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Magnesium in PDB 5k1x: Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant Y306A/N346A/C348A/Y384F in Complex with Amppnp

Enzymatic activity of Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant Y306A/N346A/C348A/Y384F in Complex with Amppnp

All present enzymatic activity of Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant Y306A/N346A/C348A/Y384F in Complex with Amppnp:
6.1.1.26;

Protein crystallography data

The structure of Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant Y306A/N346A/C348A/Y384F in Complex with Amppnp, PDB code: 5k1x was solved by A.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.18 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.017, 44.140, 64.309, 90.00, 100.01, 90.00
R / Rfree (%) 19.7 / 22.7

Other elements in 5k1x:

The structure of Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant Y306A/N346A/C348A/Y384F in Complex with Amppnp also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant Y306A/N346A/C348A/Y384F in Complex with Amppnp (pdb code 5k1x). 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 Polyspecific Pyrrolysyl-Trna Synthetase Mutant Y306A/N346A/C348A/Y384F in Complex with Amppnp, PDB code: 5k1x:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5k1x

Go back to Magnesium Binding Sites List in 5k1x
Magnesium binding site 1 out of 2 in the Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant Y306A/N346A/C348A/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 Polyspecific Pyrrolysyl-Trna Synthetase Mutant Y306A/N346A/C348A/Y384F in Complex with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:31.0
occ:1.00
 O A:HOH651 1.9 31.0 1.0
O1B A:ANP501 2.0 32.0 1.0
O A:HOH636 2.1 31.2 1.0
OE2 A:GLU396 2.1 45.8 1.0
O1A A:ANP501 2.2 30.9 1.0
OG A:SER399 2.2 46.0 1.0
CD A:GLU396 3.1 43.9 1.0
CB A:SER399 3.1 40.3 1.0
PB A:ANP501 3.2 34.4 1.0
PA A:ANP501 3.3 33.9 1.0
OE1 A:GLU396 3.4 45.3 1.0
O A:HOH604 3.4 43.7 1.0
O3A A:ANP501 3.5 34.5 1.0
N3B A:ANP501 4.0 35.3 1.0
O2A A:ANP501 4.1 33.7 1.0
OD1 A:ASP389 4.2 40.2 1.0
OD2 A:ASP389 4.2 41.6 1.0
O3' A:ANP501 4.3 27.7 1.0
CA A:SER399 4.3 34.1 1.0
O2B A:ANP501 4.4 32.5 1.0
CG A:GLU396 4.4 40.6 1.0
O5' A:ANP501 4.5 33.5 1.0
N A:SER399 4.5 33.0 1.0
CG A:ASP389 4.5 40.3 1.0
C3' A:ANP501 4.7 27.5 1.0
C5' A:ANP501 4.7 31.3 1.0
C A:SER398 5.0 32.0 1.0

Magnesium binding site 2 out of 2 in 5k1x

Go back to Magnesium Binding Sites List in 5k1x
Magnesium binding site 2 out of 2 in the Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant Y306A/N346A/C348A/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 Polyspecific Pyrrolysyl-Trna Synthetase Mutant Y306A/N346A/C348A/Y384F in Complex with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:34.3
occ:1.00
 O A:HOH643 2.0 34.2 1.0
O A:HOH647 2.0 33.4 1.0
O2G A:ANP501 2.1 35.3 1.0
O2B A:ANP501 2.1 32.5 1.0
O A:HOH620 2.2 31.5 1.0
O A:HOH703 2.4 45.9 1.0
PG A:ANP501 3.3 36.1 1.0
PB A:ANP501 3.5 34.4 1.0
O1G A:ANP501 3.7 36.5 1.0
N3B A:ANP501 3.9 35.3 1.0
NH2 A:ARG330 3.9 28.4 1.0
OE2 A:GLU332 4.2 32.9 1.0
NE2 A:HIS338 4.2 32.8 1.0
O3A A:ANP501 4.3 34.5 1.0
OE1 A:GLU332 4.4 34.6 1.0
NE2 A:GLN287 4.4 43.9 1.0
O1B A:ANP501 4.5 32.0 1.0
O3G A:ANP501 4.5 36.9 1.0
OE1 A:GLN287 4.6 46.9 1.0
CD2 A:HIS338 4.6 32.2 1.0
N7 A:ANP501 4.7 25.2 1.0
CD A:GLU332 4.7 34.9 1.0
CD A:GLN287 5.0 44.6 1.0

Reference:

Y.J.Lee, M.J.Schmidt, J.M.Tharp, A.Weber, A.L.Koenig, H.Zheng, J.Gao, M.L.Waters, D.Summerer, W.R.Liu. Genetically Encoded Fluorophenylalanines Enable Insights Into the Recognition of Lysine Trimethylation By An Epigenetic Reader. Chem.Commun.(Camb.) V. 52 12606 2016.
ISSN: ESSN 1364-548X
PubMed: 27711380
DOI: 10.1039/C6CC05959G
Page generated: Sun Sep 29 18:49:52 2024

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