Magnesium in PDB 4meg: In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex

The structure of In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex, PDB code: 4meg was solved by M.W.L.Lau, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.88 / 3.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	166.900, 40.400, 73.600, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 25.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex (pdb code 4meg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex, PDB code: 4meg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in the In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:73.2 occ:1.00 O4 A:U11 3.9 71.4 1.0 O4 A:U12 4.5 71.9 1.0 C4 A:U11 4.5 70.5 1.0 O4 B:U8 4.6 1.0 1.0 C5 A:U11 4.6 68.8 1.0 O4 B:U9 4.8 99.2 1.0

Magnesium binding site 2 out of 16 in the In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:27.0 occ:1.00 OP2 B:C17 2.0 55.5 1.0 OP2 A:C2 2.1 81.5 1.0 OP2 B:G18 2.1 50.0 1.0 O3' B:A16 3.0 54.9 1.0 P B:C17 3.0 55.4 1.0 P B:G18 3.2 49.9 1.0 O2' A:G1 3.4 87.3 1.0 OP1 B:G18 3.6 50.4 1.0 P A:C2 3.6 81.7 1.0 O5' B:C17 3.8 51.5 1.0 C3' B:C17 3.8 48.8 1.0 O3' B:C17 4.0 48.3 1.0 O2' B:A16 4.1 57.9 1.0 C5' A:C2 4.3 78.8 1.0 OP1 B:C17 4.3 56.2 1.0 C3' B:A16 4.4 54.9 1.0 C5' B:C17 4.4 50.1 1.0 OP1 A:C2 4.4 82.2 1.0 O5' A:C2 4.5 80.0 1.0 C2' A:G1 4.5 84.0 1.0 O5' B:G18 4.5 47.6 1.0 O3' A:G1 4.6 83.4 1.0 C8 B:G18 4.6 50.8 1.0 C4' B:C17 4.7 49.7 1.0 C5' B:G18 4.8 46.0 1.0 C2' B:A16 4.9 55.2 1.0 N7 B:G18 4.9 52.1 1.0 C2' B:C17 5.0 47.9 1.0

Magnesium binding site 3 out of 16 in the In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:57.2 occ:1.00 N4 B:C59 3.5 67.2 1.0 O6 B:G120 3.9 78.5 1.0 C4 B:C59 4.3 66.5 1.0 O4 B:U64 4.3 79.7 1.0 C5 B:C59 4.4 66.6 1.0 N4 B:C66 4.7 91.8 1.0

Magnesium binding site 4 out of 16 in the In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:52.6 occ:1.00 O6 B:G54 3.5 78.0 1.0 O4 B:U53 3.9 99.6 1.0 O6 B:G71 3.9 67.5 1.0 N4 B:C70 4.2 67.7 1.0 C4 B:U53 4.6 99.8 1.0 C6 B:G54 4.6 78.2 1.0 N4 B:C55 4.7 77.8 1.0 N4 B:C23 4.8 74.7 1.0 C5 B:U53 4.9 99.9 1.0 N7 B:G54 4.9 79.2 1.0 C6 B:G71 5.0 67.5 1.0

Magnesium binding site 5 out of 16 in the In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg204 b:52.8 occ:1.00 OP2 B:A85 2.2 85.9 1.0 O4 B:U107 2.6 48.2 1.0 OP2 B:A86 2.8 44.7 1.0 C4 B:U107 3.2 48.3 1.0 C5 B:U107 3.2 48.9 1.0 P B:A85 3.4 86.0 1.0 N7 B:A106 3.7 32.3 1.0 OP2 B:A106 3.8 39.5 1.0 OP1 B:A85 3.8 86.0 1.0 P B:A86 3.9 45.3 1.0 C8 B:A106 4.1 31.9 1.0 OP1 B:A86 4.2 43.8 1.0 O3' B:U84 4.4 90.6 1.0 C6 B:U107 4.5 47.4 1.0 N3 B:U107 4.5 48.5 1.0 O5' B:A85 4.6 78.8 1.0 C5 B:A106 4.6 31.4 1.0 O3' B:A85 4.7 49.0 1.0 C3' B:A85 4.8 51.5 1.0 O5' B:A106 5.0 38.8 1.0

Magnesium binding site 6 out of 16 in the In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg205 b:47.0 occ:1.00 O4 B:U102 3.2 37.9 1.0 O6 B:G101 3.3 42.7 1.0 N7 B:G101 3.4 38.9 1.0 C6 B:G101 4.0 40.3 1.0 C5 B:G101 4.0 38.8 1.0 O4 B:U100 4.1 51.1 1.0 C4 B:U102 4.1 37.1 1.0 N6 B:A91 4.3 36.6 1.0 C4 B:U100 4.3 50.2 1.0 C8 B:G101 4.5 37.1 1.0 C5 B:U102 4.5 37.6 1.0 C5 B:U100 4.6 48.8 1.0 N3 B:U100 4.9 49.6 1.0

Magnesium binding site 7 out of 16 in the In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg206 b:67.1 occ:1.00 OP1 B:A87 2.4 43.9 1.0 O6 B:G104 2.8 39.6 1.0 N7 B:G104 3.3 38.5 1.0 C6 B:G104 3.6 38.7 1.0 P B:A87 3.8 43.5 1.0 C5 B:G104 3.8 39.0 1.0 O6 B:G103 3.9 41.9 1.0 N7 B:G103 4.0 44.8 1.0 C6 B:G103 4.3 43.5 1.0 C5 B:G103 4.4 44.5 1.0 OP2 B:A87 4.4 44.0 1.0 C8 B:G104 4.5 37.3 1.0 N4 B:C89 4.6 40.0 1.0 O3' B:A86 4.7 42.8 1.0 O5' B:A87 4.8 39.0 1.0 C8 B:G103 4.9 44.4 1.0 N1 B:G104 4.9 35.7 1.0

Magnesium binding site 8 out of 16 in the In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg207 b:62.7 occ:1.00 N2 B:G75 3.0 66.7 1.0 N1 B:G75 3.0 66.3 1.0 O2' B:G118 3.0 84.2 1.0 C4' B:G119 3.3 89.7 1.0 O4' B:G119 3.3 89.3 1.0 C2 B:G75 3.4 67.0 1.0 C5' B:G119 3.6 89.7 1.0 C2' B:G118 3.8 86.2 1.0 N1 B:A76 3.9 64.3 1.0 O3' B:G118 3.9 89.9 1.0 C6 B:G75 4.1 66.5 1.0 O5' B:G119 4.2 90.0 1.0 O6 B:G75 4.3 64.1 1.0 N6 B:A76 4.3 65.0 1.0 C6 B:A76 4.4 64.7 1.0 C3' B:G118 4.5 88.0 1.0 C2 B:A76 4.6 64.9 1.0 C3' B:G119 4.7 90.1 1.0 C1' B:G119 4.7 87.8 1.0 N3 B:G75 4.8 67.2 1.0 P B:G119 4.8 90.3 1.0

Magnesium binding site 9 out of 16 in the In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg208 b:50.0 occ:1.00 OP1 B:U102 2.7 38.6 1.0 P B:U102 3.7 38.2 1.0 O3' B:G101 4.1 36.7 1.0 OP2 B:U102 4.3 40.9 1.0

Magnesium binding site 10 out of 16 in the In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of In Vitro Evolved Glms Ribozyme Triple Mutant, Magnesium Ion Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg209 b:81.9 occ:1.00 OP1 B:U84 2.4 0.3 1.0 O5' B:U84 3.0 0.6 1.0 P B:U84 3.3 0.6 1.0 C5' B:A85 3.5 66.0 1.0 C2' B:U84 3.6 98.0 1.0 C3' B:U84 4.0 96.7 1.0 O5' B:A85 4.2 78.8 1.0 C5' B:U84 4.3 0.2 1.0 OP2 B:U84 4.3 0.1 1.0 C6 B:U84 4.4 0.8 1.0 O3' B:G83 4.4 0.2 1.0 O B:HOH301 4.4 60.7 1.0 O2' B:U84 4.5 96.7 1.0 C4' B:A85 4.5 55.9 1.0 MG B:MG211 4.5 92.7 1.0 C4' B:U84 4.7 0.5 1.0 C1' B:U84 4.7 0.0 1.0 N1 B:U84 4.8 0.3 1.0 O4' B:A85 4.8 52.4 1.0 O3' B:U84 5.0 90.6 1.0

M.W.Lau, A.R.Ferre-D'amare. An in Vitro Evolved Glms Ribozyme Has the Wild-Type Fold But Loses Coenzyme Dependence. Nat.Chem.Biol. V. 9 805 2013.
ISSN: ISSN 1552-4450
PubMed: 24096303
DOI: 10.1038/NCHEMBIO.1360