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Magnesium in PDB 5d8h: Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton

Protein crystallography data

The structure of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton, PDB code: 5d8h was solved by A.G.Gabdulkhakov, I.V.Mitroshin, M.B.Garber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.55 / 2.80
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 125.070, 127.160, 132.930, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 24.5

Other elements in 5d8h:

The structure of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton (pdb code 5d8h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton, PDB code: 5d8h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 5d8h

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Magnesium binding site 1 out of 11 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton


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 the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:60.1
occ:1.00
O A:HOH1405 1.9 60.7 1.0
O A:HOH1429 1.9 65.0 1.0
O A:HOH1414 2.1 85.1 1.0
O6 A:G1166 2.2 65.8 1.0
O A:HOH1417 2.3 79.2 1.0
O A:HOH1434 2.3 72.5 1.0
C6 A:G1166 3.3 67.9 1.0
OP2 A:G1165 4.0 61.1 1.0
C5 A:G1166 4.1 65.3 1.0
N7 A:G1166 4.1 71.5 1.0
OP2 A:U1211 4.2 75.6 1.0
O A:HOH1431 4.3 66.2 1.0
N1 A:G1166 4.5 67.8 1.0
N7 A:G1165 4.6 63.8 1.0
OP2 A:G1164 4.8 62.5 1.0

Magnesium binding site 2 out of 11 in 5d8h

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Magnesium binding site 2 out of 11 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton


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 the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:71.7
occ:1.00
O4 A:U1204 2.0 68.8 1.0
O A:HOH1422 2.1 73.5 1.0
O A:HOH1428 2.1 69.5 1.0
OP2 A:A1183 2.2 71.2 1.0
O A:HOH1416 2.8 74.4 1.0
O A:HOH1409 2.8 70.3 1.0
C4 A:U1204 3.2 66.3 1.0
O6 A:G1203 3.2 65.4 1.0
P A:A1183 3.5 77.4 1.0
OP1 A:A1183 3.9 64.0 1.0
OP2 A:C1207 4.0 62.1 1.0
C6 A:G1203 4.0 62.1 1.0
N3 A:U1204 4.1 65.2 1.0
C3' A:C1182 4.2 70.8 1.0
C5 A:U1204 4.2 63.6 1.0
O3' A:C1182 4.2 79.4 1.0
OP1 A:A1206 4.3 73.8 1.0
C2' A:C1182 4.6 68.3 1.0
N1 A:G1203 4.6 57.4 1.0
O5' A:A1183 4.6 73.9 1.0
OP1 A:C1207 4.9 80.8 1.0
C2 A:A1179 4.9 72.3 1.0
P A:C1207 5.0 79.2 1.0
C5 A:G1203 5.0 60.2 1.0
C5' A:A1183 5.0 73.6 1.0

Magnesium binding site 3 out of 11 in 5d8h

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Magnesium binding site 3 out of 11 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton


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 the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1303

b:68.2
occ:1.00
O A:HOH1432 2.2 65.1 1.0
OP1 A:C1182 2.3 70.2 1.0
OP2 A:A1180 2.4 78.3 1.0
O A:HOH1437 2.6 80.3 1.0
O6 A:G1173 3.5 70.2 1.0
NA A:NA1313 3.5 84.1 1.0
O6 A:G1184 3.6 75.6 1.0
O5' A:A1180 3.7 80.1 1.0
P A:A1180 3.7 78.5 1.0
P A:C1182 3.7 80.2 1.0
N4 A:C1185 3.8 69.5 1.0
O A:HOH1401 3.9 71.7 1.0
N4 A:C1174 4.3 71.9 1.0
OP2 A:C1182 4.3 78.7 1.0
O3' A:G1181 4.4 82.1 1.0
O6 A:G1172 4.5 67.8 1.0
O3' A:A1179 4.5 87.1 1.0
C6 A:G1184 4.7 71.4 1.0
C6 A:G1173 4.7 67.7 1.0
OP1 A:A1180 4.8 81.5 1.0
O5' A:C1182 4.9 60.6 1.0
C5' A:A1180 5.0 79.3 1.0

Magnesium binding site 4 out of 11 in 5d8h

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Magnesium binding site 4 out of 11 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1304

b:65.0
occ:1.00
O A:HOH1420 2.0 63.9 1.0
O A:HOH1454 2.0 77.4 1.0
O A:HOH1442 2.1 58.7 1.0
O A:HOH1431 2.2 66.2 1.0
O A:HOH1440 2.2 77.1 1.0
O A:HOH1403 2.3 70.2 1.0
O6 A:G1164 4.0 63.0 1.0
O6 A:G1163 4.1 67.6 1.0
N7 A:G1163 4.2 70.0 1.0
N7 A:G1164 4.3 71.1 1.0
C6 A:G1163 4.5 70.3 1.0
OP2 A:C1212 4.6 69.8 1.0
C5 A:G1163 4.6 72.7 1.0
O6 A:G1165 4.6 65.3 1.0
O A:HOH1414 4.6 85.1 1.0
C6 A:G1164 4.8 64.0 1.0
C5 A:G1164 5.0 63.5 1.0
O A:HOH1405 5.0 60.7 1.0

Magnesium binding site 5 out of 11 in 5d8h

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Magnesium binding site 5 out of 11 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1305

b:64.4
occ:1.00
O A:HOH1424 2.2 63.1 1.0
O A:HOH1448 2.3 63.2 1.0
O A:HOH1425 2.4 64.8 1.0
O A:HOH1413 2.5 66.0 1.0
O A:HOH1451 2.5 72.3 1.0
O A:HOH1439 2.6 66.3 1.0
O4 A:U1191 4.0 73.8 1.0
O4 A:U1193 4.0 61.8 1.0
OP1 A:G1197 4.6 75.6 1.0
O4 A:U1192 4.6 64.5 1.0
OP2 A:A1196 4.7 58.2 1.0
C4 A:U1191 4.7 70.5 1.0
C5 A:U1191 4.8 68.9 1.0
C4 A:U1193 4.9 61.1 1.0

Magnesium binding site 6 out of 11 in 5d8h

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Magnesium binding site 6 out of 11 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1306

b:96.0
occ:1.00
O A:HOH1449 1.7 94.9 1.0
O A:HOH1446 1.7 82.8 1.0
O A:HOH1453 1.8 86.0 1.0
O A:HOH1412 1.8 84.5 1.0
O A:HOH1445 2.1 79.7 1.0
O A:HOH1436 2.1 83.3 1.0
N7 A:A1160 4.1 76.8 1.0
N6 A:A1160 4.4 79.5 1.0
OP2 A:C1159 4.6 76.1 1.0
O6 A:G1161 4.6 79.9 1.0
O4 A:U1218 4.7 72.9 1.0
O6 A:G1217 4.7 66.3 1.0
N7 A:G1161 4.8 78.5 1.0
C5 A:A1160 4.9 77.6 1.0

Magnesium binding site 7 out of 11 in 5d8h

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Magnesium binding site 7 out of 11 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1307

b:77.3
occ:1.00
O A:HOH1435 2.4 83.1 1.0
O A:HOH1427 2.5 71.9 1.0
O A:HOH1408 2.5 62.4 1.0
O A:HOH1457 3.0 69.2 1.0
OP2 A:A1208 3.6 77.1 1.0
N7 A:G1181 3.6 58.2 1.0
OP1 A:A1208 3.9 84.9 1.0
OP1 A:G1181 4.1 71.4 1.0
P A:A1208 4.2 82.4 1.0
N4 A:C1182 4.3 62.0 1.0
C8 A:G1181 4.3 59.4 1.0
O6 A:G1181 4.6 61.8 1.0
C5 A:G1181 4.7 56.1 1.0
OP2 A:G1209 4.9 77.3 1.0
O5' A:A1208 4.9 78.7 1.0

Magnesium binding site 8 out of 11 in 5d8h

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Magnesium binding site 8 out of 11 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1308

b:1.0
occ:1.00
O A:HOH1444 1.7 99.4 1.0
O A:HOH1441 1.8 95.4 1.0
O A:HOH1438 2.0 89.2 1.0
O A:HOH1421 2.2 79.0 1.0
O4 A:U1175 3.3 83.2 1.0
OP1 A:A1179 4.1 78.1 1.0
OP1 A:A1180 4.1 81.5 1.0
C4 A:U1175 4.5 75.5 1.0
O5' A:A1179 4.6 86.4 1.0
O4 A:U1176 4.6 81.1 1.0
P A:A1179 4.6 88.4 1.0
OP2 A:A1179 4.7 78.6 1.0
OP2 A:G1173 4.8 74.7 1.0
O2 A:U1171 4.9 90.5 1.0

Magnesium binding site 9 out of 11 in 5d8h

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Magnesium binding site 9 out of 11 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1309

b:82.4
occ:1.00
O A:HOH1426 2.4 73.7 1.0
O A:HOH1456 2.4 75.8 1.0
O A:HOH1452 2.5 91.2 1.0
O6 A:G1157 3.0 67.0 1.0
O A:HOH1415 3.0 69.7 1.0
O6 A:G1220 3.2 67.4 1.0
C6 A:G1157 3.5 65.6 1.0
C5 A:G1157 4.0 69.4 1.0
N7 A:G1157 4.0 72.3 1.0
C6 A:G1220 4.1 65.7 1.0
N7 A:G1220 4.1 69.7 1.0
O A:HOH1411 4.4 72.1 1.0
C5 A:G1220 4.4 66.4 1.0
N1 A:G1157 4.5 65.9 1.0

Magnesium binding site 10 out of 11 in 5d8h

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Magnesium binding site 10 out of 11 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1310

b:0.9
occ:1.00
O A:HOH1430 1.5 0.8 1.0
O A:HOH1450 1.5 0.6 1.0
O A:HOH1402 1.6 0.8 1.0
O A:HOH1458 1.6 0.7 1.0
O A:HOH1443 1.7 0.9 1.0
O A:HOH1455 1.7 0.8 1.0
O6 A:G1223 3.3 94.2 1.0
O6 A:G1222 4.2 87.0 1.0
N7 A:G1223 4.3 87.3 1.0
C6 A:G1223 4.3 87.8 1.0
N4 A:C1224 4.3 90.0 1.0
O6 A:G1151 4.3 88.5 1.0
N4 A:C1152 4.6 87.3 1.0
C5 A:G1223 4.7 83.8 1.0
C6 A:G1222 4.7 82.8 1.0
N7 A:G1222 5.0 84.8 1.0

Reference:

A.G.Gabdulkhakov, I.V.Mitroshin, M.B.Garber. Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton To Be Published.
Page generated: Mon Dec 14 20:10:31 2020

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