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Magnesium in PDB 7u0r: Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp

Enzymatic activity of Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp

All present enzymatic activity of Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp:
6.1.1.26;

Protein crystallography data

The structure of Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp, PDB code: 7u0r was solved by C.V.Swenson, L.T.Roe, R.C.B.Fricke, S.S.Smaga, C.L.Gee, A.Schepartz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.37 / 1.80
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 108.958, 108.958, 112.26, 90, 90, 90
R / Rfree (%) 18 / 21.1

Other elements in 7u0r:

The structure of Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp (pdb code 7u0r). 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 Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp, PDB code: 7u0r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7u0r

Go back to Magnesium Binding Sites List in 7u0r
Magnesium binding site 1 out of 5 in the Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp


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 Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:38.0
occ:1.00
 OE2 A:GLU218 2.0 37.8 1.0
OG A:SER221 2.0 36.4 1.0
O A:HOH528 2.1 36.3 1.0
O1B A:ANP402 2.1 42.6 1.0
O2A A:ANP402 2.1 39.5 1.0
O A:HOH609 2.2 44.2 1.0
CD A:GLU218 3.0 47.7 1.0
CB A:SER221 3.1 34.0 1.0
PB A:ANP402 3.2 60.7 1.0
PA A:ANP402 3.3 47.8 1.0
MG A:MG406 3.3 51.1 1.0
O3A A:ANP402 3.4 61.3 1.0
OE1 A:GLU218 3.4 45.0 1.0
N3B A:ANP402 3.8 52.2 1.0
OD2 A:ASP211 3.9 41.7 1.0
O3' A:ANP402 4.0 35.6 1.0
O A:HOH539 4.0 43.0 1.0
O1A A:ANP402 4.1 44.7 1.0
CG A:GLU218 4.3 38.4 1.0
OD1 A:ASP211 4.3 35.5 1.0
CA A:SER221 4.3 30.7 1.0
C3' A:ANP402 4.3 36.3 1.0
CG A:ASP211 4.5 40.7 1.0
O2B A:ANP402 4.5 56.2 1.0
O5' A:ANP402 4.5 36.0 1.0
N A:SER221 4.6 30.7 1.0
O A:HOH691 4.6 57.5 1.0
O03 A:LE0401 4.6 55.4 1.0
C5' A:ANP402 4.7 33.4 1.0
O A:CYS220 5.0 34.4 1.0

Magnesium binding site 2 out of 5 in 7u0r

Go back to Magnesium Binding Sites List in 7u0r
Magnesium binding site 2 out of 5 in the Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp


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 Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:52.9
occ:1.00
 O2B A:ANP402 2.0 56.2 1.0
O A:HOH652 2.2 60.5 1.0
O1G A:ANP402 2.3 65.0 1.0
O A:HOH592 2.3 64.6 1.0
O A:HOH506 2.3 43.4 1.0
O A:HOH654 2.4 66.5 1.0
PG A:ANP402 3.2 80.3 1.0
PB A:ANP402 3.3 60.7 1.0
O3G A:ANP402 3.6 58.5 1.0
N3B A:ANP402 3.6 52.2 1.0
NH1 A:ARG150 3.9 42.2 1.0
NE2 A:HIS158 4.0 59.0 1.0
O A:HOH676 4.0 68.8 1.0
OE2 A:GLU152 4.2 48.3 1.0
O1B A:ANP402 4.3 42.6 1.0
O3A A:ANP402 4.3 61.3 1.0
CD2 A:HIS158 4.5 59.6 1.0
OE1 A:GLU152 4.6 65.1 1.0
O2G A:ANP402 4.6 49.9 1.0
N7 A:ANP402 4.7 38.2 1.0
OE1 A:GLN107 4.8 66.2 1.0
CD A:GLU152 4.9 64.3 1.0

Magnesium binding site 3 out of 5 in 7u0r

Go back to Magnesium Binding Sites List in 7u0r
Magnesium binding site 3 out of 5 in the Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp


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 Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:51.1
occ:1.00
 O A:HOH691 2.4 57.5 1.0
O3G A:ANP402 2.4 58.5 1.0
OE1 A:GLU218 2.5 45.0 1.0
O A:HOH528 2.5 36.3 1.0
O1B A:ANP402 2.6 42.6 1.0
MG A:MG404 3.3 38.0 1.0
CD A:GLU218 3.4 47.7 1.0
N3B A:ANP402 3.4 52.2 1.0
PB A:ANP402 3.4 60.7 1.0
PG A:ANP402 3.5 80.3 1.0
OE2 A:GLU218 3.6 37.8 1.0
O A:HOH618 3.9 49.2 1.0
O2B A:ANP402 4.1 56.2 1.0
O A:HOH609 4.2 44.2 1.0
O A:HOH654 4.3 66.5 1.0
O2G A:ANP402 4.3 49.9 1.0
OD2 A:ASP211 4.4 41.7 1.0
O A:HOH563 4.4 50.6 1.0
O A:HOH539 4.6 43.0 1.0
O1G A:ANP402 4.6 65.0 1.0
CG A:GLU218 4.8 38.4 1.0
O A:HOH676 4.8 68.8 1.0
O3A A:ANP402 4.8 61.3 1.0
OG A:SER221 4.9 36.4 1.0

Magnesium binding site 4 out of 5 in 7u0r

Go back to Magnesium Binding Sites List in 7u0r
Magnesium binding site 4 out of 5 in the Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp


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 Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:58.4
occ:1.00
 O2B B:ANP402 2.0 52.0 1.0
O3G B:ANP402 2.1 59.2 1.0
O B:HOH574 2.2 63.0 1.0
O B:HOH544 2.3 63.4 1.0
O B:HOH507 2.4 56.7 1.0
O B:HOH548 2.8 66.0 1.0
PB B:ANP402 3.5 64.1 1.0
PG B:ANP402 3.5 66.2 1.0
NH1 B:ARG150 3.7 55.2 1.0
OE2 B:GLU152 3.9 60.9 1.0
N3B B:ANP402 4.0 70.2 1.0
NE2 B:HIS158 4.0 67.8 1.0
O1G B:ANP402 4.1 73.8 1.0
O B:HOH680 4.2 70.6 1.0
O3A B:ANP402 4.2 81.5 1.0
CD2 B:HIS158 4.4 62.9 1.0
O1B B:ANP402 4.5 81.0 1.0
OE1 B:GLU152 4.5 68.4 1.0
OE1 B:GLN107 4.6 67.9 1.0
CD B:GLU152 4.7 68.0 1.0
N7 B:ANP402 4.7 54.4 1.0
O2G B:ANP402 4.7 57.1 1.0
NE2 B:GLN107 4.9 66.1 1.0
CZ B:ARG150 5.0 48.1 1.0

Magnesium binding site 5 out of 5 in 7u0r

Go back to Magnesium Binding Sites List in 7u0r
Magnesium binding site 5 out of 5 in the Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp


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 Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:67.9
occ:1.00
 O B:HOH518 2.1 60.7 1.0
O1B B:ANP402 2.2 81.0 1.0
OG B:SER221 2.4 64.6 1.0
OE2 B:GLU218 2.4 63.3 1.0
O2A B:ANP402 2.4 84.9 1.0
O B:HOH529 3.2 68.1 1.0
CD B:GLU218 3.3 69.8 1.0
PB B:ANP402 3.3 64.1 1.0
O B:HOH600 3.4 86.5 1.0
PA B:ANP402 3.4 64.4 1.0
CB B:SER221 3.6 55.3 1.0
OE1 B:GLU218 3.7 65.9 1.0
O3A B:ANP402 3.7 81.5 1.0
O5' B:ANP402 3.8 76.2 1.0
N3B B:ANP402 3.9 70.2 1.0
OD2 B:ASP211 4.0 71.8 1.0
O B:HOH556 4.1 82.0 1.0
OD1 B:ASP211 4.1 69.6 1.0
CG B:ASP211 4.4 68.6 1.0
CG B:GLU218 4.6 61.0 1.0
O2B B:ANP402 4.6 52.0 1.0
O3' B:ANP402 4.6 52.8 1.0
CA B:SER221 4.8 58.0 1.0
O1A B:ANP402 4.8 58.4 1.0
C3' B:ANP402 4.9 56.6 1.0
OG1 B:THR209 5.0 84.2 1.0
N B:SER221 5.0 49.7 1.0

Reference:

R.Fricke, C.V.Swenson, L.T.Roe, N.X.Hamlish, B.Shah, Z.Zhang, E.Ficaretta, O.Ad, S.Smaga, C.L.Gee, A.Chatterjee, A.Schepartz. Expanding the Substrate Scope of Pyrrolysyl-Transfer Rna Synthetase Enzymes to Include Non-Alpha-Amino Acids in Vitro and in Vivo. Nat.Chem. 2023.
ISSN: ESSN 1755-4349
PubMed: 37264106
DOI: 10.1038/S41557-023-01224-Y
Page generated: Thu Jul 27 19:26:08 2023

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