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Magnesium in PDB 8h53: Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp

Enzymatic activity of Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp

All present enzymatic activity of Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp:
6.1.1.22;

Protein crystallography data

The structure of Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp, PDB code: 8h53 was solved by J.S.Park, B.W.Han, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.88 / 2.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 115.423, 125.842, 161.134, 90, 90, 90
R / Rfree (%) 20.3 / 23.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp (pdb code 8h53). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp, PDB code: 8h53:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8h53

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Magnesium binding site 1 out of 8 in the Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg612

b:48.6
occ:1.00
 O A:HOH714 2.0 41.6 1.0
O A:HOH716 2.1 43.8 1.0
O3 A:2PN602 2.1 54.8 1.0
O A:HOH783 2.2 36.0 1.0
O A:HOH753 2.3 32.8 1.0
O6 A:2PN602 2.4 49.9 1.0
O A:HOH738 3.4 48.5 1.0
P1 A:2PN602 3.4 55.5 1.0
P2 A:2PN602 3.5 68.8 1.0
N1 A:2PN602 3.6 49.3 1.0
OE1 A:GLU471 3.9 50.8 1.0
NH2 A:ARG330 4.0 40.0 1.0
OE1 A:GLU424 4.1 36.8 1.0
O A:HOH884 4.2 42.8 1.0
OD2 A:ASP418 4.2 42.0 1.0
O2 A:2PN602 4.3 53.3 1.0
O A:ILE419 4.3 31.4 1.0
O1 A:2PN602 4.3 51.6 1.0
O4 A:2PN602 4.4 67.3 1.0
OD1 A:ASP418 4.5 40.4 1.0
O A:HOH870 4.5 34.4 1.0
O5 A:2PN602 4.5 59.1 1.0
CG A:ASP418 4.8 39.1 1.0
O A:HOH756 4.9 34.1 1.0

Magnesium binding site 2 out of 8 in 8h53

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Magnesium binding site 2 out of 8 in the Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg613

b:52.4
occ:1.00
 O1P A:4AD601 2.0 44.7 1.0
O5 A:2PN602 2.0 59.1 1.0
O A:HOH786 2.1 33.6 1.0
OE2 A:GLU471 2.1 36.1 1.0
CD A:GLU471 2.9 39.3 1.0
O A:HOH738 2.9 48.5 1.0
OE1 A:GLU471 2.9 50.8 1.0
P2 A:2PN602 3.3 68.8 1.0
P A:4AD601 3.4 37.9 1.0
O6 A:2PN602 3.7 49.9 1.0
O2P A:4AD601 3.9 39.2 1.0
N1 A:2PN602 3.9 49.3 1.0
O3' A:4AD601 4.1 31.5 1.0
C3' A:4AD601 4.2 36.0 1.0
O A:HOH901 4.2 28.2 1.0
CG A:GLU471 4.3 35.1 1.0
OD1 A:ASP463 4.3 34.6 1.0
O3P A:4AD601 4.3 36.8 1.0
O5' A:4AD601 4.4 41.9 1.0
O4 A:2PN602 4.4 67.3 1.0
CA A:GLY474 4.5 31.3 1.0
O A:HOH714 4.6 41.6 1.0
OD2 A:ASP463 4.6 43.5 1.0
C5' A:4AD601 4.7 30.5 1.0
CG A:ASP463 4.8 35.3 1.0
O A:HOH776 5.0 48.1 1.0

Magnesium binding site 3 out of 8 in 8h53

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Magnesium binding site 3 out of 8 in the Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg609

b:49.2
occ:1.00
 O B:HOH709 2.0 45.5 1.0
O B:HOH703 2.1 40.5 1.0
O B:HOH757 2.2 35.5 1.0
O B:HOH735 2.3 29.1 1.0
O3 B:2PN602 2.3 56.4 1.0
O6 B:2PN602 2.4 51.0 1.0
O B:HOH740 3.5 45.9 1.0
P1 B:2PN602 3.6 51.7 1.0
P2 B:2PN602 3.6 65.3 1.0
N1 B:2PN602 3.8 51.2 1.0
OE1 B:GLU424 4.0 37.6 1.0
OE1 B:GLU471 4.0 53.4 1.0
OD2 B:ASP418 4.1 43.5 1.0
O B:HOH794 4.1 44.2 1.0
O B:HOH876 4.1 35.8 1.0
O B:ILE419 4.1 35.5 1.0
NH2 B:ARG330 4.2 42.0 1.0
OD1 B:ASP418 4.2 40.5 1.0
O2 B:2PN602 4.5 52.4 1.0
O1 B:2PN602 4.5 52.5 1.0
O4 B:2PN602 4.6 62.1 1.0
CG B:ASP418 4.6 36.4 1.0
O5 B:2PN602 4.6 59.8 1.0
O B:HOH724 4.8 38.1 1.0
CA B:PRO420 4.9 36.2 1.0
CD B:GLU424 5.0 38.4 1.0
O B:HOH913 5.0 49.7 1.0

Magnesium binding site 4 out of 8 in 8h53

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Magnesium binding site 4 out of 8 in the Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg610

b:48.1
occ:1.00
 O2P B:4AD601 1.9 41.2 1.0
O5 B:2PN602 2.0 59.8 1.0
OE2 B:GLU471 2.1 34.0 1.0
O B:HOH759 2.1 35.3 1.0
CD B:GLU471 2.8 40.9 1.0
OE1 B:GLU471 2.8 53.4 1.0
O B:HOH740 3.0 45.9 1.0
P2 B:2PN602 3.3 65.3 1.0
P B:4AD601 3.4 34.0 1.0
N1 B:2PN602 3.7 51.2 1.0
O3' B:4AD601 3.9 31.1 1.0
O6 B:2PN602 3.9 51.0 1.0
C3' B:4AD601 4.1 34.9 1.0
O1P B:4AD601 4.1 38.4 1.0
O5' B:4AD601 4.2 39.4 1.0
CG B:GLU471 4.2 32.7 1.0
O3P B:4AD601 4.2 38.2 1.0
OD1 B:ASP463 4.2 34.3 1.0
CA B:GLY474 4.4 28.6 1.0
O4 B:2PN602 4.4 62.1 1.0
O B:HOH885 4.5 40.2 1.0
O B:HOH893 4.5 26.6 1.0
C5' B:4AD601 4.6 30.3 1.0
OD2 B:ASP463 4.6 41.8 1.0
O B:HOH703 4.6 40.5 1.0
CG B:ASP463 4.7 36.2 1.0
N B:GLY474 4.9 30.4 1.0
C4' B:4AD601 4.9 32.9 1.0

Magnesium binding site 5 out of 8 in 8h53

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Magnesium binding site 5 out of 8 in the Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg609

b:53.2
occ:1.00
 O2 C:2PN602 1.9 63.6 1.0
O C:HOH781 2.0 52.1 1.0
O C:HOH704 2.1 51.2 1.0
O C:HOH710 2.3 49.8 1.0
O C:HOH766 2.4 50.1 1.0
O4 C:2PN602 2.4 61.4 1.0
P1 C:2PN602 3.3 65.5 1.0
P2 C:2PN602 3.6 61.1 1.0
OE1 C:GLU424 3.8 53.0 1.0
N1 C:2PN602 3.9 57.1 1.0
NH2 C:ARG330 4.0 54.0 1.0
OE1 C:GLU471 4.0 57.8 1.0
O C:ILE419 4.0 48.3 1.0
O3 C:2PN602 4.2 61.6 1.0
O1 C:2PN602 4.2 59.3 1.0
O5 C:2PN602 4.3 48.5 1.0
O C:HOH825 4.3 48.0 1.0
OD1 C:ASP418 4.4 54.9 1.0
OD2 C:ASP418 4.5 54.3 1.0
O C:HOH820 4.7 42.8 1.0
O6 C:2PN602 4.8 57.6 1.0
CD C:GLU424 4.8 50.2 1.0
CA C:PRO420 4.8 52.5 1.0
C C:PRO420 4.9 54.5 1.0
CG C:ASP418 4.9 56.3 1.0

Magnesium binding site 6 out of 8 in 8h53

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Magnesium binding site 6 out of 8 in the Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg610

b:49.5
occ:1.00
 O2P C:4AD601 1.9 37.1 1.0
O1 C:2PN602 1.9 59.3 1.0
OE2 C:GLU471 2.1 43.3 1.0
O C:HOH742 2.1 37.8 1.0
CD C:GLU471 2.8 46.5 1.0
OE1 C:GLU471 2.8 57.8 1.0
P1 C:2PN602 3.2 65.5 1.0
P C:4AD601 3.3 34.7 1.0
N1 C:2PN602 3.6 57.1 1.0
O1P C:4AD601 3.8 30.8 1.0
O2 C:2PN602 4.0 63.6 1.0
O3' C:4AD601 4.0 33.7 1.0
O5' C:4AD601 4.1 36.4 1.0
C3' C:4AD601 4.2 35.1 1.0
CG C:GLU471 4.2 39.8 1.0
O3 C:2PN602 4.3 61.6 1.0
O3P C:4AD601 4.3 31.9 1.0
O C:HOH858 4.4 33.5 1.0
OD1 C:ASP463 4.5 47.3 1.0
OD2 C:ASP463 4.6 47.9 1.0
C5' C:4AD601 4.6 28.5 1.0
O C:HOH704 4.7 51.2 1.0
CA C:GLY474 4.7 36.0 1.0
CG C:ASP463 4.8 45.1 1.0
NZ C:LYS445 4.9 51.4 1.0

Magnesium binding site 7 out of 8 in 8h53

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Magnesium binding site 7 out of 8 in the Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg608

b:56.6
occ:1.00
 O6 D:2PN602 1.9 67.4 1.0
O D:HOH775 2.1 52.2 1.0
O D:HOH704 2.2 55.3 1.0
O D:HOH742 2.3 52.9 1.0
O D:HOH748 2.3 54.0 1.0
O1 D:2PN602 2.8 64.5 1.0
P2 D:2PN602 3.3 64.8 1.0
O D:ILE419 3.8 61.0 1.0
O4 D:2PN602 3.9 62.9 1.0
P1 D:2PN602 4.0 64.4 1.0
OD1 D:ASP418 4.0 61.6 1.0
OE1 D:GLU424 4.0 51.2 1.0
N1 D:2PN602 4.0 61.1 1.0
O D:HOH815 4.1 54.2 1.0
NH2 D:ARG330 4.3 57.5 1.0
OD2 D:ASP418 4.3 64.5 1.0
O5 D:2PN602 4.4 68.4 1.0
OE1 D:GLU471 4.6 58.0 1.0
CG D:ASP418 4.6 61.5 1.0
CA D:PRO420 4.9 62.6 1.0
O2 D:2PN602 4.9 55.5 1.0
C D:PRO420 4.9 60.7 1.0
C D:ILE419 4.9 59.9 1.0
O3 D:2PN602 5.0 59.4 1.0
CD D:GLU424 5.0 58.9 1.0

Magnesium binding site 8 out of 8 in 8h53

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Magnesium binding site 8 out of 8 in the Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg609

b:52.0
occ:1.00
 O2P D:4AD601 1.9 43.5 1.0
O4 D:2PN602 2.1 62.9 1.0
O D:HOH739 2.1 43.6 1.0
OE2 D:GLU471 2.5 50.7 1.0
O D:HOH709 2.6 49.5 1.0
OE1 D:GLU471 2.7 58.0 1.0
CD D:GLU471 3.0 52.2 1.0
P D:4AD601 3.3 44.2 1.0
P2 D:2PN602 3.3 64.8 1.0
N1 D:2PN602 3.7 61.1 1.0
O1P D:4AD601 3.8 39.9 1.0
O5 D:2PN602 4.0 68.4 1.0
O D:HOH824 4.2 39.0 1.0
O3P D:4AD601 4.2 42.5 1.0
O3' D:4AD601 4.2 37.7 1.0
O5' D:4AD601 4.3 39.4 1.0
OD1 D:ASP463 4.4 48.8 1.0
C3' D:4AD601 4.4 40.5 1.0
CG D:GLU471 4.4 44.3 1.0
O6 D:2PN602 4.5 67.4 1.0
OD2 D:ASP463 4.5 49.8 1.0
O D:HOH742 4.6 52.9 1.0
CA D:GLY474 4.6 38.5 1.0
NZ D:LYS445 4.7 55.7 1.0
C5' D:4AD601 4.7 36.4 1.0
CG D:ASP463 4.7 46.8 1.0

Reference:

J.S.Park, B.W.Han. Human Asparaginyl-Trna Synthetase in Complex with Asparagine-Amp To Be Published.
Page generated: Fri Oct 4 04:24:18 2024

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