Atomistry » Magnesium » PDB 5dar-5djg » 5dar
Atomistry »
  Magnesium »
    PDB 5dar-5djg »
      5dar »

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

Go back to Magnesium Binding Sites List in 5dar
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

Go back to Magnesium Binding Sites List in 5dar
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

Go back to Magnesium Binding Sites List in 5dar
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

Go back to Magnesium Binding Sites List in 5dar
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

Go back to Magnesium Binding Sites List in 5dar
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

Go back to Magnesium Binding Sites List in 5dar
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

Go back to Magnesium Binding Sites List in 5dar
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

Go back to Magnesium Binding Sites List in 5dar
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: Sun Sep 29 02:41:23 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy