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: Wed Aug 14 11:53:03 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy