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Magnesium in PDB 2xti: Asparaginyl-Trna Synthetase From Brugia Malayi Complexed with Atp:Mg and L-Asp-Beta-Noh Adenylate:Ppi:Mg

Enzymatic activity of Asparaginyl-Trna Synthetase From Brugia Malayi Complexed with Atp:Mg and L-Asp-Beta-Noh Adenylate:Ppi:Mg

All present enzymatic activity of Asparaginyl-Trna Synthetase From Brugia Malayi Complexed with Atp:Mg and L-Asp-Beta-Noh Adenylate:Ppi:Mg:
6.1.1.4;

Protein crystallography data

The structure of Asparaginyl-Trna Synthetase From Brugia Malayi Complexed with Atp:Mg and L-Asp-Beta-Noh Adenylate:Ppi:Mg, PDB code: 2xti was solved by T.Crepin, M.Haertlein, M.Kron, S.Cusack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.22 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.920, 106.390, 161.420, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 29.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Asparaginyl-Trna Synthetase From Brugia Malayi Complexed with Atp:Mg and L-Asp-Beta-Noh Adenylate:Ppi:Mg (pdb code 2xti). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Asparaginyl-Trna Synthetase From Brugia Malayi Complexed with Atp:Mg and L-Asp-Beta-Noh Adenylate:Ppi:Mg, PDB code: 2xti:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2xti

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Magnesium binding site 1 out of 6 in the Asparaginyl-Trna Synthetase From Brugia Malayi Complexed with Atp:Mg and L-Asp-Beta-Noh Adenylate:Ppi:Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Asparaginyl-Trna Synthetase From Brugia Malayi Complexed with Atp:Mg and L-Asp-Beta-Noh Adenylate:Ppi:Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1551

b:25.7
occ:1.00
 O1P A:NB81549 1.8 24.8 1.0
O A:HOH2132 1.9 15.5 1.0
OE2 A:GLU471 2.1 23.2 1.0
O3 A:POP1550 2.4 37.8 1.0
O A:HOH2135 2.5 16.5 1.0
CD A:GLU471 2.9 24.3 1.0
OE1 A:GLU471 3.1 30.7 1.0
O2 A:POP1550 3.1 36.8 1.0
P1 A:POP1550 3.2 39.5 1.0
P A:NB81549 3.3 23.7 1.0
O3P A:NB81549 3.9 29.0 1.0
O A:HOH2053 3.9 22.5 1.0
O2P A:NB81549 4.0 24.0 1.0
O A:POP1550 4.1 37.1 1.0
O A:HOH2113 4.2 14.8 1.0
OD1 A:ASP463 4.2 26.3 1.0
O3' A:NB81549 4.3 16.9 1.0
CG A:GLU471 4.3 21.6 1.0
OD2 A:ASP463 4.3 29.4 1.0
CA A:GLY474 4.3 15.0 1.0
O5' A:NB81549 4.4 20.9 1.0
C3' A:NB81549 4.4 16.8 1.0
O1 A:POP1550 4.4 39.1 1.0
NZ A:LYS445 4.4 29.4 1.0
CG A:ASP463 4.5 23.2 1.0
C5' A:NB81549 4.7 18.5 1.0
O A:HOH2112 4.7 41.1 1.0

Magnesium binding site 2 out of 6 in 2xti

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Magnesium binding site 2 out of 6 in the Asparaginyl-Trna Synthetase From Brugia Malayi Complexed with Atp:Mg and L-Asp-Beta-Noh Adenylate:Ppi:Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Asparaginyl-Trna Synthetase From Brugia Malayi Complexed with Atp:Mg and L-Asp-Beta-Noh Adenylate:Ppi:Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1552

b:34.6
occ:1.00
 O A:HOH2136 1.9 31.6 1.0
O1 A:POP1550 2.0 39.1 1.0
O6 A:POP1550 2.0 36.8 1.0
O A:HOH2133 2.2 19.9 1.0
P1 A:POP1550 2.9 39.5 1.0
P2 A:POP1550 3.0 36.7 1.0
O A:POP1550 3.1 37.1 1.0
O2 A:POP1550 3.2 36.8 1.0
O4 A:POP1550 3.6 37.1 1.0
NE2 A:HIS330 4.2 19.3 1.0
O3 A:POP1550 4.3 37.8 1.0
O5 A:POP1550 4.4 35.6 1.0
O A:HOH2134 4.5 21.0 1.0
O A:HOH2091 4.7 22.3 1.0
O A:HOH2135 4.7 16.5 1.0
MG A:MG1553 4.9 24.8 1.0
OE2 A:GLU323 5.0 24.1 1.0
CD2 A:HIS330 5.0 22.3 1.0

Magnesium binding site 3 out of 6 in 2xti

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Magnesium binding site 3 out of 6 in the Asparaginyl-Trna Synthetase From Brugia Malayi Complexed with Atp:Mg and L-Asp-Beta-Noh Adenylate:Ppi:Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Asparaginyl-Trna Synthetase From Brugia Malayi Complexed with Atp:Mg and L-Asp-Beta-Noh Adenylate:Ppi:Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1553

b:24.8
occ:1.00
 O A:HOH2112 1.9 41.1 1.0
O4 A:POP1550 2.3 37.1 1.0
O A:HOH2097 2.4 18.7 1.0
O A:HOH2091 2.7 22.3 1.0
O3 A:POP1550 3.3 37.8 1.0
O1 A:POP1550 3.4 39.1 1.0
P2 A:POP1550 3.7 36.7 1.0
P1 A:POP1550 3.8 39.5 1.0
O A:HOH2134 3.8 21.0 1.0
O A:ILE419 3.9 23.8 1.0
O A:POP1550 3.9 37.1 1.0
OE1 A:GLU471 4.2 30.7 1.0
OE1 A:GLU424 4.2 20.0 1.0
OD2 A:ASP418 4.2 31.7 1.0
NH2 A:ARG329 4.2 21.6 1.0
OD1 A:ASP418 4.3 30.3 1.0
O A:HOH2109 4.5 21.6 1.0
O6 A:POP1550 4.6 36.8 1.0
CG A:ASP418 4.7 30.3 1.0
O5 A:POP1550 4.7 35.6 1.0
CA A:ALA420 4.8 25.2 1.0
O A:HOH2133 4.8 19.9 1.0
MG A:MG1552 4.9 34.6 1.0
C A:ILE419 4.9 25.8 1.0
N A:GLU421 5.0 23.6 1.0
CD A:GLU424 5.0 18.9 1.0
CD A:GLU471 5.0 24.3 1.0

Magnesium binding site 4 out of 6 in 2xti

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Magnesium binding site 4 out of 6 in the Asparaginyl-Trna Synthetase From Brugia Malayi Complexed with Atp:Mg and L-Asp-Beta-Noh Adenylate:Ppi:Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Asparaginyl-Trna Synthetase From Brugia Malayi Complexed with Atp:Mg and L-Asp-Beta-Noh Adenylate:Ppi:Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1550

b:37.4
occ:1.00
 O2A B:ATP1549 2.3 30.4 1.0
O1B B:ATP1549 2.3 33.2 1.0
OE2 B:GLU471 2.7 36.8 1.0
PA B:ATP1549 3.4 29.8 1.0
MG B:MG1552 3.4 41.0 1.0
O B:HOH2090 3.6 28.8 1.0
PB B:ATP1549 3.6 32.9 1.0
CD B:GLU471 3.6 36.0 1.0
OE1 B:GLU471 3.8 38.1 1.0
O3A B:ATP1549 3.9 32.5 1.0
O1A B:ATP1549 3.9 30.0 1.0
OD2 B:ASP463 4.1 38.2 1.0
NZ B:LYS445 4.2 38.7 1.0
OD1 B:ASP463 4.2 36.6 1.0
CA B:GLY474 4.3 32.9 1.0
O2B B:ATP1549 4.5 34.1 1.0
CG B:ASP463 4.5 35.9 1.0
O5' B:ATP1549 4.7 26.9 1.0
O3B B:ATP1549 4.8 32.7 1.0
C B:GLY474 4.8 32.4 1.0
O B:HOH2084 4.9 37.5 1.0
O2G B:ATP1549 4.9 33.9 1.0
O B:GLY474 5.0 31.5 1.0
CG B:GLU471 5.0 34.6 1.0

Magnesium binding site 5 out of 6 in 2xti

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Magnesium binding site 5 out of 6 in the Asparaginyl-Trna Synthetase From Brugia Malayi Complexed with Atp:Mg and L-Asp-Beta-Noh Adenylate:Ppi:Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Asparaginyl-Trna Synthetase From Brugia Malayi Complexed with Atp:Mg and L-Asp-Beta-Noh Adenylate:Ppi:Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1551

b:34.4
occ:1.00
 O1G B:ATP1549 2.0 28.6 1.0
O B:HOH2110 2.0 51.8 1.0
O B:HOH2109 2.1 31.6 1.0
O2B B:ATP1549 2.6 34.1 1.0
PG B:ATP1549 3.3 31.9 1.0
O3B B:ATP1549 3.5 32.7 1.0
PB B:ATP1549 3.7 32.9 1.0
NE2 B:HIS330 3.7 36.5 1.0
O2G B:ATP1549 4.0 33.9 1.0
OE2 B:GLU323 4.0 37.8 1.0
OE1 B:GLU323 4.0 40.8 1.0
CD2 B:HIS330 4.2 35.4 1.0
CD B:GLU323 4.4 39.0 1.0
O3A B:ATP1549 4.4 32.5 1.0
O3G B:ATP1549 4.5 26.6 1.0
CE1 B:HIS330 4.8 36.4 1.0
N7 B:ATP1549 4.9 23.1 1.0
NH1 B:ARG321 4.9 31.8 1.0
O1B B:ATP1549 5.0 33.2 1.0

Magnesium binding site 6 out of 6 in 2xti

Go back to Magnesium Binding Sites List in 2xti
Magnesium binding site 6 out of 6 in the Asparaginyl-Trna Synthetase From Brugia Malayi Complexed with Atp:Mg and L-Asp-Beta-Noh Adenylate:Ppi:Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Asparaginyl-Trna Synthetase From Brugia Malayi Complexed with Atp:Mg and L-Asp-Beta-Noh Adenylate:Ppi:Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1552

b:41.0
occ:1.00
 OE1 B:GLU471 2.1 38.1 1.0
O2G B:ATP1549 2.4 33.9 1.0
O1B B:ATP1549 2.4 33.2 1.0
CD B:GLU471 3.0 36.0 1.0
OE2 B:GLU471 3.4 36.8 1.0
MG B:MG1550 3.4 37.4 1.0
PB B:ATP1549 3.6 32.9 1.0
PG B:ATP1549 3.7 31.9 1.0
OD2 B:ASP463 3.9 38.2 1.0
O3B B:ATP1549 3.9 32.7 1.0
O2B B:ATP1549 4.2 34.1 1.0
CG B:GLU471 4.3 34.6 1.0
O3G B:ATP1549 4.4 26.6 1.0
OE2 B:GLU424 4.4 40.6 1.0
CB B:GLU471 4.6 35.2 1.0
O B:HOH2109 4.7 31.6 1.0
O2A B:ATP1549 4.8 30.4 1.0
O1G B:ATP1549 4.8 28.6 1.0
O3A B:ATP1549 4.9 32.5 1.0
CG B:ASP463 5.0 35.9 1.0

Reference:

T.Crepin, F.Peterson, M.Haertlein, D.Jensen, C.Wang, S.Cusack, M.Kron. A Hybrid Structural Model of the Complete Brugia Malayi Cytoplasmic Asparaginyl-Trna Synthetase. J.Mol.Biol. V. 405 1056 2011.
ISSN: ISSN 0022-2836
PubMed: 21134380
DOI: 10.1016/J.JMB.2010.11.049
Page generated: Wed Aug 14 07:17:47 2024

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