Magnesium in PDB 2quw: Hammerhead Ribozyme G12A Mutant After Cleavage

The structure of Hammerhead Ribozyme G12A Mutant After Cleavage, PDB code: 2quw was solved by Y.I.Chi, W.G.Scott, S.H.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.46 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	28.030, 53.140, 72.050, 74.24, 81.37, 75.65
R / Rfree (%)	19.9 / 26.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Magnesium atom in the Hammerhead Ribozyme G12A Mutant After Cleavage (pdb code 2quw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 17 binding sites of Magnesium where determined in the Hammerhead Ribozyme G12A Mutant After Cleavage, PDB code: 2quw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 17 in the Hammerhead Ribozyme G12A Mutant After Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hammerhead Ribozyme G12A Mutant After Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg13 b:69.0 occ:1.00 O1C A:CCC12 2.6 64.5 1.0 OP1 B:C14 2.9 62.5 1.0 P B:C14 3.7 61.4 1.0 PC A:CCC12 3.7 65.0 1.0 C3' A:CCC12 3.8 61.5 1.0 O3' B:A13 3.9 61.7 1.0 OP2 B:C14 4.0 61.5 1.0 O3' A:CCC12 4.0 64.8 1.0 O2' A:CCC12 4.1 65.3 1.0 C2' A:CCC12 4.3 62.6 1.0 C5' B:A13 4.6 61.1 1.0 O5' B:A13 4.7 64.1 1.0 C3' B:A13 4.9 60.4 1.0 O2C A:CCC12 5.0 66.6 1.0 C4' B:A13 5.0 60.5 1.0

Magnesium binding site 2 out of 17 in the Hammerhead Ribozyme G12A Mutant After Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hammerhead Ribozyme G12A Mutant After Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1 b:69.3 occ:1.00 O B:HOH78 2.3 53.4 1.0 O6 B:G17 3.7 60.7 1.0 N7 B:G16 4.1 58.1 1.0 N7 B:G17 4.1 60.8 1.0 O2' B:A46 4.2 70.9 1.0 O6 B:G16 4.2 58.6 1.0 OP1 B:G47 4.3 72.9 1.0 C6 B:G17 4.6 59.9 1.0 C5 B:G16 4.7 59.3 1.0 OP2 B:G47 4.7 72.1 1.0 C6 B:G16 4.7 59.6 1.0 C5 B:G17 4.8 60.1 1.0 O B:HOH76 4.9 64.1 1.0 P B:G47 5.0 72.9 1.0 C8 B:G16 5.0 58.9 1.0

Magnesium binding site 3 out of 17 in the Hammerhead Ribozyme G12A Mutant After Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hammerhead Ribozyme G12A Mutant After Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2 b:67.9 occ:1.00 N1 B:G22 2.6 82.1 1.0 OP2 B:G45 2.8 87.8 1.0 N2 B:G22 3.0 82.1 1.0 C2 B:G22 3.3 82.3 1.0 C6 B:G22 3.6 81.3 1.0 O6 B:G22 3.6 81.9 1.0 O2 B:C23 3.7 87.8 1.0 O3' B:U44 3.9 84.8 1.0 O2 B:U21 4.0 73.8 1.0 P B:G45 4.0 86.9 1.0 N3 B:U24 4.0 75.0 1.0 O2 B:U24 4.1 75.9 1.0 C2 B:U24 4.1 76.5 1.0 C2 B:C23 4.4 88.7 1.0 O2' B:U24 4.6 81.3 1.0 C2 B:U21 4.6 74.3 1.0 N3 B:G22 4.6 82.0 1.0 O2' B:U44 4.6 82.7 1.0 N3 B:C23 4.6 88.4 1.0 C4 B:U24 4.7 75.3 1.0 N1 B:A46 4.7 69.6 1.0 N1 B:U24 4.7 76.9 1.0 N3 B:U21 4.8 73.5 1.0 C5 B:G22 4.8 81.2 1.0 C2 B:A46 4.8 70.5 1.0

Magnesium binding site 4 out of 17 in the Hammerhead Ribozyme G12A Mutant After Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Hammerhead Ribozyme G12A Mutant After Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4 b:85.8 occ:1.00 N1 B:A38 2.6 69.3 1.0 O4' B:A51 2.9 70.1 1.0 C1' B:A51 2.9 68.1 1.0 O3' B:A51 3.3 71.3 1.0 C4' B:A51 3.5 70.1 1.0 C2 B:A38 3.5 70.1 1.0 C8 B:A52 3.5 65.8 1.0 C6 B:A38 3.5 70.2 1.0 N6 B:A38 3.6 70.3 1.0 C2 B:G39 3.6 70.0 1.0 N2 B:G39 3.7 70.1 1.0 N3 B:A51 3.7 66.4 1.0 N1 B:G39 3.7 70.3 1.0 N7 B:A52 3.7 64.7 1.0 C3' B:A51 3.7 70.6 1.0 N9 B:A51 3.9 66.7 1.0 C2' B:A51 3.9 70.2 1.0 N3 B:G39 4.1 70.0 1.0 C4 B:A51 4.2 65.9 1.0 O4' B:A52 4.3 66.5 1.0 O2 B:C50 4.3 67.2 1.0 C6 B:G39 4.3 70.2 1.0 N9 B:A52 4.3 65.8 1.0 O2' B:A51 4.5 71.1 1.0 C4 B:G39 4.6 69.8 1.0 O B:HOH73 4.7 57.8 1.0 C5 B:A52 4.7 66.0 1.0 N3 B:C50 4.7 65.2 1.0 C5 B:G39 4.7 69.7 1.0 P B:A52 4.8 70.2 1.0 C2 B:C50 4.8 66.3 1.0 N3 B:A38 4.8 70.3 1.0 O5' B:A52 4.8 68.6 1.0 C5 B:A38 4.9 70.3 1.0 C2 B:A51 4.9 66.0 1.0 C5' B:A51 4.9 70.8 1.0 C1' B:A52 4.9 66.2 1.0 O6 B:G39 4.9 69.8 1.0

Magnesium binding site 5 out of 17 in the Hammerhead Ribozyme G12A Mutant After Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Hammerhead Ribozyme G12A Mutant After Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg6 b:74.7 occ:1.00 OP2 B:A38 2.2 71.5 1.0 P B:A38 3.6 69.3 1.0 O5' B:A38 4.0 70.0 1.0 O2C A:CCC12 4.2 66.6 1.0 N7 B:A38 4.3 70.6 1.0 O3' B:G37 4.3 68.5 1.0 N7 B:G39 4.5 69.6 1.0 O2' B:G37 4.5 65.0 1.0 O1C A:CCC12 4.6 64.5 1.0 C8 B:A38 4.6 70.2 1.0 OP1 B:A38 4.7 70.3 1.0 OP2 B:G39 4.8 75.7 1.0 C2' B:G37 4.8 65.7 1.0

Magnesium binding site 6 out of 17 in the Hammerhead Ribozyme G12A Mutant After Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Hammerhead Ribozyme G12A Mutant After Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg7 b:70.9 occ:1.00 O2 A:U11 2.7 63.2 1.0 O2 B:C55 2.8 63.0 1.0 N9 B:G34 2.9 61.2 1.0 C4 B:G34 3.1 60.9 1.0 C1' B:G34 3.3 61.6 1.0 C8 B:G34 3.3 61.0 1.0 O4' B:G34 3.5 64.1 1.0 N2 A:G10 3.6 68.8 1.0 N3 B:G34 3.6 60.5 1.0 C2 A:U11 3.6 63.9 1.0 C5 B:G34 3.6 61.2 1.0 C2 B:A54 3.7 62.8 1.0 N7 B:G34 3.8 61.1 1.0 C2 B:C55 3.8 63.1 1.0 N1 B:A54 4.3 62.0 1.0 C2 B:G34 4.3 60.8 1.0 N3 A:U11 4.3 63.2 1.0 N1 A:U11 4.4 63.5 1.0 C1' B:C55 4.4 65.2 1.0 C1' A:U11 4.4 64.3 1.0 C6 B:G34 4.5 61.1 1.0 N3 B:A54 4.5 63.8 1.0 N1 B:C55 4.5 64.4 1.0 C2 A:G10 4.6 68.9 1.0 N3 B:C55 4.6 62.6 1.0 C2' B:G34 4.7 63.6 1.0 N1 B:G34 4.7 61.4 1.0 O2' A:U11 4.9 65.1 1.0 O2' B:C55 4.9 70.0 1.0 C4' B:G34 5.0 64.2 1.0

Magnesium binding site 7 out of 17 in the Hammerhead Ribozyme G12A Mutant After Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Hammerhead Ribozyme G12A Mutant After Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg10 b:83.0 occ:1.00 O3' B:A66 3.7 59.7 1.0 O B:HOH89 3.8 58.4 1.0 OP1 B:A67 3.9 59.7 1.0 O2' B:A66 4.1 63.8 1.0 OP1 D:U24 4.3 84.7 1.0 P B:A67 4.5 59.7 1.0 C4' B:A66 4.5 62.9 1.0 C5' B:A67 4.6 61.5 1.0 C3' B:A66 4.6 61.7 1.0 O3' D:C23 4.7 86.0 1.0 C1' D:C23 4.7 83.0 1.0 O4' D:C23 5.0 85.0 1.0 C2' B:A66 5.0 63.2 1.0

Magnesium binding site 8 out of 17 in the Hammerhead Ribozyme G12A Mutant After Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Hammerhead Ribozyme G12A Mutant After Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg70 b:86.0 occ:1.00 N3 B:G22 1.9 82.0 1.0 O4' B:C23 2.2 90.2 1.0 N2 B:G22 2.2 82.1 1.0 C2 B:G22 2.4 82.3 1.0 N1 B:C23 2.7 89.4 1.0 O5' B:C23 2.9 94.4 1.0 C6 B:C23 2.9 88.8 1.0 C1' B:C23 3.0 89.9 1.0 C3' B:G22 3.1 88.9 1.0 C5' B:C23 3.1 93.2 1.0 C4' B:C23 3.2 91.5 1.0 C4 B:G22 3.2 81.7 1.0 C2' B:G22 3.3 87.6 1.0 C2 B:C23 3.3 88.7 1.0 C5 B:U24 3.4 75.8 1.0 C5 B:C23 3.6 88.7 1.0 N1 B:G22 3.8 82.1 1.0 C6 B:U24 3.8 76.8 1.0 O2 B:C23 3.9 87.8 1.0 N3 B:C23 3.9 88.4 1.0 N9 B:G22 4.0 82.5 1.0 O3' B:G22 4.0 92.3 1.0 C1' B:G22 4.0 83.8 1.0 C4 B:C23 4.0 89.2 1.0 P B:C23 4.1 94.7 1.0 C2' B:C23 4.1 91.2 1.0 C4' B:G22 4.1 88.0 1.0 C4 B:U24 4.2 75.3 1.0 O4' B:G22 4.2 87.3 1.0 C3' B:C23 4.3 91.5 1.0 C5 B:G22 4.4 81.2 1.0 C5' B:G22 4.4 87.7 1.0 O2' B:G22 4.5 88.2 1.0 O4 B:U24 4.5 75.0 1.0 OP2 B:C23 4.6 93.2 1.0 C6 B:G22 4.7 81.3 1.0 N1 B:U24 4.7 76.9 1.0 O B:HOH95 4.9 76.2 1.0 N3 B:U24 5.0 75.0 1.0

Magnesium binding site 9 out of 17 in the Hammerhead Ribozyme G12A Mutant After Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Hammerhead Ribozyme G12A Mutant After Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg71 b:90.0 occ:1.00 N7 B:G57 2.4 75.2 1.0 C8 B:G57 3.1 75.3 1.0 OP2 B:G57 3.2 80.4 1.0 N7 B:A56 3.3 68.8 1.0 C8 B:A56 3.4 69.0 1.0 C5 B:G57 3.7 74.8 1.0 C5 B:A56 3.8 68.1 1.0 N9 B:A56 3.8 69.6 1.0 C3' B:A56 4.0 73.4 1.0 O6 B:G57 4.1 75.4 1.0 C4 B:A56 4.1 68.8 1.0 O5' B:A56 4.3 73.7 1.0 C6 B:G57 4.3 75.5 1.0 P B:G57 4.3 80.8 1.0 C2' B:A56 4.3 72.3 1.0 O5' B:G57 4.4 78.7 1.0 N9 B:G57 4.4 75.7 1.0 OP2 B:A56 4.4 74.1 1.0 C6 B:A56 4.6 69.4 1.0 C1' B:A56 4.6 70.3 1.0 C4 B:G57 4.7 75.0 1.0 O3' B:A56 4.7 77.8 1.0

Magnesium binding site 10 out of 17 in the Hammerhead Ribozyme G12A Mutant After Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Hammerhead Ribozyme G12A Mutant After Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg72 b:88.1 occ:1.00 N7 B:G29 2.6 58.7 1.0 C5 B:C28 3.3 58.7 1.0 C8 B:G29 3.5 59.5 1.0 C4 B:C28 3.6 59.2 1.0 C5 B:G29 3.8 59.6 1.0 C6 B:C28 3.8 59.1 1.0 N4 B:C28 3.8 59.7 1.0 O6 B:G29 4.0 59.7 1.0 OP2 B:G29 4.2 65.7 1.0 C6 B:G29 4.3 59.1 1.0 N3 B:C28 4.3 58.5 1.0 N1 B:C28 4.5 61.3 1.0 C2 B:C28 4.7 61.0 1.0 N9 B:G29 4.7 59.8 1.0 C4 B:G29 4.9 60.5 1.0

Y.I.Chi, M.Martick, M.Lares, R.Kim, W.G.Scott, S.H.Kim. Capturing Hammerhead Ribozyme Structures in Action By Modulating General Base Catalysis. Plos Biol. V. 6 E234 2008.
ISSN: ISSN 1544-9173
PubMed: 18834200
DOI: 10.1371/JOURNAL.PBIO.0060234