Magnesium in PDB 4cs4: Catalytic Domain of Pyrrolysyl-Trna Synthetase Mutant Y306A, Y384F in Complex with Amppnp

All present enzymatic activity of Catalytic Domain of Pyrrolysyl-Trna Synthetase Mutant Y306A, Y384F in Complex with Amppnp:
6.1.1.26;

The structure of Catalytic Domain of Pyrrolysyl-Trna Synthetase Mutant Y306A, Y384F in Complex with Amppnp, PDB code: 4cs4 was solved by M.J.Schmidt, A.Weber, M.Pott, W.Welte, D.Summerer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.100 / 1.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.075, 44.533, 64.359, 90.00, 99.66, 90.00
R / Rfree (%)	14.83 / 17.56

The binding sites of Magnesium atom in the Catalytic Domain of Pyrrolysyl-Trna Synthetase Mutant Y306A, Y384F in Complex with Amppnp (pdb code 4cs4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Catalytic Domain of Pyrrolysyl-Trna Synthetase Mutant Y306A, Y384F in Complex with Amppnp, PDB code: 4cs4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Catalytic Domain of Pyrrolysyl-Trna Synthetase Mutant Y306A, Y384F in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Catalytic Domain of Pyrrolysyl-Trna Synthetase Mutant Y306A, Y384F in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1478 b:31.6 occ:0.69 OG A:SER399 2.2 29.6 1.0 O A:HOH2104 2.4 41.3 1.0 O2A A:ANP1457 2.4 28.3 1.0 O1B A:ANP1457 2.4 31.2 1.0 OE2 A:GLU396 2.4 27.7 1.0 O A:HOH2107 2.6 51.7 1.0 HB2 A:SER399 3.1 32.1 1.0 CD A:GLU396 3.1 29.4 1.0 CB A:SER399 3.2 26.7 1.0 OE1 A:GLU396 3.2 33.5 1.0 O A:HOH2106 3.3 54.1 1.0 PB A:ANP1457 3.3 29.0 1.0 O3A A:ANP1457 3.3 28.7 1.0 PA A:ANP1457 3.4 27.1 1.0 HO3' A:ANP1457 3.6 26.8 1.0 HB3 A:SER399 3.8 32.1 1.0 N3B A:ANP1457 3.8 31.0 1.0 H5'1 A:ANP1457 4.0 28.7 1.0 OXT A:AXZ1480 4.0 46.4 0.9 HNB1 A:ANP1457 4.1 37.2 1.0 H3' A:ANP1457 4.2 24.6 1.0 O A:HOH2120 4.3 40.6 1.0 CA A:SER399 4.3 22.7 1.0 OD1 A:ASP389 4.4 32.2 1.0 O3' A:ANP1457 4.4 22.4 1.0 O1A A:ANP1457 4.4 26.3 1.0 N A:SER399 4.4 21.8 1.0 H A:SER399 4.4 26.1 1.0 CG A:GLU396 4.5 25.8 1.0 O5' A:ANP1457 4.5 25.5 1.0 HG2 A:GLU396 4.6 31.0 1.0 HA A:SER399 4.6 27.3 1.0 C5' A:ANP1457 4.7 23.9 1.0 OD2 A:ASP389 4.7 37.4 1.0 HG3 A:GLU396 4.7 31.0 1.0 O2B A:ANP1457 4.7 28.4 1.0 C3' A:ANP1457 4.7 20.5 1.0 CG A:ASP389 4.8 33.2 1.0 H A:AXZ1480 4.9 36.5 0.9 C A:SER398 5.0 22.5 1.0

Magnesium binding site 2 out of 2 in the Catalytic Domain of Pyrrolysyl-Trna Synthetase Mutant Y306A, Y384F in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Catalytic Domain of Pyrrolysyl-Trna Synthetase Mutant Y306A, Y384F in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1479 b:31.7 occ:0.62 O A:HOH2121 2.0 53.0 1.0 O A:HOH2074 2.0 28.4 1.0 O2G A:ANP1457 2.1 32.8 1.0 O A:HOH2057 2.1 35.9 1.0 O2B A:ANP1457 2.1 28.4 1.0 O A:HOH2056 2.2 37.2 1.0 PG A:ANP1457 3.3 32.4 1.0 HH11 A:ARG330 3.3 27.5 1.0 HE2 A:HIS338 3.4 33.2 1.0 PB A:ANP1457 3.5 29.0 1.0 O3G A:ANP1457 3.7 38.9 1.0 N3B A:ANP1457 3.8 31.0 1.0 HE22 A:GLN287 3.9 53.8 1.0 HH12 A:ARG330 3.9 27.5 1.0 NH1 A:ARG330 4.0 22.5 1.0 HD2 A:HIS338 4.0 32.2 1.0 NE2 A:HIS338 4.0 27.7 1.0 OE2 A:GLU332 4.1 28.0 1.0 HNB1 A:ANP1457 4.3 37.2 1.0 CD2 A:HIS338 4.4 26.8 1.0 O1B A:ANP1457 4.4 31.2 1.0 OE1 A:GLN287 4.4 44.6 1.0 O3A A:ANP1457 4.5 28.7 1.0 OE1 A:GLU332 4.5 30.6 1.0 N7 A:ANP1457 4.5 20.3 1.0 HD3 A:ARG330 4.6 26.3 1.0 NE2 A:GLN287 4.6 44.8 1.0 O1G A:ANP1457 4.7 30.7 1.0 CD A:GLU332 4.8 28.8 1.0 H8 A:ANP1457 4.9 21.7 1.0 HN62 A:ANP1457 4.9 24.1 1.0 CD A:GLN287 5.0 42.2 1.0

M.J.Schmidt, A.Weber, M.Pott, W.Welte, D.Summerer. Structural Basis of Furan-Amino Acid Recognition By A Polyspecific Aminoacyl-Trna-Synthetase and Its Genetic Encoding in Human Cells. Chembiochem V. 15 1755 2014.
ISSN: ISSN 1439-4227
PubMed: 24737732
DOI: 10.1002/CBIC.201402006