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Magnesium in PDB 3qtc: Crystal Structure of the Catalytic Domain of Mmomers, An O-Methyl Tyrosyl-Trna Synthetase Evolved From Methanosarcina Mazei Pylrs, Complexed with O-Methyl Tyrosine and Amp-Pnp

Enzymatic activity of Crystal Structure of the Catalytic Domain of Mmomers, An O-Methyl Tyrosyl-Trna Synthetase Evolved From Methanosarcina Mazei Pylrs, Complexed with O-Methyl Tyrosine and Amp-Pnp

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Mmomers, An O-Methyl Tyrosyl-Trna Synthetase Evolved From Methanosarcina Mazei Pylrs, Complexed with O-Methyl Tyrosine and Amp-Pnp:
6.1.1.26;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Mmomers, An O-Methyl Tyrosyl-Trna Synthetase Evolved From Methanosarcina Mazei Pylrs, Complexed with O-Methyl Tyrosine and Amp-Pnp, PDB code: 3qtc was solved by N.Dellas, J.K.Takimoto, J.P.Noel, L.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.30 / 1.75
Space group P 64
Cell size a, b, c (Å), α, β, γ (°) 104.809, 104.809, 71.674, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 21.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of Mmomers, An O-Methyl Tyrosyl-Trna Synthetase Evolved From Methanosarcina Mazei Pylrs, Complexed with O-Methyl Tyrosine and Amp-Pnp (pdb code 3qtc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Catalytic Domain of Mmomers, An O-Methyl Tyrosyl-Trna Synthetase Evolved From Methanosarcina Mazei Pylrs, Complexed with O-Methyl Tyrosine and Amp-Pnp, PDB code: 3qtc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3qtc

Go back to Magnesium Binding Sites List in 3qtc
Magnesium binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Mmomers, An O-Methyl Tyrosyl-Trna Synthetase Evolved From Methanosarcina Mazei Pylrs, Complexed with O-Methyl Tyrosine 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 the Catalytic Domain of Mmomers, An O-Methyl Tyrosyl-Trna Synthetase Evolved From Methanosarcina Mazei Pylrs, Complexed with O-Methyl Tyrosine and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg800

b:24.4
occ:1.00
O1G A:ANP810 2.0 28.0 1.0
O2B A:ANP810 2.0 27.7 1.0
O A:HOH487 2.1 27.4 1.0
O A:HOH492 2.1 20.8 1.0
O A:HOH490 2.1 23.9 1.0
O A:HOH494 2.2 27.2 1.0
PB A:ANP810 3.3 27.4 1.0
PG A:ANP810 3.3 26.3 1.0
N3B A:ANP810 3.7 26.1 1.0
NH1 A:ARG330 3.9 23.9 1.0
O2G A:ANP810 3.9 27.1 1.0
NE2 A:HIS338 3.9 27.5 1.0
O A:HOH75 3.9 35.9 1.0
OE1 A:GLU332 4.1 25.3 1.0
O A:HOH130 4.2 49.5 1.0
O1B A:ANP810 4.2 29.6 1.0
OE1 A:GLU283 4.3 50.2 1.0
CD2 A:HIS338 4.4 26.8 1.0
O3A A:ANP810 4.4 26.2 1.0
OE2 A:GLU283 4.4 49.8 1.0
OE2 A:GLU332 4.4 26.2 1.0
NE2 A:GLN287 4.5 31.1 1.0
N7 A:ANP810 4.5 22.9 1.0
O3G A:ANP810 4.5 25.2 1.0
OE1 A:GLN287 4.6 33.2 1.0
CD A:GLU283 4.7 50.0 1.0
CD A:GLU332 4.7 28.1 1.0

Magnesium binding site 2 out of 2 in 3qtc

Go back to Magnesium Binding Sites List in 3qtc
Magnesium binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Mmomers, An O-Methyl Tyrosyl-Trna Synthetase Evolved From Methanosarcina Mazei Pylrs, Complexed with O-Methyl Tyrosine 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 the Catalytic Domain of Mmomers, An O-Methyl Tyrosyl-Trna Synthetase Evolved From Methanosarcina Mazei Pylrs, Complexed with O-Methyl Tyrosine and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:32.4
occ:1.00
O A:HOH521 2.0 51.5 1.0
OG A:SER399 2.2 24.3 0.5
O1B A:ANP810 2.4 29.6 1.0
O2A A:ANP810 2.5 28.8 1.0
OE2 A:GLU396 2.6 29.9 1.0
O A:HOH498 2.9 36.4 1.0
OE1 A:GLU396 3.2 33.0 1.0
CD A:GLU396 3.2 31.0 1.0
O A:HOH497 3.2 48.1 1.0
CB A:SER399 3.3 25.5 0.5
CB A:SER399 3.3 25.2 0.5
PB A:ANP810 3.4 27.4 1.0
O3A A:ANP810 3.4 26.2 1.0
PA A:ANP810 3.5 25.5 1.0
O A:HOH79 3.7 47.5 1.0
N3B A:ANP810 3.8 26.1 1.0
OG A:SER399 3.8 26.1 0.5
O A:HOH545 3.9 54.5 1.0
O1A A:ANP810 4.4 23.6 1.0
CA A:SER399 4.4 25.1 0.5
OD2 A:ASP389 4.5 41.4 1.0
CA A:SER399 4.5 24.8 0.5
O3' A:ANP810 4.5 23.7 1.0
CG A:GLU396 4.6 28.2 1.0
O5' A:ANP810 4.7 24.3 1.0
N A:SER399 4.7 24.9 1.0
O2B A:ANP810 4.7 27.7 1.0
O A:HOH138 4.8 38.2 1.0
C5' A:ANP810 4.9 22.7 1.0
C3' A:ANP810 4.9 23.6 1.0

Reference:

J.K.Takimoto, N.Dellas, J.P.Noel, L.Wang. Stereochemical Basis For Engineered Pyrrolysyl-Trna Synthetase and the Efficient in Vivo Incorporation of Structurally Divergent Non-Native Amino Acids. Acs Chem.Biol. V. 6 733 2011.
ISSN: ISSN 1554-8929
PubMed: 21545173
DOI: 10.1021/CB200057A
Page generated: Mon Dec 14 08:43:12 2020

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