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Magnesium in PDB 2iy5: Phenylalanyl-Trna Synthetase From Thermus Thermophilus Complexed with Trna and A Phenylalanyl-Adenylate Analog

Enzymatic activity of Phenylalanyl-Trna Synthetase From Thermus Thermophilus Complexed with Trna and A Phenylalanyl-Adenylate Analog

All present enzymatic activity of Phenylalanyl-Trna Synthetase From Thermus Thermophilus Complexed with Trna and A Phenylalanyl-Adenylate Analog:
6.1.1.20;

Protein crystallography data

The structure of Phenylalanyl-Trna Synthetase From Thermus Thermophilus Complexed with Trna and A Phenylalanyl-Adenylate Analog, PDB code: 2iy5 was solved by N.Moor, O.Kotik-Kogan, D.Tworowski, M.Sukhanova, M.Safro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 9.99 / 3.10
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 173.400, 173.400, 139.400, 90.00, 90.00, 120.00
R / Rfree (%) 23.8 / 29.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Phenylalanyl-Trna Synthetase From Thermus Thermophilus Complexed with Trna and A Phenylalanyl-Adenylate Analog (pdb code 2iy5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Phenylalanyl-Trna Synthetase From Thermus Thermophilus Complexed with Trna and A Phenylalanyl-Adenylate Analog, PDB code: 2iy5:

Magnesium binding site 1 out of 1 in 2iy5

Go back to Magnesium Binding Sites List in 2iy5
Magnesium binding site 1 out of 1 in the Phenylalanyl-Trna Synthetase From Thermus Thermophilus Complexed with Trna and A Phenylalanyl-Adenylate Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Phenylalanyl-Trna Synthetase From Thermus Thermophilus Complexed with Trna and A Phenylalanyl-Adenylate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1781

b:19.8
occ:1.00
 OE1 B:GLU461 2.5 15.1 1.0
O B:ASP452 3.2 20.4 1.0
OD1 B:ASP452 3.4 13.4 1.0
OD2 B:ASP458 3.7 19.8 1.0
CD B:GLU461 3.8 16.7 1.0
ND2 B:ASN163 3.9 27.4 1.0
CB B:ASP452 3.9 14.9 1.0
CG B:ASP452 4.0 12.7 1.0
CD A:GLU262 4.0 35.3 1.0
OE1 A:GLU262 4.1 37.2 1.0
OE2 A:GLU262 4.1 38.3 1.0
CD2 B:LEU453 4.2 8.4 1.0
C B:ASP452 4.3 18.1 1.0
CG B:ASP458 4.3 21.3 1.0
CB B:ASP458 4.5 22.4 1.0
OE2 B:GLU461 4.5 14.8 1.0
CA B:ASP458 4.6 23.1 1.0
CG A:GLU262 4.7 31.8 1.0
O B:ASP458 4.7 21.9 1.0
CA B:ASP452 4.7 17.5 1.0
CG B:GLU461 4.8 15.2 1.0
OE2 B:GLU462 4.8 31.0 1.0
CB B:GLU461 4.9 16.4 1.0

Reference:

N.Moor, O.Kotik-Kogan, D.Tworowski, M.Sukhanova, M.Safro. The Crystal Structure of the Ternary Complex of Phenylalanyl-Trna Synthetase with Trnaphe and A Phenylalanyl-Adenylate Analogue Reveals A Conformational Switch of the Cca End. Biochemistry V. 45 10572 2006.
ISSN: ISSN 0006-2960
PubMed: 16939209
DOI: 10.1021/BI060491L
Page generated: Sun Aug 10 11:42:27 2025

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