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Magnesium in PDB 4hvc: Crystal Structure of Human Prolyl-Trna Synthetase in Complex with Halofuginone and Atp Analogue

Enzymatic activity of Crystal Structure of Human Prolyl-Trna Synthetase in Complex with Halofuginone and Atp Analogue

All present enzymatic activity of Crystal Structure of Human Prolyl-Trna Synthetase in Complex with Halofuginone and Atp Analogue:
6.1.1.15; 6.1.1.17;

Protein crystallography data

The structure of Crystal Structure of Human Prolyl-Trna Synthetase in Complex with Halofuginone and Atp Analogue, PDB code: 4hvc was solved by H.Zhou, L.Sun, X.L.Yang, P.Schimmel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.43 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.544, 93.100, 87.004, 90.00, 107.95, 90.00
R / Rfree (%) 20.4 / 22.7

Other elements in 4hvc:

The structure of Crystal Structure of Human Prolyl-Trna Synthetase in Complex with Halofuginone and Atp Analogue also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Chlorine (Cl) 2 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Prolyl-Trna Synthetase in Complex with Halofuginone and Atp Analogue (pdb code 4hvc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Prolyl-Trna Synthetase in Complex with Halofuginone and Atp Analogue, PDB code: 4hvc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4hvc

Go back to Magnesium Binding Sites List in 4hvc
Magnesium binding site 1 out of 2 in the Crystal Structure of Human Prolyl-Trna Synthetase in Complex with Halofuginone and Atp Analogue


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 Human Prolyl-Trna Synthetase in Complex with Halofuginone and Atp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1603

b:39.1
occ:1.00
O1G A:ANP1601 1.9 51.3 1.0
O1B A:ANP1601 2.1 46.6 1.0
O A:HOH1794 2.2 40.3 1.0
O A:HOH1793 2.3 35.1 1.0
O A:HOH1795 2.4 42.7 1.0
PG A:ANP1601 3.0 53.1 1.0
O3G A:ANP1601 3.3 53.0 1.0
PB A:ANP1601 3.4 47.5 1.0
N3B A:ANP1601 3.6 50.5 1.0
NH1 A:ARG1152 3.8 34.4 1.0
NH1 A:ARG1163 3.9 40.4 1.0
OE2 A:GLU1154 4.2 44.2 1.0
OE1 A:GLU1154 4.4 45.1 1.0
OE2 A:GLU1100 4.4 45.0 1.0
O2B A:ANP1601 4.4 48.6 1.0
O2G A:ANP1601 4.4 52.5 1.0
N7 A:ANP1601 4.4 37.9 1.0
OE1 A:GLU1100 4.5 39.8 1.0
O3A A:ANP1601 4.5 47.7 1.0
NZ A:LYS1156 4.5 56.7 1.0
N1 A:HFG1602 4.6 37.9 1.0
CE1 A:PHE1097 4.7 44.9 1.0
CD A:GLU1154 4.8 44.0 1.0
C2 A:HFG1602 4.8 37.2 1.0
C8 A:ANP1601 4.9 38.9 1.0
CD A:GLU1100 4.9 42.9 1.0
CD A:ARG1152 4.9 35.6 1.0
CZ A:ARG1152 5.0 35.2 1.0

Magnesium binding site 2 out of 2 in 4hvc

Go back to Magnesium Binding Sites List in 4hvc
Magnesium binding site 2 out of 2 in the Crystal Structure of Human Prolyl-Trna Synthetase in Complex with Halofuginone and Atp Analogue


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 Human Prolyl-Trna Synthetase in Complex with Halofuginone and Atp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1603

b:40.5
occ:1.00
O2G B:ANP1601 2.0 51.8 1.0
O B:HOH1706 2.1 41.0 1.0
O1B B:ANP1601 2.1 48.5 1.0
O B:HOH1778 2.1 49.5 1.0
O B:HOH1784 2.2 47.2 1.0
O B:HOH1719 2.2 38.9 1.0
PG B:ANP1601 3.2 53.2 1.0
PB B:ANP1601 3.4 49.1 1.0
O3G B:ANP1601 3.6 54.6 1.0
N3B B:ANP1601 3.7 50.9 1.0
O B:HOH1743 3.8 48.9 1.0
NH1 B:ARG1152 3.9 36.0 1.0
NH1 B:ARG1163 4.2 45.2 1.0
OE2 B:GLU1154 4.3 42.4 1.0
OE2 B:GLU1100 4.4 50.2 1.0
O2B B:ANP1601 4.4 48.7 1.0
OE1 B:GLU1154 4.4 45.4 1.0
OE1 B:GLU1100 4.4 47.1 1.0
O1G B:ANP1601 4.5 52.9 1.0
N7 B:ANP1601 4.5 42.8 1.0
N1 B:HFG1602 4.5 40.5 1.0
O3A B:ANP1601 4.5 47.7 1.0
CE1 B:PHE1097 4.7 53.2 1.0
C2 B:HFG1602 4.8 40.1 1.0
CD B:GLU1154 4.8 43.5 1.0
CD B:GLU1100 4.9 48.3 1.0
CD B:ARG1152 4.9 35.0 1.0
C8 B:ANP1601 4.9 43.5 1.0

Reference:

H.Zhou, L.Sun, X.L.Yang, P.Schimmel. Atp-Directed Capture of Bioactive Herbal-Based Medicine on Human Trna Synthetase. Nature V. 494 121 2012.
ISSN: ISSN 0028-0836
PubMed: 23263184
DOI: 10.1038/NATURE11774
Page generated: Mon Dec 14 18:50:45 2020

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