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Magnesium in PDB 1e22: Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and the Non-Hydrolysable Atp Analogue Amp-Pcp

Enzymatic activity of Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and the Non-Hydrolysable Atp Analogue Amp-Pcp

All present enzymatic activity of Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and the Non-Hydrolysable Atp Analogue Amp-Pcp:
6.1.1.6;

Protein crystallography data

The structure of Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and the Non-Hydrolysable Atp Analogue Amp-Pcp, PDB code: 1e22 was solved by G.Desogus, F.Todone, P.Brick, S.Onesti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.0 / 2.43
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 142.020, 142.020, 175.390, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 22.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and the Non-Hydrolysable Atp Analogue Amp-Pcp (pdb code 1e22). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and the Non-Hydrolysable Atp Analogue Amp-Pcp, PDB code: 1e22:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1e22

Go back to Magnesium Binding Sites List in 1e22
Magnesium binding site 1 out of 3 in the Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and the Non-Hydrolysable Atp Analogue Amp-Pcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and the Non-Hydrolysable Atp Analogue Amp-Pcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg515

b:53.6
occ:1.00
 O1A A:ACP512 2.3 26.8 1.0
OE2 A:GLU414 2.3 31.0 1.0
O1B A:ACP512 2.4 31.6 1.0
OE2 A:GLU421 2.8 26.6 1.0
PA A:ACP512 3.3 27.0 1.0
CD A:GLU414 3.3 27.8 1.0
NH2 A:ARG412 3.5 6.0 1.0
MG A:MG517 3.5 44.1 1.0
O2A A:ACP512 3.6 32.0 1.0
CD A:GLU421 3.6 22.2 1.0
OE1 A:GLU414 3.6 30.7 1.0
OE1 A:GLU421 3.6 22.9 1.0
PB A:ACP512 3.7 26.3 1.0
O3A A:ACP512 3.9 33.7 1.0
O A:HOH2256 4.1 25.3 1.0
ND2 A:ASN424 4.2 12.4 1.0
C1 A:GOL523 4.4 44.7 1.0
O2B A:ACP512 4.6 29.4 1.0
O5' A:ACP512 4.7 25.0 1.0
CG A:GLU414 4.7 21.6 1.0
CG A:ASN424 4.7 17.4 1.0
O1 A:GOL523 4.7 46.3 1.0
CZ A:ARG412 4.8 12.5 1.0
C2 A:GOL523 4.8 47.4 1.0
CB A:ASN424 5.0 14.4 1.0
CG A:GLU421 5.0 20.2 1.0

Magnesium binding site 2 out of 3 in 1e22

Go back to Magnesium Binding Sites List in 1e22
Magnesium binding site 2 out of 3 in the Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and the Non-Hydrolysable Atp Analogue Amp-Pcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and the Non-Hydrolysable Atp Analogue Amp-Pcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg516

b:61.1
occ:1.00
 O2B A:ACP512 2.5 29.4 1.0
O1G A:ACP512 2.8 23.3 1.0
O A:HOH2303 2.8 52.5 1.0
O A:HOH2172 2.9 41.7 1.0
OE2 A:GLU264 3.5 45.6 1.0
PB A:ACP512 3.7 26.3 1.0
OE1 A:GLU264 3.8 45.4 1.0
NE2 A:HIS270 3.9 30.1 1.0
CD A:GLU264 4.0 46.5 1.0
PG A:ACP512 4.0 26.9 1.0
C3B A:ACP512 4.0 31.1 1.0
CD2 A:HIS270 4.4 30.0 1.0
N7 A:ACP512 4.6 19.6 1.0
O3A A:ACP512 4.7 33.7 1.0
O3G A:ACP512 4.8 25.4 1.0
O1B A:ACP512 4.8 31.6 1.0
CE1 A:HIS270 4.8 30.4 1.0

Magnesium binding site 3 out of 3 in 1e22

Go back to Magnesium Binding Sites List in 1e22
Magnesium binding site 3 out of 3 in the Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and the Non-Hydrolysable Atp Analogue Amp-Pcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Lysyl-Trna Synthetase (Lysu) Hexagonal Form Complexed with Lysine and the Non-Hydrolysable Atp Analogue Amp-Pcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg517

b:44.1
occ:1.00
 OE1 A:GLU421 2.3 22.9 1.0
O3G A:ACP512 2.4 25.4 1.0
O1B A:ACP512 2.4 31.6 1.0
CD A:GLU421 3.4 22.2 1.0
MG A:MG515 3.5 53.6 1.0
PB A:ACP512 3.6 26.3 1.0
PG A:ACP512 3.7 26.9 1.0
OE2 A:GLU421 3.9 26.6 1.0
OE2 A:GLU380 4.0 48.6 1.0
C3B A:ACP512 4.1 31.1 1.0
OD2 A:ASP376 4.1 38.4 1.0
OD1 A:ASP376 4.1 36.0 1.0
OE1 A:GLU414 4.1 30.7 1.0
O2B A:ACP512 4.2 29.4 1.0
O1G A:ACP512 4.4 23.3 1.0
CG A:ASP376 4.5 33.4 1.0
CG A:GLU421 4.7 20.2 1.0
OE2 A:GLU414 4.7 31.0 1.0
O2G A:ACP512 4.8 27.2 1.0
CD A:GLU414 4.8 27.8 1.0
O1A A:ACP512 4.9 26.8 1.0
O3A A:ACP512 4.9 33.7 1.0
CB A:GLU421 4.9 17.9 1.0
O A:HOH2230 4.9 44.3 1.0
CD A:GLU380 5.0 44.7 1.0

Reference:

G.Desogus, F.Todone, P.Brick, S.Onesti. Active Site of Lysyl-Trna Synthetase: Structural Studies of the Adenylation Reaction Biochemistry V. 39 8418 2000.
ISSN: ISSN 0006-2960
PubMed: 10913247
DOI: 10.1021/BI0006722
Page generated: Mon Dec 14 05:51:13 2020

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