Atomistry » Magnesium » PDB 3cpw-3d19 » 3cul
Atomistry »
  Magnesium »
    PDB 3cpw-3d19 »
      3cul »

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

Go back to Magnesium Binding Sites List in 3cul
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

Go back to Magnesium Binding Sites List in 3cul
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

Go back to Magnesium Binding Sites List in 3cul
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

Go back to Magnesium Binding Sites List in 3cul
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

Go back to Magnesium Binding Sites List in 3cul
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

Go back to Magnesium Binding Sites List in 3cul
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

Go back to Magnesium Binding Sites List in 3cul
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

Go back to Magnesium Binding Sites List in 3cul
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

Go back to Magnesium Binding Sites List in 3cul
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

Go back to Magnesium Binding Sites List in 3cul
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: Mon Dec 14 08:02:25 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy