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Magnesium in PDB 3cul: Aminoacyl-Trna Synthetase Ribozyme

Protein crystallography data

The structure of Aminoacyl-Trna Synthetase Ribozyme, PDB code: 3cul was solved by H.Xiao, H.Murakami, H.Suga, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.57 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 192.151, 48.725, 90.515, 90.00, 93.50, 90.00
R / Rfree (%) 22.7 / 28.3

Other elements in 3cul:

The structure of Aminoacyl-Trna Synthetase Ribozyme also contains other interesting chemical elements:

Potassium (K) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Aminoacyl-Trna Synthetase Ribozyme (pdb code 3cul). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Aminoacyl-Trna Synthetase Ribozyme, PDB code: 3cul:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3cul

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Magnesium binding site 1 out of 10 in the Aminoacyl-Trna Synthetase Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Aminoacyl-Trna Synthetase Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:63.5
occ:1.00
 O C:HOH601 1.9 59.2 1.0
O6 C:G5 3.7 75.6 1.0
O6 C:G6 4.1 58.0 1.0
N7 C:G6 4.1 56.0 1.0
C6 C:G5 4.3 69.3 1.0
N7 C:G5 4.3 69.8 1.0
N4 C:C7 4.4 60.4 1.0
C5 C:G5 4.6 70.8 1.0
O6 C:G8 4.7 80.8 1.0
C6 C:G6 4.8 53.3 1.0
C5 C:G6 4.8 54.5 1.0

Magnesium binding site 2 out of 10 in 3cul

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Magnesium binding site 2 out of 10 in the Aminoacyl-Trna Synthetase Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Aminoacyl-Trna Synthetase Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:72.1
occ:1.00
 O C:HOH602 1.9 87.8 1.0
O C:HOH603 2.0 70.5 1.0
N7 C:G24 3.9 83.2 1.0
OP2 C:A23 4.0 71.3 1.0
C8 C:G24 4.2 83.7 1.0
OP2 C:G24 4.3 82.9 1.0
N1 C:A45 4.3 0.4 1.0
N7 C:G25 4.4 68.6 1.0
N6 C:A45 4.6 0.1 1.0
O6 C:G25 4.6 70.1 1.0
C6 C:A45 4.9 0.7 1.0
N4 C:C26 4.9 76.0 1.0

Magnesium binding site 3 out of 10 in 3cul

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Magnesium binding site 3 out of 10 in the Aminoacyl-Trna Synthetase Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Aminoacyl-Trna Synthetase Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg505

b:82.4
occ:1.00
 O4 C:U71 2.0 0.6 1.0
OP2 C:U70 2.1 93.0 1.0
C4 C:U71 2.8 0.2 1.0
C5 C:U71 3.1 0.7 1.0
P C:U70 3.5 96.5 1.0
N3 C:U71 4.2 0.8 1.0
O5' C:U70 4.2 97.7 1.0
C5 C:U70 4.3 91.0 1.0
OP1 C:U70 4.4 96.8 1.0
O3' C:G69 4.5 91.8 1.0
C6 C:U71 4.5 0.5 1.0
O5' C:G69 4.7 96.4 1.0
C3' C:G69 4.7 91.9 1.0
C6 C:U70 4.7 91.1 1.0
OP2 C:A74 5.0 88.8 1.0

Magnesium binding site 4 out of 10 in 3cul

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Magnesium binding site 4 out of 10 in the Aminoacyl-Trna Synthetase Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Aminoacyl-Trna Synthetase Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg506

b:89.5
occ:1.00
 O C:HOH604 2.0 62.4 1.0
OP2 C:A75 3.6 0.2 1.0
O6 C:G68 4.2 85.6 1.0
N7 C:G68 4.2 85.6 1.0
O4 C:U70 4.6 91.9 1.0
P C:A75 4.6 0.6 1.0
OP1 C:A75 4.7 0.3 1.0
O6 C:G69 4.7 76.1 1.0
N7 C:G69 4.9 77.0 1.0
C6 C:G68 4.9 84.3 1.0
C5 C:G68 5.0 85.5 1.0

Magnesium binding site 5 out of 10 in 3cul

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Magnesium binding site 5 out of 10 in the Aminoacyl-Trna Synthetase Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Aminoacyl-Trna Synthetase Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg507

b:68.4
occ:1.00
 O C:HOH609 2.0 83.4 1.0
O2B C:GTP1 2.1 89.9 1.0
OP2 C:G2 2.7 79.1 1.0
PB C:GTP1 3.1 87.0 1.0
O2A C:GTP1 3.2 86.2 1.0
O3A C:GTP1 3.2 90.0 1.0
P C:G2 3.6 81.8 1.0
O3B C:GTP1 3.7 98.4 1.0
PA C:GTP1 3.8 84.7 1.0
O3G C:GTP1 4.1 0.9 1.0
O5' C:G2 4.2 80.2 1.0
N7 C:G2 4.4 76.9 1.0
O3' C:GTP1 4.4 81.8 1.0
C3' C:GTP1 4.4 75.0 1.0
O1B C:GTP1 4.5 85.3 1.0
PG C:GTP1 4.6 0.0 1.0
C5' C:GTP1 4.6 74.1 1.0
O5' C:GTP1 4.6 89.2 1.0
C8 C:G2 4.7 76.9 1.0
N7 C:A3 4.7 72.0 1.0
N6 C:A3 4.8 69.5 1.0
OP1 C:G2 4.9 86.8 1.0

Magnesium binding site 6 out of 10 in 3cul

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Magnesium binding site 6 out of 10 in the Aminoacyl-Trna Synthetase Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Aminoacyl-Trna Synthetase Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg508

b:1.0
occ:1.00
 OP1 C:C22 3.6 74.8 1.0
P C:C22 4.6 70.0 1.0
OP2 C:C22 4.7 68.1 1.0
OP2 C:G42 4.8 79.3 1.0
OP2 C:A23 4.9 71.3 1.0

Magnesium binding site 7 out of 10 in 3cul

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Magnesium binding site 7 out of 10 in the Aminoacyl-Trna Synthetase Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Aminoacyl-Trna Synthetase Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg509

b:95.4
occ:1.00
 OP2 C:G8 2.3 85.1 1.0
OP2 C:C7 2.8 70.2 1.0
O5' C:C7 3.2 71.0 1.0
N7 C:G8 3.5 85.0 1.0
P C:C7 3.5 73.8 1.0
P C:G8 3.6 88.4 1.0
C3' C:C7 3.7 75.4 1.0
C6 C:C7 3.7 58.0 1.0
C8 C:G8 3.9 84.9 1.0
C5 C:C7 3.9 56.6 1.0
C5' C:C7 4.0 67.5 1.0
O3' C:C7 4.0 85.9 1.0
O5' C:G8 4.2 85.1 1.0
C4' C:C7 4.3 71.1 1.0
OP1 C:C7 4.4 69.9 1.0
N1 C:C7 4.6 63.6 1.0
C5 C:G8 4.8 83.4 1.0
C2' C:C7 4.8 73.0 1.0
O3' C:G6 4.8 76.7 1.0
O4' C:C7 4.8 70.8 1.0
OP1 C:G8 4.9 87.4 1.0
C4 C:C7 5.0 57.4 1.0

Magnesium binding site 8 out of 10 in 3cul

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Magnesium binding site 8 out of 10 in the Aminoacyl-Trna Synthetase Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Aminoacyl-Trna Synthetase Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg510

b:61.1
occ:1.00
 O1B C:GTP1 2.4 85.3 1.0
O1G C:GTP1 2.8 0.1 1.0
O3G C:GTP1 3.0 0.9 1.0
O2B C:GTP1 3.0 89.9 1.0
PB C:GTP1 3.1 87.0 1.0
PG C:GTP1 3.3 0.0 1.0
N4 C:C13 3.6 62.2 1.0
O3B C:GTP1 3.8 98.4 1.0
C5 C:C13 3.8 64.5 1.0
N4 C:C14 4.0 57.2 1.0
C4 C:C13 4.0 63.9 1.0
C5 C:C14 4.5 52.1 1.0
O3A C:GTP1 4.6 90.0 1.0
C4 C:C14 4.7 57.5 1.0
O2G C:GTP1 4.8 0.4 1.0
C6 C:C13 4.8 65.5 1.0
O1A C:GTP1 5.0 87.1 1.0

Magnesium binding site 9 out of 10 in 3cul

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Magnesium binding site 9 out of 10 in the Aminoacyl-Trna Synthetase Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Aminoacyl-Trna Synthetase Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:71.1
occ:1.00
 O D:HOH610 2.1 72.0 1.0
O6 D:G169 3.9 54.1 1.0
N7 D:G168 4.0 66.5 1.0
O6 D:G168 4.0 63.8 1.0
N7 D:G169 4.1 64.0 1.0
O4 D:U170 4.2 64.3 1.0
OP2 D:A175 4.2 66.5 1.0
C6 D:G168 4.6 63.5 1.0
C5 D:G168 4.6 62.5 1.0
C6 D:G169 4.7 62.4 1.0
C5 D:G169 4.8 63.3 1.0
OP1 D:A175 4.9 62.0 1.0
P D:A175 5.0 68.5 1.0
C8 D:G168 5.0 68.4 1.0
C4 D:U170 5.0 62.4 1.0

Magnesium binding site 10 out of 10 in 3cul

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Magnesium binding site 10 out of 10 in the Aminoacyl-Trna Synthetase Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Aminoacyl-Trna Synthetase Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg504

b:66.8
occ:1.00
 O4 D:U171 2.0 74.6 1.0
OP2 D:U170 2.4 65.0 1.0
C4 D:U171 3.0 73.2 1.0
C5 D:U171 3.4 74.0 1.0
P D:U170 3.7 62.4 1.0
N3 D:U171 4.2 69.5 1.0
OP1 D:U170 4.3 63.6 1.0
O5' D:U170 4.6 57.9 1.0
O3' D:G169 4.7 65.4 1.0
C6 D:U171 4.7 72.6 1.0
C5 D:U170 4.9 60.9 1.0

Reference:

H.Xiao, H.Murakami, H.Suga, A.R.Ferre-D'amare. Structural Basis of Specific Trna Aminoacylation By A Small in Vitro Selected Ribozyme. Nature V. 454 358 2008.
ISSN: ISSN 0028-0836
PubMed: 18548004
DOI: 10.1038/NATURE07033
Page generated: Wed Aug 14 11:53:03 2024

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