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Magnesium in PDB 1j1u: Crystal Structure of Archaeal Tyrosyl-Trna Synthetase Complexed with Trna(Tyr) and L-Tyrosine

Enzymatic activity of Crystal Structure of Archaeal Tyrosyl-Trna Synthetase Complexed with Trna(Tyr) and L-Tyrosine

All present enzymatic activity of Crystal Structure of Archaeal Tyrosyl-Trna Synthetase Complexed with Trna(Tyr) and L-Tyrosine:
6.1.1.1;

Protein crystallography data

The structure of Crystal Structure of Archaeal Tyrosyl-Trna Synthetase Complexed with Trna(Tyr) and L-Tyrosine, PDB code: 1j1u was solved by T.Kobayashi, O.Nureki, R.Ishitani, M.Tukalo, S.Cusack, K.Sakamoto, S.Yokoyama, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.63 / 1.95
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 86.805, 86.805, 156.075, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Archaeal Tyrosyl-Trna Synthetase Complexed with Trna(Tyr) and L-Tyrosine (pdb code 1j1u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Archaeal Tyrosyl-Trna Synthetase Complexed with Trna(Tyr) and L-Tyrosine, PDB code: 1j1u:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1j1u

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Magnesium binding site 1 out of 4 in the Crystal Structure of Archaeal Tyrosyl-Trna Synthetase Complexed with Trna(Tyr) and L-Tyrosine


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 Archaeal Tyrosyl-Trna Synthetase Complexed with Trna(Tyr) and L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1501

b:53.5
occ:1.00
 OP1 B:A509 2.1 45.1 1.0
O B:HOH350 2.2 56.0 1.0
OP2 B:G510 2.2 51.1 1.0
O B:HOH60 2.4 49.9 1.0
OP1 B:U548 2.4 61.7 1.0
P B:A509 3.5 45.5 1.0
P B:G510 3.6 51.0 1.0
P B:U548 3.7 61.1 1.0
C5' B:A509 3.9 46.2 1.0
O B:HOH351 4.1 64.1 1.0
O5' B:A509 4.1 42.5 1.0
OP2 B:U548 4.1 71.3 1.0
OP1 B:G510 4.1 53.6 1.0
C4' B:A509 4.2 43.5 1.0
O B:HOH120 4.4 33.7 1.0
O5' B:U548 4.4 67.9 1.0
O3' B:U508 4.4 44.5 1.0
OP2 B:A509 4.5 46.9 1.0
O3' B:A509 4.5 48.3 1.0
O5' B:G510 4.6 53.6 1.0
O2' B:G547 4.7 64.7 1.0
C4' B:G547 4.8 50.0 1.0
OP2 B:U511 4.9 56.0 1.0
C3' B:A509 4.9 39.0 1.0
C5' B:G510 5.0 57.3 1.0
O3' B:G547 5.0 68.5 1.0

Magnesium binding site 2 out of 4 in 1j1u

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Magnesium binding site 2 out of 4 in the Crystal Structure of Archaeal Tyrosyl-Trna Synthetase Complexed with Trna(Tyr) and L-Tyrosine


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 Archaeal Tyrosyl-Trna Synthetase Complexed with Trna(Tyr) and L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1502

b:42.5
occ:1.00
 O B:HOH61 2.0 38.9 1.0
O B:HOH288 2.1 37.1 1.0
O B:HOH292 2.1 45.5 1.0
O B:HOH289 2.2 49.9 1.0
O B:HOH291 2.2 41.8 1.0
O B:HOH290 2.3 37.0 1.0
O B:HOH155 3.9 57.5 1.0
O B:HOH311 3.9 46.7 1.0
O6 B:G503 4.2 45.2 1.0
O6 B:G504 4.3 38.5 1.0
O6 B:G569 4.3 37.9 1.0
N7 B:G503 4.3 47.8 1.0
O B:HOH207 4.4 45.8 1.0
O B:HOH157 4.5 52.2 1.0
O B:HOH169 4.7 46.1 1.0
C6 B:G503 4.8 50.5 1.0
N4 B:C570 4.8 30.7 1.0
C5 B:G503 4.9 54.7 1.0
N4 B:C502 4.9 43.7 1.0

Magnesium binding site 3 out of 4 in 1j1u

Go back to Magnesium Binding Sites List in 1j1u
Magnesium binding site 3 out of 4 in the Crystal Structure of Archaeal Tyrosyl-Trna Synthetase Complexed with Trna(Tyr) and L-Tyrosine


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 Archaeal Tyrosyl-Trna Synthetase Complexed with Trna(Tyr) and L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1503

b:59.3
occ:1.00
 O B:HOH278 2.0 42.2 1.0
O B:HOH359 2.2 69.3 1.0
O B:HOH18 2.2 43.3 1.0
O B:HOH77 2.3 43.7 1.0
O B:HOH360 2.4 49.9 1.0
O B:HOH361 2.6 62.2 1.0
O B:HOH362 3.7 56.5 1.0
O2' B:A559 4.2 32.2 1.0
O B:HOH59 4.3 40.1 1.0
O4 B:U555 4.4 38.4 1.0
N7 B:G554 4.4 37.4 1.0
O B:HOH163 4.4 55.1 1.0
O6 B:G554 4.5 35.3 1.0
C2' B:A559 4.7 28.0 1.0
OP1 B:A559 4.7 48.0 1.0

Magnesium binding site 4 out of 4 in 1j1u

Go back to Magnesium Binding Sites List in 1j1u
Magnesium binding site 4 out of 4 in the Crystal Structure of Archaeal Tyrosyl-Trna Synthetase Complexed with Trna(Tyr) and L-Tyrosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Archaeal Tyrosyl-Trna Synthetase Complexed with Trna(Tyr) and L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:29.9
occ:1.00
 O A:HOH723 2.1 48.6 1.0
NE2 A:HIS160 2.2 46.4 1.0
O A:HOH722 2.3 32.5 1.0
CD2 A:HIS160 3.1 35.6 1.0
CE1 A:HIS160 3.2 34.6 1.0
CG A:HIS160 4.2 35.4 1.0
ND1 A:HIS160 4.3 41.7 1.0
CG A:ASN117 4.4 36.1 1.0
OD1 A:ASN117 4.5 33.8 1.0
ND2 A:ASN117 4.5 38.3 1.0
CB A:ASN117 4.8 28.7 1.0
O A:HOH559 4.8 40.8 1.0
O A:HOH729 4.9 56.9 1.0
O A:HOH533 5.0 40.3 1.0

Reference:

T.Kobayashi, O.Nureki, R.Ishitani, A.Yaremchuk, M.Tukalo, S.Cusack, K.Sakamoto, S.Yokoyama. Structural Basis For Orthogonal Trna Specificities of Tyrosyl-Trna Synthetases For Genetic Code Expansion Nat.Struct.Biol. V. 10 425 2003.
ISSN: ISSN 1072-8368
PubMed: 12754495
DOI: 10.1038/NSB934
Page generated: Sat Aug 9 22:48:39 2025

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