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Magnesium in PDB 5k1p: Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant N346A/C348A in Complex with Amppnp

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

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

Protein crystallography data

The structure of Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant N346A/C348A in Complex with Amppnp, PDB code: 5k1p was solved by A.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.28 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.493, 44.358, 64.314, 90.00, 99.92, 90.00
R / Rfree (%) 16.5 / 19.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant N346A/C348A in Complex with Amppnp (pdb code 5k1p). 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 N346A/C348A in Complex with Amppnp, PDB code: 5k1p:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5k1p

Go back to Magnesium Binding Sites List in 5k1p
Magnesium binding site 1 out of 2 in the Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant N346A/C348A 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 N346A/C348A in Complex with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:23.2
occ:1.00
O A:HOH784 2.1 41.8 1.0
O A:HOH642 2.2 40.2 1.0
O1B A:ANP501 2.3 34.4 0.9
OG A:SER399 2.3 28.3 1.0
OE2 A:GLU396 2.5 26.1 1.0
O1A A:ANP501 2.5 29.2 0.9
OE1 A:GLU396 2.5 30.5 1.0
CD A:GLU396 2.9 31.4 1.0
O A:HOH666 3.1 45.1 1.0
PB A:ANP501 3.4 30.4 0.9
HNB1 A:ANP501 3.4 33.2 0.9
CB A:SER399 3.5 25.5 1.0
HB2 A:SER399 3.5 30.6 1.0
PA A:ANP501 3.6 28.1 0.9
O3A A:ANP501 3.6 30.5 0.9
HB3 A:SER399 3.9 30.6 1.0
N3B A:ANP501 3.9 27.7 0.9
HO3' A:ANP501 4.0 27.1 0.9
O A:HOH762 4.0 59.9 1.0
OD1 A:ASP389 4.1 31.0 1.0
O A:HOH604 4.1 36.8 1.0
CG A:GLU396 4.4 23.3 1.0
O2A A:ANP501 4.4 26.5 0.9
H5'2 A:ANP501 4.5 31.3 0.9
H3' A:ANP501 4.6 23.7 0.9
CA A:SER399 4.6 19.6 1.0
CG A:ASP389 4.7 30.5 1.0
HG2 A:GLU396 4.7 27.9 1.0
HG3 A:GLU396 4.7 27.9 1.0
O3' A:ANP501 4.7 22.6 0.9
OD2 A:ASP389 4.7 38.2 1.0
O2B A:ANP501 4.7 31.6 0.9
HG1 A:THR387 4.8 48.7 1.0
HA A:SER399 4.8 23.6 1.0
N A:SER399 4.8 20.9 1.0
O5' A:ANP501 4.8 24.4 0.9
H A:SER399 4.9 25.0 1.0

Magnesium binding site 2 out of 2 in 5k1p

Go back to Magnesium Binding Sites List in 5k1p
Magnesium binding site 2 out of 2 in the Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant N346A/C348A 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 N346A/C348A in Complex with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:23.2
occ:1.00
O A:HOH725 2.1 32.1 1.0
O2G A:ANP501 2.1 28.1 0.9
O A:HOH722 2.2 34.8 1.0
O2B A:ANP501 2.2 31.6 0.9
O A:HOH670 2.2 26.4 1.0
HE2 A:HIS338 3.3 31.6 1.0
PG A:ANP501 3.5 29.2 0.9
PB A:ANP501 3.6 30.4 0.9
HH21 A:ARG330 3.6 27.7 1.0
HE22 A:GLN287 3.9 43.7 1.0
N3B A:ANP501 4.0 27.7 0.9
NE2 A:HIS338 4.0 26.3 1.0
HD2 A:HIS338 4.0 28.3 1.0
O1G A:ANP501 4.1 35.3 0.9
HH22 A:ARG330 4.2 27.7 1.0
NH2 A:ARG330 4.2 23.1 1.0
O A:HOH829 4.3 45.1 1.0
OE2 A:GLU332 4.3 27.3 1.0
CD2 A:HIS338 4.3 23.6 1.0
O1B A:ANP501 4.4 34.4 0.9
OE1 A:GLN287 4.5 41.3 1.0
OE1 A:GLU332 4.6 34.5 1.0
O3A A:ANP501 4.6 30.5 0.9
NE2 A:GLN287 4.7 36.4 1.0
O3G A:ANP501 4.7 35.0 0.9
HNB1 A:ANP501 4.8 33.2 0.9
HD3 A:ARG330 4.8 28.3 1.0
CD A:GLU332 4.9 30.5 1.0
N7 A:ANP501 4.9 20.2 0.9
HD2 A:ARG330 5.0 28.3 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: Mon Dec 14 20:36:42 2020

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