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Magnesium in PDB 4cs3: Catalytic Domain of Pyrrolysyl-Trna Synthetase Mutant Y306A, Y384F in Complex with An Adenylated Furan-Bearing Noncanonical Amino Acid and Pyrophosphate

Enzymatic activity of Catalytic Domain of Pyrrolysyl-Trna Synthetase Mutant Y306A, Y384F in Complex with An Adenylated Furan-Bearing Noncanonical Amino Acid and Pyrophosphate

All present enzymatic activity of Catalytic Domain of Pyrrolysyl-Trna Synthetase Mutant Y306A, Y384F in Complex with An Adenylated Furan-Bearing Noncanonical Amino Acid and Pyrophosphate:
6.1.1.26;

Protein crystallography data

The structure of Catalytic Domain of Pyrrolysyl-Trna Synthetase Mutant Y306A, Y384F in Complex with An Adenylated Furan-Bearing Noncanonical Amino Acid and Pyrophosphate, PDB code: 4cs3 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) 36.489 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.335, 44.345, 64.165, 90.00, 99.85, 90.00
R / Rfree (%) 15.5 / 18.49

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Catalytic Domain of Pyrrolysyl-Trna Synthetase Mutant Y306A, Y384F in Complex with An Adenylated Furan-Bearing Noncanonical Amino Acid and Pyrophosphate (pdb code 4cs3). 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 An Adenylated Furan-Bearing Noncanonical Amino Acid and Pyrophosphate, PDB code: 4cs3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4cs3

Go back to Magnesium Binding Sites List in 4cs3
Magnesium binding site 1 out of 2 in the Catalytic Domain of Pyrrolysyl-Trna Synthetase Mutant Y306A, Y384F in Complex with An Adenylated Furan-Bearing Noncanonical Amino Acid and Pyrophosphate


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 An Adenylated Furan-Bearing Noncanonical Amino Acid and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1463

b:43.6
occ:1.00
 O A:HOH2140 2.1 32.5 1.0
O A:HOH2101 2.1 41.9 1.0
O A:HOH2100 2.1 40.6 1.0
O6 A:POP1462 2.2 51.3 0.8
O1 A:POP1462 2.4 0.3 0.8
HH11 A:ARG330 3.4 30.1 1.0
HE2 A:HIS338 3.5 37.6 1.0
P2 A:POP1462 3.5 47.3 0.8
P1 A:POP1462 3.6 0.5 0.8
O A:POP1462 3.9 51.5 0.8
HE22 A:GLN287 4.0 65.3 1.0
HD2 A:HIS338 4.0 33.8 1.0
OE2 A:GLU332 4.1 33.9 1.0
NH1 A:ARG330 4.1 23.5 1.0
O3 A:POP1462 4.1 0.8 0.8
HH12 A:ARG330 4.1 30.1 1.0
NE2 A:HIS338 4.1 31.3 1.0
O4 A:POP1462 4.2 53.6 0.8
CD2 A:HIS338 4.4 28.2 1.0
OE1 A:GLN287 4.5 57.8 1.0
OE1 A:GLU332 4.5 54.7 1.0
O5 A:POP1462 4.6 41.8 0.8
HD3 A:ARG330 4.7 28.5 1.0
NE2 A:GLN287 4.7 54.4 1.0
CD A:GLU332 4.7 44.6 1.0
O2 A:POP1462 4.8 0.1 0.8
N7 A:AMP1459 4.8 18.9 0.9
HD2 A:ARG330 4.8 28.5 1.0

Magnesium binding site 2 out of 2 in 4cs3

Go back to Magnesium Binding Sites List in 4cs3
Magnesium binding site 2 out of 2 in the Catalytic Domain of Pyrrolysyl-Trna Synthetase Mutant Y306A, Y384F in Complex with An Adenylated Furan-Bearing Noncanonical Amino Acid and Pyrophosphate


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 An Adenylated Furan-Bearing Noncanonical Amino Acid and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1464

b:23.3
occ:1.00
 O5 A:POP1462 1.9 41.8 0.8
HG A:SER399 2.0 33.7 1.0
O A:HOH2209 2.1 45.4 1.0
O A:HOH2202 2.1 42.5 1.0
O1P A:AMP1459 2.3 27.4 0.9
OG A:SER399 2.3 28.1 1.0
OE2 A:GLU396 2.3 28.6 1.0
OE1 A:GLU396 2.6 36.2 1.0
CD A:GLU396 2.8 31.7 1.0
O A:HOH2208 3.1 43.7 1.0
P2 A:POP1462 3.2 47.3 0.8
HB2 A:SER399 3.3 30.6 1.0
CB A:SER399 3.4 25.5 1.0
O4 A:POP1462 3.6 53.6 0.8
P A:AMP1459 3.7 25.9 0.9
O A:HOH2195 3.9 36.3 1.0
HB3 A:SER399 3.9 30.6 1.0
O A:POP1462 3.9 51.5 0.8
O2P A:AMP1459 4.2 24.5 0.9
H3' A:AMP1459 4.2 26.6 0.9
OD1 A:ASP389 4.3 34.8 1.0
CG A:GLU396 4.3 24.1 1.0
O6 A:POP1462 4.4 51.3 0.8
O3' A:AMP1459 4.4 23.6 0.9
O3P A:AMP1459 4.4 26.7 0.9
H5'1 A:AMP1459 4.5 27.6 0.9
CA A:SER399 4.5 22.3 1.0
OD2 A:ASP389 4.6 44.6 1.0
HG2 A:GLU396 4.6 28.9 1.0
N A:SER399 4.6 22.6 1.0
H A:SER399 4.7 27.1 1.0
CG A:ASP389 4.7 33.7 1.0
O3 A:POP1462 4.7 0.8 0.8
HA A:SER399 4.7 26.8 1.0
HG3 A:GLU396 4.7 28.9 1.0
O5' A:AMP1459 4.8 25.3 0.9
C3' A:AMP1459 4.8 22.1 0.9
HO3' A:AMP1459 4.9 28.3 0.9

Reference:

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
Page generated: Mon Aug 11 07:18:46 2025

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