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Magnesium in PDB 5dar: Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii

Protein crystallography data

The structure of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii, PDB code: 5dar 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) 20.00 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.396, 88.451, 95.231, 90.00, 102.19, 90.00
R / Rfree (%) 26.4 / 29.7

Other elements in 5dar:

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

Potassium (K) 5 atoms
Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 5dar

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Magnesium binding site 1 out of 8 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:2.0
occ:1.00
 OP1 A:A1183 2.6 10.2 1.0
OP1 A:C1182 2.9 9.8 1.0
OP2 A:A1180 3.1 13.6 1.0
O3' A:A1179 3.3 14.1 1.0
P A:C1182 3.3 10.1 1.0
OP2 A:C1182 3.4 10.4 1.0
O5' A:C1182 3.5 9.8 1.0
P A:A1180 3.6 13.6 1.0
O2' A:A1179 3.7 15.2 1.0
O5' A:A1180 3.8 13.1 1.0
P A:A1183 4.0 10.0 1.0
C2 A:A1183 4.1 11.4 1.0
C1' A:A1179 4.2 14.4 1.0
C2' A:A1179 4.4 14.5 1.0
C5' A:A1180 4.4 12.5 1.0
C5' A:C1182 4.4 9.7 1.0
C3' A:A1179 4.4 14.3 1.0
OP1 A:C1207 4.5 14.2 1.0
OP2 A:A1183 4.6 10.7 1.0
N3 A:A1179 4.7 13.8 1.0
O3' A:C1182 4.7 9.7 1.0
O6 A:G1184 4.8 9.7 1.0
N3 A:A1183 4.8 11.2 1.0
N1 A:A1183 4.8 11.6 1.0
C3' A:C1182 4.9 9.6 1.0
O3' A:G1181 4.9 10.1 1.0

Magnesium binding site 2 out of 8 in 5dar

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Magnesium binding site 2 out of 8 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:7.1
occ:1.00
 O6 A:G1166 2.2 10.0 1.0
C6 A:G1166 3.4 9.6 1.0
OP1 A:U1211 3.7 13.5 1.0
OP2 A:G1164 4.1 10.1 1.0
N1 A:G1166 4.2 9.5 1.0
OP2 A:U1211 4.3 14.2 1.0
OP2 A:G1165 4.4 10.3 1.0
C5 A:G1166 4.4 9.4 1.0
P A:U1211 4.5 13.9 1.0
N7 A:G1166 4.7 9.7 1.0
N7 A:G1165 4.9 8.5 1.0

Magnesium binding site 3 out of 8 in 5dar

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Magnesium binding site 3 out of 8 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1303

b:5.8
occ:1.00
 O4 A:U1204 2.2 13.7 1.0
OP2 A:A1183 2.2 10.7 1.0
C4 A:U1204 3.2 13.2 1.0
P A:A1183 3.7 10.0 1.0
O6 A:G1203 3.8 9.8 1.0
OP1 A:A1206 3.9 16.4 1.0
C5 A:U1204 4.0 13.1 1.0
N3 A:U1204 4.2 13.1 1.0
C5' A:A1183 4.3 10.8 1.0
OP1 A:A1183 4.4 10.2 1.0
O5' A:A1183 4.5 10.4 1.0
C6 A:G1203 4.5 9.5 1.0
C2 A:A1179 4.6 13.7 1.0
O3' A:C1182 4.6 9.7 1.0
OP2 A:C1207 4.6 13.4 1.0
C3' A:C1182 4.7 9.6 1.0
C2' A:C1182 4.8 9.7 1.0
P A:A1206 4.9 16.6 1.0

Magnesium binding site 4 out of 8 in 5dar

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Magnesium binding site 4 out of 8 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1304

b:4.5
occ:1.00
 N7 A:G1197 2.4 8.2 1.0
O2' A:A1196 2.6 7.3 1.0
C5 A:G1197 3.4 8.1 1.0
O6 A:G1197 3.4 7.7 1.0
OP2 A:A1167 3.4 9.1 1.0
O2' A:G1166 3.5 9.7 1.0
C8 A:G1197 3.5 8.2 1.0
O6 A:G1199 3.7 9.3 1.0
C2' A:A1196 3.7 7.6 1.0
C6 A:G1197 3.7 8.0 1.0
C6 A:G1199 3.8 9.6 1.0
O3' A:A1196 3.9 7.6 1.0
C5 A:G1199 4.1 9.5 1.0
N1 A:G1199 4.3 10.0 1.0
N7 A:G1199 4.4 9.5 1.0
N1 A:A1213 4.4 7.5 1.0
C3' A:A1196 4.4 7.6 1.0
C2' A:G1166 4.6 9.3 1.0
C4 A:G1197 4.6 8.1 1.0
N9 A:G1197 4.6 8.1 1.0
P A:A1167 4.7 9.0 1.0
O3' A:G1166 4.8 9.0 1.0
C4 A:G1199 4.8 9.7 1.0
N7 A:A1167 4.8 7.7 1.0
C2 A:A1213 4.9 7.5 1.0
OP2 A:G1197 5.0 7.7 1.0

Magnesium binding site 5 out of 8 in 5dar

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Magnesium binding site 5 out of 8 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1305

b:30.0
occ:1.00
 O A:HOH1402 1.8 30.0 1.0
O A:HOH1405 1.8 30.0 1.0
OP2 A:A1196 3.5 7.6 1.0
O4 A:U1193 3.5 6.2 1.0
O4 A:U1192 3.5 7.1 1.0
O4 A:U1191 3.6 7.5 1.0
C4 A:U1193 4.1 6.4 1.0
C4 A:U1191 4.1 7.2 1.0
C5 A:U1191 4.2 7.3 1.0
N3 A:U1193 4.3 6.5 1.0
C4 A:U1192 4.6 6.9 1.0
P A:A1196 4.8 7.5 1.0
OP1 A:G1197 4.8 7.7 1.0
O3' A:A1195 5.0 7.7 1.0
C5 A:U1192 5.0 6.8 1.0

Magnesium binding site 6 out of 8 in 5dar

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Magnesium binding site 6 out of 8 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1301

b:2.4
occ:1.00
 O4 D:U1204 2.2 11.3 1.0
OP2 D:A1183 2.7 13.4 1.0
C4 D:U1204 3.2 11.3 1.0
N3 D:U1204 3.7 11.3 1.0
OP1 D:A1206 3.7 14.6 1.0
P D:A1183 3.8 13.6 1.0
O5' D:A1183 3.8 13.3 1.0
C2 D:A1179 4.2 13.0 1.0
O6 D:G1203 4.2 14.2 1.0
OP2 D:C1207 4.2 17.6 1.0
OP1 D:C1207 4.3 17.4 1.0
N3 D:A1179 4.4 13.1 1.0
C5 D:U1204 4.4 11.5 1.0
O3' D:C1182 4.4 13.1 1.0
C3' D:C1182 4.6 13.4 1.0
P D:A1206 4.7 15.2 1.0
P D:C1207 4.7 16.6 1.0
O5' D:A1206 4.8 15.1 1.0
C5' D:A1183 4.9 13.2 1.0
C6 D:G1203 4.9 13.3 1.0

Magnesium binding site 7 out of 8 in 5dar

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Magnesium binding site 7 out of 8 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1302

b:17.3
occ:1.00
 OP1 D:C1182 2.1 11.8 1.0
OP2 D:A1180 2.7 14.6 1.0
P D:C1182 3.6 11.5 1.0
O6 D:G1172 3.7 10.9 1.0
O6 D:G1173 3.7 18.3 1.0
N4 D:C1185 3.8 20.1 1.0
P D:A1180 4.0 15.5 1.0
O6 D:G1184 4.1 11.5 1.0
O3' D:G1181 4.1 12.3 1.0
O5' D:C1182 4.3 11.9 1.0
K D:K1304 4.4 11.8 1.0
C6 D:G1172 4.5 11.4 1.0
OP1 D:A1180 4.6 15.2 1.0
OP2 D:C1182 4.7 11.5 1.0
O5' D:A1180 4.7 14.7 1.0
N4 D:C1174 4.7 21.5 1.0
C6 D:G1173 4.8 18.7 1.0
N4 D:C1186 4.9 16.6 1.0
N7 D:G1172 5.0 12.3 1.0

Magnesium binding site 8 out of 8 in 5dar

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1303

b:20.2
occ:1.00
 O D:HOH1407 1.8 35.2 1.0
O D:HOH1404 1.9 6.3 1.0
O D:HOH1401 1.9 33.1 1.0
O D:HOH1406 2.6 19.5 1.0
O D:HOH1405 2.7 5.2 1.0
O D:HOH1402 2.7 56.8 1.0
OP2 D:A1196 3.9 14.5 1.0
O4 D:U1191 4.1 11.8 1.0
O4 D:U1193 4.2 12.2 1.0
O4 D:U1192 4.8 12.3 1.0
C4 D:U1191 4.8 11.9 1.0
C5 D:U1191 4.8 12.5 1.0
OP1 D:G1197 4.9 16.0 1.0
C4 D:U1193 5.0 12.0 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 To Be Published.
Page generated: Tue Aug 12 06:52:03 2025

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