Magnesium in PDB 8dqg: Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Amppnp and Acridone

Protein crystallography data

The structure of Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Amppnp and Acridone, PDB code: 8dqg was solved by I.Gottfried-Lee, P.A.Karplus, R.A.Mehl, R.B.Cooley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.47 / 1.49
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 110.953, 110.953, 113.587, 90, 90, 90
R / Rfree (%) 13.6 / 16.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Amppnp and Acridone (pdb code 8dqg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Amppnp and Acridone, PDB code: 8dqg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 8dqg

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Magnesium binding site 1 out of 5 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Amppnp and Acridone


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 Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Amppnp and Acridone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:29.2
occ:0.67
 O1B D:ANP301 2.2 28.4 0.8
OE2 D:GLU218 2.3 31.1 1.0
O1A D:ANP301 2.4 29.3 0.8
O D:HOH454 2.4 35.5 1.0
OG D:SER221 2.4 27.8 0.6
HB3 D:SER221 2.7 31.6 0.4
HG D:SER221 2.8 35.1 0.4
HG D:SER221 2.9 33.3 0.6
OG D:SER221 3.2 29.2 0.4
PB D:ANP301 3.2 28.1 0.8
MG D:MG305 3.2 33.6 0.6
CD D:GLU218 3.2 30.8 1.0
O3A D:ANP301 3.2 27.3 0.8
HB2 D:SER221 3.3 31.2 0.6
PA D:ANP301 3.3 26.1 0.8
CB D:SER221 3.3 26.3 0.4
CB D:SER221 3.4 26.0 0.6
OE1 D:GLU218 3.5 32.5 1.0
N3B D:ANP301 3.7 28.5 0.8
HB2 D:SER221 3.8 31.6 0.4
HB3 D:SER221 3.9 31.2 0.6
H3' D:ANP301 3.9 27.6 0.8
O D:HOH472 4.0 37.0 1.0
OD2 D:ASP211 4.2 28.7 1.0
HNB1 D:ANP301 4.2 34.2 0.8
H5'2 D:ANP301 4.2 26.3 0.8
O3' D:ANP301 4.2 25.4 0.8
O2A D:ANP301 4.3 25.2 0.8
HN2 D:T7Q302 4.4 68.8 0.8
HG1 D:THR209 4.5 36.7 1.0
O5' D:ANP301 4.5 24.9 0.8
CG D:GLU218 4.5 27.2 1.0
HA D:T7Q302 4.5 59.8 0.8
OD1 D:ASP211 4.5 25.5 1.0
C3' D:ANP301 4.5 23.0 0.8
O2B D:ANP301 4.6 28.0 0.8
CA D:SER221 4.6 23.3 0.6
HG3 D:GLU218 4.6 32.6 1.0
CA D:SER221 4.6 23.5 0.4
HN3 D:T7Q302 4.6 68.8 0.8
O D:HOH632 4.7 53.1 1.0
CG D:ASP211 4.7 25.3 1.0
HG2 D:GLU218 4.7 32.6 1.0
C5' D:ANP301 4.8 21.9 0.8
HA D:SER221 4.8 28.0 0.6
N D:SER221 4.8 22.1 1.0
HA D:SER221 4.8 28.2 0.4
HG21 D:THR209 4.9 35.0 1.0
N D:T7Q302 4.9 57.3 0.8
H D:SER221 4.9 26.6 0.4
H D:SER221 4.9 26.6 0.6

Magnesium binding site 2 out of 5 in 8dqg

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Magnesium binding site 2 out of 5 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Amppnp and Acridone


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 Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Amppnp and Acridone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg304

b:25.3
occ:0.65
 O D:HOH487 2.0 28.3 0.8
O2B D:ANP301 2.1 28.0 0.8
O3G D:ANP301 2.1 29.7 0.8
O D:HOH574 2.1 28.2 0.7
O D:HOH558 2.1 32.5 0.6
O D:HOH547 2.1 36.9 1.0
HE2 D:HIS158 3.1 42.1 1.0
HH11 D:ARG150 3.2 31.6 1.0
PG D:ANP301 3.3 28.7 0.8
PB D:ANP301 3.4 28.1 0.8
N3B D:ANP301 3.7 28.5 0.8
HH12 D:ARG150 3.7 31.6 1.0
NH1 D:ARG150 3.8 26.3 1.0
O2G D:ANP301 3.8 31.5 0.8
NE2 D:HIS158 3.8 35.1 1.0
HNB1 D:ANP301 3.9 34.2 0.8
HE22 D:GLN107 4.0 43.3 1.0
O D:HOH638 4.2 51.3 1.0
OE2 D:GLU152 4.3 35.0 1.0
O1B D:ANP301 4.3 28.4 0.8
O3A D:ANP301 4.4 27.3 0.8
HD2 D:HIS158 4.5 40.7 1.0
CD2 D:HIS158 4.5 33.9 1.0
O1G D:ANP301 4.6 29.7 0.8
OE1 D:GLU152 4.6 38.1 1.0
N7 D:ANP301 4.6 23.8 0.8
OE1 D:GLN107 4.6 35.9 1.0
HD3 D:ARG150 4.6 29.6 1.0
HD2 D:ARG150 4.8 29.6 1.0
CE1 D:HIS158 4.8 37.4 1.0
NE2 D:GLN107 4.8 36.0 1.0
H8 D:ANP301 4.9 27.8 0.8
CD D:GLU152 4.9 35.6 1.0
HE1 D:HIS158 4.9 44.8 1.0

Magnesium binding site 3 out of 5 in 8dqg

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Magnesium binding site 3 out of 5 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Amppnp and Acridone


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 Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Amppnp and Acridone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg305

b:33.6
occ:0.64
 OE1 D:GLU218 2.4 32.5 1.0
O D:HOH454 2.5 35.5 1.0
O D:HOH632 2.5 53.1 1.0
O2G D:ANP301 2.5 31.5 0.8
O1B D:ANP301 2.6 28.4 0.8
O D:HOH637 2.8 58.4 1.0
MG D:MG303 3.2 29.2 0.7
N3B D:ANP301 3.2 28.5 0.8
CD D:GLU218 3.3 30.8 1.0
PB D:ANP301 3.4 28.1 0.8
PG D:ANP301 3.5 28.7 0.8
OE2 D:GLU218 3.5 31.1 1.0
O D:HOH566 3.8 50.1 1.0
HNB1 D:ANP301 4.1 34.2 0.8
O1G D:ANP301 4.3 29.7 0.8
O2B D:ANP301 4.4 28.0 0.8
O D:HOH444 4.5 39.0 1.0
OD2 D:ASP211 4.5 28.7 1.0
O D:HOH558 4.6 32.5 0.6
O3A D:ANP301 4.6 27.3 0.8
O3G D:ANP301 4.7 29.7 0.8
O D:HOH472 4.7 37.0 1.0
CG D:GLU218 4.7 27.2 1.0
HB2 D:GLU218 5.0 31.4 1.0

Magnesium binding site 4 out of 5 in 8dqg

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Magnesium binding site 4 out of 5 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Amppnp and Acridone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Amppnp and Acridone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:37.3
occ:0.59
 HG A:SER221 2.0 52.4 1.0
O A:HOH573 2.3 46.7 1.0
O1B A:ANP303 2.3 36.2 0.7
O1A A:ANP303 2.4 34.0 0.7
OE2 A:GLU218 2.5 48.4 1.0
OG A:SER221 2.6 43.7 1.0
PB A:ANP303 3.2 35.6 0.7
CD A:GLU218 3.2 48.6 1.0
O3A A:ANP303 3.3 35.5 0.7
PA A:ANP303 3.4 34.1 0.7
OE1 A:GLU218 3.4 52.1 1.0
HB2 A:SER221 3.5 47.3 1.0
CB A:SER221 3.6 39.4 1.0
N3B A:ANP303 3.7 35.9 0.7
H3' A:ANP303 4.0 35.7 0.7
HB3 A:SER221 4.0 47.3 1.0
H5'2 A:ANP303 4.1 38.4 0.7
HNB1 A:ANP303 4.1 43.1 0.7
OD2 A:ASP211 4.2 55.7 1.0
O3' A:ANP303 4.3 31.7 0.7
O2A A:ANP303 4.4 34.4 0.7
O5' A:ANP303 4.5 33.3 0.7
CG A:GLU218 4.5 43.9 1.0
HG3 A:GLU218 4.6 52.7 1.0
C3' A:ANP303 4.6 29.8 0.7
O2B A:ANP303 4.6 34.7 0.7
C5' A:ANP303 4.7 32.0 0.7
HG2 A:GLU218 4.8 52.7 1.0
CA A:SER221 4.9 35.5 1.0
CG A:ASP211 5.0 52.0 1.0

Magnesium binding site 5 out of 5 in 8dqg

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Magnesium binding site 5 out of 5 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Amppnp and Acridone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Amppnp and Acridone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:35.9
occ:0.68
 O2G A:ANP303 2.0 35.9 0.7
O2B A:ANP303 2.0 34.7 0.7
O A:HOH413 2.1 35.5 0.8
O A:HOH555 2.2 37.5 0.7
O A:HOH429 2.3 41.4 0.8
HE2 A:HIS158 3.2 54.5 1.0
HH11 A:ARG150 3.2 43.8 1.0
PG A:ANP303 3.2 36.3 0.7
PB A:ANP303 3.4 35.6 0.7
N3B A:ANP303 3.7 35.9 0.7
HH12 A:ARG150 3.8 43.8 1.0
O1G A:ANP303 3.8 36.0 0.7
NH1 A:ARG150 3.8 36.5 1.0
NE2 A:HIS158 3.9 45.4 1.0
HNB1 A:ANP303 4.0 43.1 0.7
HE22 A:GLN107 4.3 55.2 1.0
O1B A:ANP303 4.3 36.2 0.7
OE2 A:GLU152 4.3 47.0 1.0
O3A A:ANP303 4.4 35.5 0.7
HD2 A:HIS158 4.4 55.2 1.0
OE1 A:GLN107 4.4 44.0 1.0
CD2 A:HIS158 4.5 46.0 1.0
O3G A:ANP303 4.6 35.3 0.7
N7 A:ANP303 4.6 28.2 0.7
HD3 A:ARG150 4.7 36.4 1.0
OE1 A:GLU152 4.7 44.2 1.0
HD2 A:ARG150 4.8 36.4 1.0
CE1 A:HIS158 4.9 46.2 1.0
H8 A:ANP303 4.9 34.5 0.7
NE2 A:GLN107 5.0 46.0 1.0
CD A:GLU152 5.0 44.1 1.0

Reference:

I.Gottfried-Lee, J.J.Perona, P.A.Karplus, R.A.Mehl, R.B.Cooley. Structures of Methanomethylophilus Alvus Pyrrolysine Trna-Synthetases Support the Need For De Novo Selections When Altering the Substrate Specificity. Acs Chem.Biol. V. 17 3470 2022.
ISSN: ESSN 1554-8937
PubMed: 36395426
DOI: 10.1021/ACSCHEMBIO.2C00640
Page generated: Fri Apr 7 09:00:57 2023

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