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Magnesium in PDB 1dk1: Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex

Protein crystallography data

The structure of Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex, PDB code: 1dk1 was solved by A.Nikulin, A.Serganov, E.Ennifar, S.Tischenko, N.Nevskaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.80
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 128.800, 128.800, 65.100, 90.00, 90.00, 120.00
R / Rfree (%) 21.3 / 29.1

Other elements in 1dk1:

The structure of Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex also contains other interesting chemical elements:

Potassium (K) 1 atom
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex (pdb code 1dk1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex, PDB code: 1dk1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 1dk1

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Magnesium binding site 1 out of 9 in the Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg200

b:67.9
occ:1.00
 N7 B:G13 3.8 54.2 1.0
N7 B:G14 4.1 53.0 1.0
C8 B:G13 4.4 36.3 1.0
C5 B:G13 4.5 32.7 1.0
O6 B:G13 4.7 62.0 1.0
OP2 B:G14 4.8 63.4 1.0
C6 B:G13 4.8 41.8 1.0
MG B:MG203 4.9 53.4 1.0
C8 B:G14 4.9 54.3 1.0

Magnesium binding site 2 out of 9 in 1dk1

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Magnesium binding site 2 out of 9 in the Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:82.5
occ:1.00
 OP2 B:G26 3.5 68.5 1.0
N7 B:G25 4.6 53.9 1.0
N7 B:G26 4.6 60.9 1.0
C8 B:G25 4.7 42.6 1.0
C8 B:G26 4.9 57.2 1.0

Magnesium binding site 3 out of 9 in 1dk1

Go back to Magnesium Binding Sites List in 1dk1
Magnesium binding site 3 out of 9 in the Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:67.4
occ:0.98
 N7 B:G49 3.2 51.1 1.0
N4 B:C48 3.6 40.0 1.0
C4 B:C48 3.6 38.2 1.0
C5 B:C48 3.8 24.5 1.0
O6 B:G49 4.1 34.9 1.0
C8 B:G49 4.1 37.2 1.0
N3 B:C48 4.2 26.4 1.0
C5 B:G49 4.2 40.5 1.0
C6 B:C48 4.4 26.2 1.0
C6 B:G49 4.5 46.4 1.0
OP2 B:C48 4.5 71.0 1.0
O B:HOH307 4.5 55.1 1.0
C2 B:C48 4.8 37.8 1.0
N1 B:C48 4.9 45.2 1.0
OP2 B:G49 4.9 44.5 1.0

Magnesium binding site 4 out of 9 in 1dk1

Go back to Magnesium Binding Sites List in 1dk1
Magnesium binding site 4 out of 9 in the Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:53.4
occ:1.00
 OP1 B:G51 4.8 45.0 1.0
C3' B:G51 4.8 34.8 1.0
MG B:MG200 4.9 67.9 1.0

Magnesium binding site 5 out of 9 in 1dk1

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Magnesium binding site 5 out of 9 in the Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex within 5.0Å range:

Magnesium binding site 6 out of 9 in 1dk1

Go back to Magnesium Binding Sites List in 1dk1
Magnesium binding site 6 out of 9 in the Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg205

b:70.2
occ:1.00
 O4 B:U39 3.7 73.5 1.0
C4 B:U39 3.7 64.4 1.0
O B:HOH316 3.9 66.3 1.0
C5 B:U39 4.1 51.2 1.0
N3 B:U39 4.2 50.9 1.0
N7 B:G40 4.4 34.9 1.0
O6 B:G40 4.6 54.7 1.0
C6 B:U39 4.7 47.5 1.0
C2 B:U39 4.9 52.6 1.0

Magnesium binding site 7 out of 9 in 1dk1

Go back to Magnesium Binding Sites List in 1dk1
Magnesium binding site 7 out of 9 in the Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg206

b:68.7
occ:0.97
 O B:HOH315 4.9 49.9 0.9
O6 B:G31 5.0 25.8 1.0

Magnesium binding site 8 out of 9 in 1dk1

Go back to Magnesium Binding Sites List in 1dk1
Magnesium binding site 8 out of 9 in the Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg208

b:62.2
occ:0.97
 OP2 B:U42 3.7 21.7 1.0
OP1 B:G21 3.8 50.2 1.0
OP2 B:G21 3.8 48.4 1.0
P B:G21 4.3 50.5 1.0
OP1 B:C20 4.6 50.0 1.0
P B:U42 4.9 42.5 1.0
O3' B:C20 4.9 51.6 1.0
O B:HOH322 4.9 53.6 1.0

Magnesium binding site 9 out of 9 in 1dk1

Go back to Magnesium Binding Sites List in 1dk1
Magnesium binding site 9 out of 9 in the Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg209

b:78.1
occ:1.00
 O2' B:A52 3.4 46.7 1.0
N1 B:G5 3.8 35.1 1.0
C2 B:G5 4.0 34.4 1.0
O B:HOH310 4.2 67.7 0.9
C6 B:G5 4.2 38.2 1.0
N2 B:G5 4.3 33.0 1.0
O3' B:A52 4.3 48.0 1.0
OP2 B:C53 4.4 38.4 1.0
N3 B:G5 4.4 40.4 1.0
C2' B:A52 4.5 42.0 1.0
O6 B:G5 4.6 53.9 1.0
C5 B:G5 4.6 35.9 1.0
C4 B:G5 4.7 47.6 1.0
P B:C53 4.7 54.9 1.0
C3' B:A52 4.8 38.5 1.0
N7 B:G6 4.8 38.8 1.0
OP1 B:C53 4.9 62.9 1.0

Reference:

A.Nikulin, A.Serganov, E.Ennifar, S.Tishchenko, N.Nevskaya, W.Shepard, C.Portier, M.Garber, B.Ehresmann, C.Ehresmann, S.Nikonov, P.Dumas. Crystal Structure of the S15-Rrna Complex. Nat.Struct.Biol. V. 7 273 2000.
ISSN: ISSN 1072-8368
PubMed: 10742169
DOI: 10.1038/74028
Page generated: Tue Aug 13 02:40:14 2024

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