Magnesium in PDB 6ab2: Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Oclzlys

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

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

Protein crystallography data

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Oclzlys, PDB code: 6ab2 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) 35.07 / 1.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.419, 43.887, 72.386, 90.00, 119.45, 90.00
R / Rfree (%) 17 / 19.8

Other elements in 6ab2:

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

Potassium (K) 2 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Oclzlys (pdb code 6ab2). 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 Oclzlys, PDB code: 6ab2:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6ab2

Go back to Magnesium Binding Sites List in 6ab2
Magnesium binding site 1 out of 3 in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Oclzlys


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 Oclzlys within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:36.4
occ:1.00
O2B A:ATP504 1.9 42.9 1.0
O A:HOH647 2.0 24.6 1.0
O A:HOH690 2.1 47.3 1.0
O2G A:ATP504 2.1 47.9 1.0
O A:HOH649 2.2 33.0 1.0
O A:HOH747 2.5 33.8 1.0
PB A:ATP504 3.1 39.0 1.0
PG A:ATP504 3.2 48.4 1.0
O3B A:ATP504 3.3 46.1 1.0
O1G A:ATP504 3.8 53.5 1.0
NE2 A:HIS338 4.0 23.7 1.0
NH1 A:ARG330 4.0 21.1 1.0
OE2 A:GLU332 4.1 25.8 1.0
O3A A:ATP504 4.2 38.7 1.0
O1B A:ATP504 4.2 41.6 1.0
OE1 A:GLU332 4.3 39.2 1.0
CD2 A:HIS338 4.4 23.2 1.0
O3G A:ATP504 4.5 50.5 1.0
N7 A:ATP504 4.6 17.8 1.0
CD A:GLU332 4.6 47.6 1.0

Magnesium binding site 2 out of 3 in 6ab2

Go back to Magnesium Binding Sites List in 6ab2
Magnesium binding site 2 out of 3 in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Oclzlys


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 Oclzlys within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:36.8
occ:1.00
O1B A:ATP504 2.0 41.6 1.0
O1A A:ATP504 2.0 32.3 1.0
OG A:SER399 2.1 29.4 1.0
O A:HOH722 2.1 55.3 1.0
O A:HOH693 2.2 36.5 1.0
OE2 A:GLU396 2.3 25.1 1.0
MG A:MG503 3.1 37.8 1.0
CB A:SER399 3.1 24.2 1.0
CD A:GLU396 3.2 27.4 1.0
PA A:ATP504 3.3 30.7 1.0
PB A:ATP504 3.3 39.0 1.0
OE1 A:GLU396 3.5 32.5 1.0
O3A A:ATP504 3.5 38.7 1.0
O3B A:ATP504 4.1 46.1 1.0
O A:HOH684 4.2 41.1 1.0
CA A:SER399 4.3 17.6 1.0
O5' A:ATP504 4.3 23.9 1.0
O2A A:ATP504 4.4 36.8 1.0
O3' A:ATP504 4.4 19.1 1.0
OD1 A:ASP389 4.4 29.9 1.0
O2B A:ATP504 4.5 42.9 1.0
N A:SER399 4.5 17.1 1.0
C5' A:ATP504 4.5 23.8 1.0
OD2 A:ASP389 4.6 63.8 1.0
CG A:GLU396 4.6 21.1 1.0
O1G A:ATP504 4.6 53.5 1.0
C3' A:ATP504 4.7 17.8 1.0
CG A:ASP389 4.8 40.1 1.0

Magnesium binding site 3 out of 3 in 6ab2

Go back to Magnesium Binding Sites List in 6ab2
Magnesium binding site 3 out of 3 in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Oclzlys


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 Oclzlys within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:37.8
occ:1.00
O1G A:ATP504 2.0 53.5 1.0
O A:HOH693 2.1 36.5 1.0
O1B A:ATP504 2.2 41.6 1.0
OE1 A:GLU396 2.3 32.5 1.0
MG A:MG502 3.1 36.8 1.0
CD A:GLU396 3.2 27.4 1.0
PB A:ATP504 3.3 39.0 1.0
PG A:ATP504 3.3 48.4 1.0
O3B A:ATP504 3.4 46.1 1.0
OE2 A:GLU396 3.4 25.1 1.0
O A:HOH772 3.7 42.1 1.0
O2B A:ATP504 4.0 42.9 1.0
O A:HOH686 4.1 37.8 1.0
O A:HOH722 4.1 55.3 1.0
O3G A:ATP504 4.2 50.5 1.0
O A:HOH690 4.3 47.3 1.0
OD2 A:ASP389 4.3 63.8 1.0
O2G A:ATP504 4.3 47.9 1.0
CG A:GLU396 4.6 21.1 1.0
O3A A:ATP504 4.6 38.7 1.0
OG A:SER399 4.7 29.4 1.0
O1A A:ATP504 4.8 32.3 1.0
O A:HOH684 4.9 41.1 1.0
CB A:GLU396 5.0 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 22:19:51 2020

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