4.7 25.8 1.0
CD1 G:TRP92 4.7 27.4 1.0
CD1 H:TRP92 4.8 26.4 1.0
CD1 E:TRP92 4.8 27.3 1.0
CD1 F:TRP92 4.9 28.3 1.0
CE2 G:TRP92 4.9 27.2 1.0
CE2 E:TRP92 5.0 24.0 1.0

Magnesium binding site 9 out of 10 in 7qnq

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Magnesium binding site 9 out of 10 in the Structure of the AUX2 Relaxosome Protein of Plasmid PLS20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the AUX2 Relaxosome Protein of Plasmid PLS20 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg205

b:48.0
occ:1.00
 O G:HOH325 2.2 48.9 1.0
OD1 G:ASN99 2.5 26.5 1.0
O G:HOH314 2.5 30.6 1.0
O B:HOH333 2.5 29.2 1.0
OD1 A:ASN99 2.7 28.1 1.0
O B:HOH341 2.9 40.4 1.0
CG G:ASN99 3.4 31.9 1.0
CG A:ASN99 3.5 29.3 1.0
ND2 A:ASN99 3.6 24.9 1.0
CB G:ASN99 3.7 26.2 1.0
O B:HOH330 3.9 44.7 1.0
O A:HOH332 3.9 50.0 1.0
CA G:ASN99 4.0 27.0 1.0
MG A:MG203 4.1 49.2 1.0
O G:ALA98 4.4 26.1 1.0
O B:PRO100 4.5 28.0 1.0
ND2 G:ASN99 4.6 26.1 1.0
MG F:MG205 4.7 50.3 1.0
O B:ASN99 4.7 25.8 1.0
CB B:ASN99 4.8 26.6 1.0
O F:HOH353 4.8 46.8 1.0
CB A:ASN99 4.9 24.0 1.0
O A:HOH329 5.0 32.4 1.0

Magnesium binding site 10 out of 10 in 7qnq

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Magnesium binding site 10 out of 10 in the Structure of the AUX2 Relaxosome Protein of Plasmid PLS20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the AUX2 Relaxosome Protein of Plasmid PLS20 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg203

b:50.7
occ:1.00
 O H:HOH345 2.2 40.6 1.0
O A:HOH322 2.3 38.7 1.0
O H:HOH324 2.4 35.1 1.0
O D:HOH342 2.4 29.3 1.0
OD1 H:ASN99 2.6 31.1 1.0
OD1 D:ASN99 2.7 30.9 1.0
CG H:ASN99 3.5 32.2 1.0
CG D:ASN99 3.5 32.8 1.0
ND2 D:ASN99 3.6 25.9 1.0
O A:HOH362 3.7 46.3 1.0
CB H:ASN99 3.8 28.4 1.0
O H:HOH330 3.8 41.5 1.0
CA H:ASN99 4.0 25.8 1.0
O A:HOH332 4.1 50.0 1.0
O D:HOH339 4.2 41.6 1.0
MG D:MG203 4.2 52.4 1.0
O H:ALA98 4.2 24.7 1.0
O A:PRO100 4.4 28.7 1.0
O A:ASN99 4.7 26.6 1.0
ND2 H:ASN99 4.7 26.6 1.0
MG A:MG203 4.7 49.2 1.0
CB A:ASN99 4.8 24.0 1.0
O D:HOH325 4.8 38.2 1.0
CB D:ASN99 4.9 25.9 1.0
N H:ASN99 5.0 23.6 1.0

Reference:

I.Crespo, N.Bernardo, A.Cuppari, B.M.Calisto, J.Val-Calvo, A.Miguel-Arribas, W.J.J.Meijer, X.Carpena, F.Gil-Ortiz, M.Malfois, D.R.Boer. Structural and Biochemical Characterization of the Relaxosome Auxiliary Proteins Encoded on the Bacillus Subtilis Plasmid PLS20. Comput Struct Biotechnol J V. 20 757 2022.
ISSN: ESSN 2001-0370
PubMed: 35198129
DOI: 10.1016/J.CSBJ.2021.12.041
Page generated: Thu Oct 3 05:10:07 2024

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