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Magnesium in PDB 3cun: Aminoacyl-Trna Synthetase Ribozyme

Protein crystallography data

The structure of Aminoacyl-Trna Synthetase Ribozyme, PDB code: 3cun 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) 28.75 / 3.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 191.368, 48.076, 90.645, 90.00, 93.50, 90.00
R / Rfree (%) 25.2 / 30.3

Other elements in 3cun:

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

Cobalt (Co) 1 atom
Potassium (K) 1 atom

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 9 in 3cun

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Magnesium binding site 1 out of 9 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:61.6
occ:1.00
 O6 C:G5 3.9 82.3 1.0
O6 C:G6 4.0 65.8 1.0
N7 C:G5 4.2 80.3 1.0
N7 C:G6 4.4 62.9 1.0
O6 C:G8 4.4 96.9 1.0
C6 C:G5 4.5 81.1 1.0
C5 C:G5 4.6 80.0 1.0
O4 C:U4 4.8 85.0 1.0
C6 C:G6 4.9 57.7 1.0
N4 C:C7 4.9 65.8 1.0

Magnesium binding site 2 out of 9 in 3cun

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Magnesium binding site 2 out of 9 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
D:Mg502

b:61.9
occ:1.00
 N7 D:G168 3.9 73.6 1.0
N7 D:G169 3.9 70.8 1.0
O6 D:G169 4.1 80.4 1.0
O4 D:U170 4.1 65.3 1.0
O6 D:G168 4.4 71.9 1.0
C5 D:G168 4.6 71.8 1.0
OP2 D:A175 4.7 80.0 1.0
C8 D:G168 4.7 75.9 1.0
C5 D:G169 4.7 73.4 1.0
C6 D:G169 4.8 78.0 1.0
C6 D:G168 4.8 72.7 1.0
C8 D:G169 5.0 71.9 1.0
OP1 D:A175 5.0 75.8 1.0
C4 D:U170 5.0 62.2 1.0

Magnesium binding site 3 out of 9 in 3cun

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Magnesium binding site 3 out of 9 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:Mg503

b:63.8
occ:1.00
 N7 C:G25 3.9 83.7 1.0
N7 C:G24 4.2 90.8 1.0
OP2 C:G24 4.2 74.0 1.0
OP2 C:A23 4.3 78.5 1.0
N1 C:A45 4.4 0.9 1.0
O6 C:G25 4.4 85.1 1.0
C8 C:G24 4.6 90.6 1.0
N6 C:A45 4.7 0.8 1.0
N4 C:C26 4.8 92.4 1.0
C5 C:G25 4.8 82.0 1.0
C8 C:G25 4.8 85.1 1.0
C6 C:A45 4.9 0.1 1.0
C6 C:G25 5.0 82.4 1.0

Magnesium binding site 4 out of 9 in 3cun

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Magnesium binding site 4 out of 9 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
D:Mg504

b:92.0
occ:1.00
 O4 D:U171 2.0 66.8 1.0
OP2 D:U170 2.3 69.5 1.0
C4 D:U171 3.1 65.1 1.0
C5 D:U171 3.7 65.5 1.0
P D:U170 3.7 71.9 1.0
O5' D:G169 4.2 76.5 1.0
N3 D:U171 4.2 64.2 1.0
C5 D:U170 4.3 62.4 1.0
O3' D:G169 4.3 70.1 1.0
OP2 D:G169 4.4 82.3 1.0
C3' D:G169 4.5 68.3 1.0
OP1 D:G169 4.5 72.5 1.0
O5' D:U170 4.6 65.5 1.0
P D:G169 4.6 80.5 1.0
OP1 D:U170 4.7 71.6 1.0
C6 D:U170 4.8 65.1 1.0
C5' D:G169 5.0 70.4 1.0
OP2 D:A174 5.0 71.9 1.0

Magnesium binding site 5 out of 9 in 3cun

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Magnesium binding site 5 out of 9 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:Mg506

b:91.4
occ:1.00
 O6 C:G68 3.5 75.0 1.0
N7 C:G68 3.9 79.8 1.0
O6 C:G69 4.0 97.2 1.0
OP2 C:A75 4.0 0.0 1.0
N7 C:G69 4.2 93.5 1.0
C6 C:G68 4.2 78.4 1.0
C5 C:G68 4.4 81.6 1.0
O4 C:U70 4.5 87.4 1.0
OP1 C:A75 4.6 0.1 1.0
C6 C:G69 4.7 92.9 1.0
P C:A75 4.8 0.2 1.0
C5 C:G69 4.8 93.2 1.0
C8 C:G68 5.0 84.0 1.0

Magnesium binding site 6 out of 9 in 3cun

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Magnesium binding site 6 out of 9 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:Mg507

b:56.0
occ:1.00
 O2B C:GTP1 2.0 0.1 1.0
OP2 C:G2 3.1 97.2 1.0
O2A C:GTP1 3.1 0.0 1.0
PB C:GTP1 3.5 0.7 1.0
O3G C:GTP1 3.7 0.7 1.0
N7 C:A3 3.9 81.4 1.0
P C:G2 3.9 94.4 1.0
O3A C:GTP1 4.0 0.3 1.0
O5' C:G2 4.1 89.5 1.0
O3B C:GTP1 4.2 1.0 1.0
PA C:GTP1 4.2 0.6 1.0
OP1 C:G2 4.2 91.9 1.0
OP2 C:A3 4.3 86.3 1.0
N7 C:G2 4.4 78.0 1.0
O1B C:GTP1 4.5 0.7 1.0
N6 C:A3 4.5 78.8 1.0
C8 C:G2 4.6 80.1 1.0
PG C:GTP1 4.6 0.2 1.0
C8 C:A3 4.8 84.7 1.0
C5 C:A3 4.9 83.4 1.0
O4 C:U4 5.0 85.0 1.0

Magnesium binding site 7 out of 9 in 3cun

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Magnesium binding site 7 out of 9 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:Mg510

b:48.5
occ:1.00
 O1G C:GTP1 3.0 0.1 1.0
O1B C:GTP1 3.0 0.7 1.0
O3G C:GTP1 3.8 0.7 1.0
N4 C:C13 3.8 75.6 1.0
PG C:GTP1 3.9 0.2 1.0
O2B C:GTP1 4.0 0.1 1.0
PB C:GTP1 4.0 0.7 1.0
N4 C:C14 4.1 79.1 1.0
C5 C:C13 4.1 79.5 1.0
C4 C:C13 4.3 76.5 1.0
C5 C:C14 4.5 76.9 1.0
O3B C:GTP1 4.6 1.0 1.0
C4 C:C14 4.8 76.4 1.0

Magnesium binding site 8 out of 9 in 3cun

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Magnesium binding site 8 out of 9 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
D:Mg512

b:0.5
occ:1.00
 O2G D:GTP101 3.8 1.0 1.0
O6 D:G112 4.0 73.8 1.0
OP2 D:A111 4.1 68.6 1.0
N7 D:G112 4.2 71.0 1.0
C6 D:G112 4.8 72.0 1.0
C5 D:G112 4.9 69.4 1.0

Magnesium binding site 9 out of 9 in 3cun

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Magnesium binding site 9 out of 9 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:Mg513

b:0.3
occ:1.00
 OP2 D:C129 2.1 0.2 1.0
OP1 D:C128 2.9 0.7 1.0
P D:C129 3.1 0.2 1.0
O3' D:C128 3.6 0.5 1.0
OP1 D:C129 3.6 0.2 1.0
P D:C128 3.6 0.2 1.0
O5' D:C128 3.7 0.8 1.0
C5' D:C128 3.9 0.9 1.0
OP2 D:C128 3.9 0.7 1.0
C3' D:C128 3.9 0.0 1.0
C4' D:C128 4.5 0.1 1.0
O5' D:C129 4.5 0.4 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: Mon Dec 14 08:02:25 2020

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