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Magnesium in PDB 1ffy: Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin

Enzymatic activity of Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin

All present enzymatic activity of Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin:
6.1.1.5;

Protein crystallography data

The structure of Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin, PDB code: 1ffy was solved by L.F.Silvian, J.Wang, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.000, 100.000, 186.000, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 28.1

Other elements in 1ffy:

The structure of Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin also contains other interesting chemical elements:

Potassium (K) 1 atom
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin (pdb code 1ffy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin, PDB code: 1ffy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 1ffy

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Magnesium binding site 1 out of 10 in the Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg1201

b:37.5
occ:1.00
 O T:HOH1296 2.2 37.0 1.0
O T:HOH1297 2.2 36.1 1.0
O T:HOH1295 2.2 37.1 1.0
O T:HOH1293 2.2 36.6 1.0
O T:HOH1292 2.2 37.6 1.0
O T:HOH1294 2.2 37.4 1.0
C5 T:U55 4.3 24.9 1.0
OP2 T:U55 4.3 33.5 1.0
OP2 T:A57 4.3 28.4 1.0
OP2 T:C56 4.4 35.2 1.0
OP1 T:A57 4.4 26.1 1.0
O T:HOH1291 4.5 35.4 1.0
OP2 T:U54 4.5 39.2 1.0
C6 T:U55 4.7 25.4 1.0
P T:A57 4.8 28.5 1.0

Magnesium binding site 2 out of 10 in 1ffy

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Magnesium binding site 2 out of 10 in the Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg1202

b:54.3
occ:1.00
 O T:HOH1299 2.2 54.0 1.0
O T:HOH1301 2.2 54.0 1.0
O T:HOH1302 2.2 54.1 1.0
O T:HOH1298 2.2 53.5 1.0
O T:HOH1303 2.2 54.4 1.0
O T:HOH1300 2.2 53.0 1.0
O T:HOH1271 3.6 37.0 1.0
O T:HOH1279 3.9 39.0 1.0
O T:HOH1264 4.1 60.9 1.0
N7 T:G53 4.3 33.3 1.0
O4 T:U54 4.4 32.0 1.0
O4 T:U55 4.5 24.9 1.0
OP1 T:A58 4.5 28.1 1.0
OP2 T:A58 4.7 30.4 1.0

Magnesium binding site 3 out of 10 in 1ffy

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Magnesium binding site 3 out of 10 in the Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg1203

b:37.2
occ:1.00
 OP2 T:A14 2.0 31.5 1.0
O T:HOH1306 2.2 33.8 1.0
O A:HOH2198 2.2 34.8 1.0
O T:HOH1304 2.2 34.5 1.0
O T:HOH1305 2.2 35.5 1.0
O T:HOH1307 2.2 34.5 1.0
P T:A14 3.5 28.6 1.0
OD2 A:ASP626 4.2 27.4 1.0
O3' T:C13 4.2 27.7 1.0
C3' T:C13 4.2 22.6 1.0
OP1 T:A14 4.3 32.1 1.0
O4 T:U8 4.4 27.8 1.0
OP1 T:G7 4.4 29.7 1.0
O5' T:A14 4.5 29.9 1.0
C5' T:C13 4.5 20.0 1.0
O T:HOH1222 4.8 18.0 1.0
C4' T:C13 4.9 22.9 1.0

Magnesium binding site 4 out of 10 in 1ffy

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Magnesium binding site 4 out of 10 in the Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg1204

b:30.7
occ:1.00
 O T:HOH1308 2.2 32.4 1.0
O T:HOH1309 2.2 32.6 1.0
O T:HOH1310 2.2 30.1 1.0
O T:HOH1311 2.2 31.5 1.0
O6 T:G43 2.2 28.2 1.0
O T:HOH1218 2.9 14.8 1.0
O6 T:G26 3.0 28.6 1.0
C6 T:G43 3.2 24.9 1.0
N6 T:A44 3.4 27.3 1.0
O T:HOH1270 3.8 18.3 1.0
N4 T:C27 4.0 18.0 1.0
N1 T:G43 4.0 25.1 1.0
C5 T:G43 4.2 27.1 1.0
C6 T:G26 4.2 23.1 1.0
O T:HOH1269 4.2 23.7 1.0
C6 T:A44 4.5 29.8 1.0
O T:HOH1223 4.5 27.9 1.0
N7 T:G43 4.5 25.6 1.0
N7 T:G26 4.8 23.8 1.0
C4 T:C27 4.9 20.0 1.0
C5 T:G26 4.9 24.7 1.0
N4 T:C25 4.9 17.4 1.0
N3 T:C27 5.0 20.8 1.0
C5 T:C25 5.0 18.8 1.0

Magnesium binding site 5 out of 10 in 1ffy

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Magnesium binding site 5 out of 10 in the Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg1205

b:29.0
occ:1.00
 O A:HOH2199 2.2 30.0 1.0
O T:HOH1312 2.2 27.3 1.0
O T:HOH1313 2.2 27.7 1.0
O T:HOH1314 2.2 28.3 1.0
OP1 T:C25 2.3 23.0 1.0
O T:HOH1233 3.5 33.1 1.0
OD1 A:ASN718 3.5 24.5 1.0
OD1 A:ASN713 3.6 25.3 1.0
P T:C25 3.8 19.7 1.0
O T:HOH1231 4.3 23.4 1.0
CG A:ASN713 4.4 24.4 1.0
CG A:ASN718 4.4 21.5 1.0
CB A:ASN713 4.4 19.6 1.0
O5' T:C25 4.4 16.0 1.0
ND2 A:ASN718 4.4 22.4 1.0
OP2 T:G40 4.6 21.4 1.0
O T:HOH1223 4.6 27.9 1.0
OP2 T:C25 4.7 16.4 1.0
O3' T:G24 4.8 16.2 1.0
C5' T:C25 4.8 16.9 1.0
OP1 T:G40 5.0 21.8 1.0
CA A:ASN713 5.0 17.7 1.0

Magnesium binding site 6 out of 10 in 1ffy

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Magnesium binding site 6 out of 10 in the Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg1206

b:37.8
occ:1.00
 OP1 T:U8 2.1 34.0 1.0
OP1 T:A9 2.1 39.0 1.0
O T:HOH1318 2.2 35.4 1.0
O T:HOH1315 2.2 38.9 1.0
O T:HOH1316 2.2 37.1 1.0
O T:HOH1317 2.2 38.1 1.0
P T:U8 3.4 29.4 1.0
P T:A9 3.5 40.5 1.0
O T:HOH1213 3.7 46.9 1.0
MG T:MG1210 3.8 36.5 1.0
O3' T:G7 3.8 29.9 1.0
C5' T:U8 3.8 31.7 1.0
O5' T:U8 3.9 31.9 1.0
O T:HOH1245 4.1 29.3 1.0
O T:HOH1329 4.1 37.8 1.0
OP2 T:A9 4.2 39.0 1.0
O3' T:U8 4.2 36.9 1.0
O2' T:G7 4.4 38.5 1.0
OP2 T:U8 4.6 31.5 1.0
O5' T:A9 4.6 41.5 1.0
O T:HOH1330 4.6 36.6 1.0
C3' T:U8 4.6 32.4 1.0
C4' T:U8 4.7 31.5 1.0

Magnesium binding site 7 out of 10 in 1ffy

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Magnesium binding site 7 out of 10 in the Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg1207

b:37.3
occ:1.00
 O T:HOH1319 2.2 41.8 1.0
O T:HOH1320 2.2 40.7 1.0
OP2 T:G16 2.2 43.0 1.0
O2 T:U60 2.2 38.8 1.0
O6 T:G59 2.9 37.4 1.0
OP1 T:G19 3.0 41.5 1.0
O T:HOH1250 3.0 41.0 1.0
C2 T:U60 3.1 36.3 1.0
N3 T:U60 3.3 35.8 1.0
C6 T:G59 3.5 31.6 1.0
N1 T:G59 3.6 31.1 1.0
P T:G16 3.7 46.5 1.0
P T:G19 3.8 44.2 1.0
OP2 T:G19 4.0 45.9 1.0
O5' T:G16 4.2 53.1 1.0
O3' T:G18 4.2 47.1 1.0
C5' T:G16 4.2 63.0 1.0
OP2 T:U17 4.3 79.1 1.0
O3' T:G15 4.4 42.4 1.0
N1 T:U60 4.4 37.0 1.0
C4 T:U60 4.6 36.0 1.0
O2' T:G18 4.7 49.4 1.0
C5 T:G59 4.7 30.8 1.0
OP1 T:G16 4.7 46.2 1.0
C2 T:G59 4.8 30.9 1.0
C4' T:G18 4.9 51.3 1.0
C1' T:U60 5.0 37.4 1.0

Magnesium binding site 8 out of 10 in 1ffy

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Magnesium binding site 8 out of 10 in the Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg1208

b:33.5
occ:1.00
 O T:HOH1321 2.2 35.8 1.0
O A:HOH2200 2.2 35.2 1.0
O T:HOH1322 2.2 32.5 1.0
O A:HOH2201 2.2 36.1 1.0
OD1 A:ASN703 2.3 30.2 1.0
OP1 T:A14 2.3 32.1 1.0
P T:A14 3.4 28.6 1.0
CG A:ASN703 3.5 23.2 1.0
O3' T:C13 3.6 27.7 1.0
O A:HOH2060 3.6 30.0 1.0
O5' T:A14 3.7 29.9 1.0
ND2 A:ASN703 4.1 27.3 1.0
CG A:LEU702 4.5 21.2 1.0
CB A:LEU702 4.6 19.1 1.0
N A:ASN703 4.6 19.3 1.0
C5' T:A14 4.6 31.6 1.0
O2' T:C13 4.7 22.0 1.0
CB A:ASN703 4.7 21.5 1.0
CA A:ASN703 4.8 19.3 1.0
OP2 T:A14 4.8 31.5 1.0
CD2 A:LEU702 5.0 18.4 1.0
C3' T:C13 5.0 22.6 1.0

Magnesium binding site 9 out of 10 in 1ffy

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Magnesium binding site 9 out of 10 in the Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg1209

b:45.8
occ:1.00
 O T:HOH1323 2.2 46.0 1.0
O T:HOH1326 2.2 44.6 1.0
O T:HOH1324 2.2 45.1 1.0
OP1 T:G50 2.2 39.1 1.0
O T:HOH1325 2.2 44.7 1.0
OP1 T:C48 3.0 47.9 1.0
O3' T:U47 3.5 56.1 1.0
P T:G50 3.7 31.2 1.0
P T:C48 3.8 53.8 1.0
O5' T:C48 4.1 49.9 1.0
O5' T:G50 4.3 29.6 1.0
C5' T:G50 4.3 30.9 1.0
C3' T:U47 4.5 60.6 1.0
OP2 T:G50 4.6 28.4 1.0
O3' T:G49 4.6 30.1 1.0
OP2 T:U51 4.7 38.8 1.0
C5' T:C48 4.8 44.2 1.0

Magnesium binding site 10 out of 10 in 1ffy

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Magnesium binding site 10 out of 10 in the Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Insights Into Editing From An Ile-Trna Synthetase Structure with Trna(Ile) and Mupirocin within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg1210

b:36.5
occ:1.00
 O T:HOH1328 2.2 33.3 1.0
O T:HOH1318 2.2 35.4 1.0
O T:HOH1329 2.2 37.8 1.0
O T:HOH1327 2.2 35.4 1.0
O T:HOH1330 2.2 36.6 1.0
OP1 T:U8 3.3 34.0 1.0
OP2 T:U12 3.6 22.9 1.0
MG T:MG1206 3.8 37.8 1.0
OP2 T:A9 3.9 39.0 1.0
OP2 T:U8 4.1 31.5 1.0
P T:U8 4.1 29.4 1.0
OP1 T:A9 4.2 39.0 1.0
O T:HOH1219 4.3 17.1 1.0
OP2 T:C11 4.3 20.4 1.0
O T:HOH1317 4.4 38.1 1.0
O T:HOH1245 4.6 29.3 1.0
P T:A9 4.6 40.5 1.0
O T:HOH1213 4.6 46.9 1.0
O5' T:U8 4.9 31.9 1.0
P T:U12 5.0 23.0 1.0

Reference:

L.F.Silvian, J.Wang, T.A.Steitz. Insights Into Editing From An Ile-Trna Synthetase Structure with Trnaile and Mupirocin. Science V. 285 1074 1999.
ISSN: ISSN 0036-8075
PubMed: 10446055
DOI: 10.1126/SCIENCE.285.5430.1074
Page generated: Tue Aug 13 03:15:07 2024

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