Magnesium in PDB 6abk: Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Teoclys

Enzymatic activity of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Teoclys

All present enzymatic activity of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Teoclys:
6.1.1.26;

Protein crystallography data

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Teoclys, PDB code: 6abk was solved by T.Yanagisawa, M.Kuratani, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.99 / 1.58
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.245, 43.906, 72.451, 90.00, 118.69, 90.00
R / Rfree (%) 15.9 / 18.9

Other elements in 6abk:

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Teoclys also contains other interesting chemical elements:

Silicon (Si) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Teoclys (pdb code 6abk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Teoclys, PDB code: 6abk:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6abk

Go back to Magnesium Binding Sites List in 6abk
Magnesium binding site 1 out of 3 in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Teoclys


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 Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Teoclys within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:18.1
occ:1.00
O2B A:ATP504 2.0 17.8 1.0
O A:HOH747 2.1 22.7 1.0
O A:HOH650 2.1 15.7 1.0
O2G A:ATP504 2.1 18.7 1.0
O A:HOH737 2.1 22.2 1.0
O A:HOH663 2.1 23.1 1.0
PG A:ATP504 3.2 18.6 1.0
PB A:ATP504 3.3 16.9 1.0
O3B A:ATP504 3.5 17.4 1.0
O1G A:ATP504 3.8 21.8 1.0
NH1 A:ARG330 3.9 15.9 1.0
NE2 A:HIS338 4.0 19.9 1.0
O A:HOH823 4.1 38.5 1.0
O A:HOH818 4.1 40.0 1.0
O A:HOH887 4.2 50.5 1.0
OE2 A:GLU332 4.2 19.2 1.0
O3A A:ATP504 4.3 16.4 1.0
O1B A:ATP504 4.4 18.6 1.0
OE1 A:GLU332 4.4 24.1 1.0
O3G A:ATP504 4.5 18.5 1.0
CD2 A:HIS338 4.5 17.2 1.0
NE2 A:GLN287 4.6 39.5 1.0
N7 A:ATP504 4.6 14.5 1.0
OE1 A:GLN287 4.7 42.6 1.0
O A:HOH782 4.7 34.2 1.0
CD A:GLU332 4.8 23.3 1.0

Magnesium binding site 2 out of 3 in 6abk

Go back to Magnesium Binding Sites List in 6abk
Magnesium binding site 2 out of 3 in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Teoclys


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 Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Teoclys within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:19.2
occ:1.00
O1B A:ATP504 2.1 18.6 1.0
O1A A:ATP504 2.1 20.9 1.0
OG A:SER399 2.1 20.4 1.0
O A:HOH760 2.2 23.5 1.0
OE2 A:GLU396 2.2 19.2 1.0
O A:HOH656 2.2 19.4 1.0
CD A:GLU396 3.1 19.6 1.0
CB A:SER399 3.2 20.9 1.0
PA A:ATP504 3.3 16.8 1.0
MG A:MG503 3.3 21.2 1.0
PB A:ATP504 3.3 16.9 1.0
OE1 A:GLU396 3.4 19.9 1.0
O3A A:ATP504 3.4 16.4 1.0
O A:HOH704 4.0 24.9 1.0
O3B A:ATP504 4.1 17.4 1.0
OD2 A:ASP389 4.1 25.0 1.0
O A:HOH782 4.1 34.2 1.0
O2A A:ATP504 4.1 17.7 1.0
OD1 A:ASP389 4.2 21.5 1.0
CA A:SER399 4.2 16.1 1.0
O A:9VF505 4.3 17.7 0.3
O3' A:ATP504 4.3 15.8 1.0
N A:SER399 4.3 15.7 1.0
CG A:GLU396 4.4 15.7 1.0
CG A:ASP389 4.5 21.9 1.0
O5' A:ATP504 4.5 15.9 1.0
O2B A:ATP504 4.5 17.8 1.0
C3' A:ATP504 4.7 14.8 1.0
C5' A:ATP504 4.7 18.1 1.0
O1G A:ATP504 4.8 21.8 1.0
C A:SER398 4.9 17.2 1.0

Magnesium binding site 3 out of 3 in 6abk

Go back to Magnesium Binding Sites List in 6abk
Magnesium binding site 3 out of 3 in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Teoclys


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 Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Teoclys within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:21.2
occ:1.00
O A:HOH783 2.1 26.2 1.0
O1G A:ATP504 2.2 21.8 1.0
OE1 A:GLU396 2.3 19.9 1.0
O1B A:ATP504 2.3 18.6 1.0
O A:HOH656 2.4 19.4 1.0
CD A:GLU396 3.3 19.6 1.0
MG A:MG502 3.3 19.2 1.0
PB A:ATP504 3.4 16.9 1.0
PG A:ATP504 3.4 18.6 1.0
O3B A:ATP504 3.4 17.4 1.0
OE2 A:GLU396 3.6 19.2 1.0
O A:HOH738 3.6 24.2 1.0
O A:HOH615 3.7 44.7 1.0
O A:HOH782 4.1 34.2 1.0
OD2 A:ASP389 4.2 25.0 1.0
O A:HOH760 4.2 23.5 1.0
O2B A:ATP504 4.2 17.8 1.0
O3G A:ATP504 4.2 18.5 1.0
O A:HOH658 4.4 38.0 1.0
O2G A:ATP504 4.5 18.7 1.0
O A:HOH747 4.5 22.7 1.0
CG A:GLU396 4.6 15.7 1.0
O A:HOH843 4.6 41.5 1.0
O3A A:ATP504 4.7 16.4 1.0
O A:HOH704 4.8 24.9 1.0
OG A:SER399 4.9 20.4 1.0

Reference:

T.Yanagisawa, M.Kuratani, E.Seki, N.Hino, K.Sakamoto, S.Yokoyama. Structural Basis For Genetic-Code Expansion with Bulky Lysine Derivatives By An Engineered Pyrrolysyl-Trna Synthetase. Cell Chem Biol V. 26 936 2019.
ISSN: ESSN 2451-9456
PubMed: 31031143
DOI: 10.1016/J.CHEMBIOL.2019.03.008
Page generated: Mon Dec 14 22:19:53 2020

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