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Magnesium in PDB 3wqy: Crystal Structure of Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with Wild-Type Trna(Ala) Having G3.U70

Enzymatic activity of Crystal Structure of Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with Wild-Type Trna(Ala) Having G3.U70

All present enzymatic activity of Crystal Structure of Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with Wild-Type Trna(Ala) Having G3.U70:
6.1.1.7;

Protein crystallography data

The structure of Crystal Structure of Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with Wild-Type Trna(Ala) Having G3.U70, PDB code: 3wqy was solved by M.Naganuma, S.Sekine, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.77 / 3.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.742, 169.836, 175.260, 90.00, 90.00, 90.00
R / Rfree (%) 25 / 28.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with Wild-Type Trna(Ala) Having G3.U70 (pdb code 3wqy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with Wild-Type Trna(Ala) Having G3.U70, PDB code: 3wqy:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3wqy

Go back to Magnesium Binding Sites List in 3wqy
Magnesium binding site 1 out of 3 in the Crystal Structure of Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with Wild-Type Trna(Ala) Having G3.U70


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with Wild-Type Trna(Ala) Having G3.U70 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1701

b:52.8
occ:1.00
 N7 C:A1659 2.9 40.2 1.0
C8 C:A1659 3.6 37.1 1.0
N4 C:C1648 3.7 33.6 1.0
O4 C:U1660 3.8 47.4 1.0
C5 C:A1659 4.1 44.4 1.0
OP2 C:A1621 4.2 68.0 1.0
N6 C:A1659 4.4 62.9 1.0
OP1 C:A1659 4.5 26.7 1.0
O4' C:A1621 4.6 84.4 1.0
C5' C:G1620 4.6 58.8 1.0
C4 C:U1660 4.6 48.0 1.0
C4 C:C1648 4.7 27.1 1.0
C6 C:A1659 4.7 52.2 1.0
C5' C:A1621 4.8 70.2 1.0
N9 C:A1659 4.9 37.1 1.0

Magnesium binding site 2 out of 3 in 3wqy

Go back to Magnesium Binding Sites List in 3wqy
Magnesium binding site 2 out of 3 in the Crystal Structure of Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with Wild-Type Trna(Ala) Having G3.U70


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with Wild-Type Trna(Ala) Having G3.U70 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1702

b:13.5
occ:1.00
 OP2 C:U1612 3.3 49.9 1.0
OP1 C:A1609 3.4 47.9 1.0
OP2 C:U1608 3.5 20.0 1.0
OP2 C:C1611 3.9 75.0 1.0
OP1 C:U1608 3.9 43.4 1.0
P C:U1608 4.2 24.9 1.0
OP1 C:C1611 4.4 35.8 1.0
P C:A1609 4.5 46.1 1.0
P C:C1611 4.5 49.2 1.0
OP2 C:A1609 4.5 36.1 1.0
O5' C:C1611 4.5 44.1 1.0
P C:U1612 4.8 58.1 1.0

Magnesium binding site 3 out of 3 in 3wqy

Go back to Magnesium Binding Sites List in 3wqy
Magnesium binding site 3 out of 3 in the Crystal Structure of Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with Wild-Type Trna(Ala) Having G3.U70


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Archaeoglobus Fulgidus Alanyl-Trna Synthetase in Complex with Wild-Type Trna(Ala) Having G3.U70 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1703

b:63.8
occ:1.00
 O6 C:G1639 2.5 0.0 1.0
N7 C:G1639 3.2 0.8 1.0
C6 C:G1639 3.3 0.6 1.0
C5 C:G1639 3.5 0.6 1.0
O6 C:G1640 3.7 0.2 1.0
N4 C:C1630 4.1 1.0 1.0
N7 C:A1638 4.3 1.0 1.0
C8 C:G1639 4.4 0.1 1.0
N1 C:G1639 4.6 0.4 1.0
O6 C:G1629 4.6 0.7 1.0
C6 C:G1640 4.7 97.0 1.0
C8 C:A1638 4.7 0.9 1.0
N7 C:G1640 4.8 1.0 1.0
C5 C:A1638 4.8 0.5 1.0
C4 C:G1639 4.9 0.8 1.0

Reference:

M.Naganuma, S.Sekine, Y.E.Chong, M.Guo, X.L.Yang, H.Gamper, Y.M.Hou, P.Schimmel, S.Yokoyama. The Selective Trna Aminoacylation Mechanism Based on A Single G.U Pair Nature V. 510 507 2014.
ISSN: ISSN 0028-0836
PubMed: 24919148
DOI: 10.1038/NATURE13440
Page generated: Mon Dec 14 09:01:45 2020

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