Atomistry » Magnesium » PDB 1duh-1e9a » 1e22
Atomistry »
  Magnesium »
    PDB 1duh-1e9a »
      1e22 »

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: Tue Aug 13 02:49:44 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy