Calcium in PDB 4meh: In Vitro Evolved Glms Ribozyme Triple Mutant, Calcium Ion Complex

The structure of In Vitro Evolved Glms Ribozyme Triple Mutant, Calcium Ion Complex, PDB code: 4meh 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)	28.86 / 3.12
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	177.910, 41.170, 75.850, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 27.3

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

Calcium binding site 1 out of 9 in the In Vitro Evolved Glms Ribozyme Triple Mutant, Calcium Ion Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of In Vitro Evolved Glms Ribozyme Triple Mutant, Calcium Ion Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:0.1 occ:1.00 OP1 A:G1 2.8 92.2 1.0 N2 B:G47 2.9 0.1 1.0 C2 B:G47 3.8 0.2 1.0 P A:G1 3.8 94.4 1.0 O5' A:G1 4.0 92.4 1.0 N3 A:G1 4.0 84.7 1.0 C4 A:G1 4.0 83.6 1.0 N1 B:G47 4.1 0.7 1.0 O3' A:DA0 4.1 90.6 1.0 C2 A:G1 4.1 84.6 1.0 C5 A:G1 4.3 83.6 1.0 N1 A:G1 4.3 83.5 1.0 C6 A:G1 4.4 82.7 1.0 C5' A:G1 4.5 88.0 1.0 O4' A:G1 4.5 84.6 1.0 N9 A:G1 4.6 83.1 1.0 N2 A:G1 4.7 83.3 1.0 N3 B:G47 4.8 0.1 1.0 C5 A:C2 4.9 88.1 1.0 N7 A:G1 4.9 83.3 1.0

Calcium binding site 2 out of 9 in the In Vitro Evolved Glms Ribozyme Triple Mutant, Calcium Ion Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of In Vitro Evolved Glms Ribozyme Triple Mutant, Calcium Ion Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:0.6 occ:1.00 OP2 B:U48 2.3 0.9 1.0 C3' B:G47 2.6 0.6 1.0 C2' B:G47 3.1 0.3 1.0 N1 B:A30 3.1 0.6 1.0 N6 B:A30 3.3 0.5 1.0 P B:U48 3.3 0.3 1.0 O3' B:G47 3.3 0.6 1.0 O5' B:G47 3.4 0.1 1.0 C8 B:G47 3.6 0.1 1.0 N9 B:G47 3.6 0.1 1.0 C4' B:G47 3.7 0.5 1.0 C6 B:A30 3.7 0.1 1.0 C1' B:G47 3.7 0.9 1.0 O5' B:U48 3.9 0.2 1.0 O4' B:G47 4.0 0.8 1.0 C5' B:G47 4.0 0.5 1.0 C2 B:A30 4.2 0.9 1.0 N7 B:G47 4.3 0.1 1.0 O2' B:G47 4.3 0.3 1.0 C4 B:G47 4.4 0.6 1.0 N7 B:G49 4.5 0.7 1.0 OP1 B:U48 4.7 0.8 1.0 OP2 B:G47 4.7 0.2 1.0 P B:G47 4.7 0.2 1.0 C5 B:G47 4.7 0.5 1.0 O6 B:G49 4.8 0.3 1.0 O4 B:U28 4.9 0.6 1.0

Calcium binding site 3 out of 9 in the In Vitro Evolved Glms Ribozyme Triple Mutant, Calcium Ion Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of In Vitro Evolved Glms Ribozyme Triple Mutant, Calcium Ion Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:0.5 occ:1.00 OP2 B:C41 2.6 81.0 1.0 OP2 B:G42 2.9 90.0 1.0 OP1 B:C41 2.9 80.0 1.0 P B:C41 3.1 81.7 1.0 O5' B:C41 3.5 81.4 1.0 N6 B:A16 3.6 84.1 1.0 P B:G42 4.3 92.4 1.0 N7 B:A16 4.3 78.9 1.0 C6 B:A16 4.5 81.8 1.0 N7 B:G42 4.6 91.9 1.0 C4' B:U40 4.6 72.2 1.0 O3' B:U40 4.6 80.3 1.0 C5 B:A16 4.7 79.8 1.0 C3' B:C41 4.7 84.9 1.0 O3' B:C41 4.8 88.0 1.0 O5' B:G42 4.8 91.1 1.0 C8 B:G42 4.9 92.3 1.0 C5' B:C41 4.9 84.0 1.0 C5' B:U40 4.9 71.5 1.0

Calcium binding site 4 out of 9 in the In Vitro Evolved Glms Ribozyme Triple Mutant, Calcium Ion Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of In Vitro Evolved Glms Ribozyme Triple Mutant, Calcium Ion Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:0.6 occ:1.00 O2 B:U48 2.3 0.3 1.0 O2' B:U48 2.6 0.2 1.0 OP2 B:G22 2.6 85.0 1.0 C2' B:G21 2.7 78.7 1.0 C3' B:G21 2.9 79.3 1.0 C2 B:U48 3.3 0.6 1.0 O3' B:G21 3.3 81.8 1.0 O4' B:G22 3.4 0.7 1.0 C2' B:U48 3.4 0.5 1.0 N9 B:G21 3.4 78.2 1.0 P B:G22 3.5 86.8 1.0 C1' B:U48 3.6 0.3 1.0 O2' B:G21 3.6 78.7 1.0 C1' B:G21 3.6 78.1 1.0 C4 B:G21 3.7 77.8 1.0 C8 B:G21 3.7 77.7 1.0 C8 B:G22 3.8 0.1 1.0 N1 B:U48 3.9 0.7 1.0 N9 B:G22 3.9 0.8 1.0 C5 B:G21 4.0 78.1 1.0 N7 B:G21 4.1 78.0 1.0 O5' B:G22 4.1 89.9 1.0 C1' B:G22 4.2 0.9 1.0 N3 B:G21 4.2 79.5 1.0 N7 B:G22 4.2 0.4 1.0 C4' B:G21 4.3 77.5 1.0 C5' B:G22 4.3 98.6 1.0 N3 B:U48 4.4 0.3 1.0 C4 B:G22 4.4 0.4 1.0 C4' B:G22 4.5 0.7 1.0 O4' B:G21 4.5 76.4 1.0 C5 B:G22 4.6 0.2 1.0 C3' B:U48 4.8 0.5 1.0 O4' B:U48 4.8 0.7 1.0 OP1 B:G22 4.8 83.9 1.0 C6 B:G21 4.9 78.8 1.0 O5' B:G21 4.9 75.0 1.0 C2 B:G21 4.9 80.6 1.0

Calcium binding site 5 out of 9 in the In Vitro Evolved Glms Ribozyme Triple Mutant, Calcium Ion Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of In Vitro Evolved Glms Ribozyme Triple Mutant, Calcium Ion Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:66.8 occ:1.00 OP2 A:C2 2.5 79.2 1.0 OP2 B:G18 2.5 64.4 1.0 OP2 B:C17 2.7 62.8 1.0 O3' B:A16 3.1 64.4 1.0 P B:C17 3.5 60.6 1.0 O3' A:G1 3.5 80.3 1.0 P A:C2 3.5 78.3 1.0 P B:G18 3.6 62.8 1.0 OP1 B:G18 3.9 59.1 1.0 C5' A:C2 4.0 83.5 1.0 O5' B:C17 4.0 62.1 1.0 O2' B:A16 4.1 81.8 1.0 O5' A:C2 4.3 79.7 1.0 C3' B:C17 4.4 59.6 1.0 C3' B:A16 4.4 70.3 1.0 O3' B:C17 4.5 60.4 1.0 C2' B:A16 4.8 74.8 1.0 OP1 A:C2 4.8 81.4 1.0 OP1 B:C17 4.8 64.5 1.0 O5' B:G18 4.9 58.9 1.0 O2' A:G1 4.9 83.4 1.0 C3' A:G1 4.9 83.1 1.0 C5' B:C17 4.9 61.0 1.0

Calcium binding site 6 out of 9 in the In Vitro Evolved Glms Ribozyme Triple Mutant, Calcium Ion Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of In Vitro Evolved Glms Ribozyme Triple Mutant, Calcium Ion Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca205 b:0.7 occ:1.00 C5' B:G22 3.2 98.6 1.0 O5' B:G22 3.3 89.9 1.0 OP1 B:G22 3.4 83.9 1.0 OP1 B:G71 3.8 0.3 1.0 P B:G22 3.8 86.8 1.0 O5' B:G71 3.8 0.7 1.0 O3' B:G21 3.9 81.8 1.0 P B:G71 4.2 1.0 1.0 C4' B:G22 4.5 0.7 1.0 C5' B:G71 4.5 0.7 1.0 OP2 B:C23 4.6 0.5 1.0 OP2 B:G71 4.6 0.1 1.0 OP1 B:C23 4.6 0.5 1.0 P B:C23 4.9 0.6 1.0 OP1 B:U72 5.0 0.0 1.0 C3' B:G71 5.0 0.7 1.0

Calcium binding site 7 out of 9 in the In Vitro Evolved Glms Ribozyme Triple Mutant, Calcium Ion Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of In Vitro Evolved Glms Ribozyme Triple Mutant, Calcium Ion Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca206 b:0.6 occ:1.00 OP1 A:C2 2.2 81.4 1.0 O6 B:G20 2.3 74.6 1.0 C6 B:G20 3.5 73.0 1.0 P A:C2 3.6 78.3 1.0 N7 B:A19 4.0 71.9 1.0 O5' A:C2 4.3 79.7 1.0 C5 B:G20 4.3 71.6 1.0 O6 B:G21 4.3 79.1 1.0 OP2 A:C2 4.3 79.2 1.0 OP2 B:A19 4.3 64.7 1.0 N7 B:G20 4.3 71.3 1.0 N1 B:G20 4.5 73.1 1.0 O3' A:G1 4.6 80.3 1.0 N6 B:A19 4.7 72.4 1.0 C3' A:G1 4.7 83.1 1.0 C8 B:A19 4.8 69.6 1.0 C6 B:G21 4.9 78.8 1.0 C5 B:A19 4.9 71.6 1.0

Calcium binding site 8 out of 9 in the In Vitro Evolved Glms Ribozyme Triple Mutant, Calcium Ion Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of In Vitro Evolved Glms Ribozyme Triple Mutant, Calcium Ion Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca207 b:0.1 occ:1.00 N2 B:G27 2.8 0.8 1.0 O2 B:C50 3.1 0.3 1.0 C1' B:C51 3.4 0.7 1.0 O2 B:C51 3.5 0.5 1.0 N1 B:C51 3.7 0.7 1.0 C2 B:C51 3.8 0.9 1.0 C2 B:G27 3.8 0.6 1.0 C2 B:C50 3.8 0.9 1.0 O4' B:C51 3.9 0.7 1.0 N3 B:C50 3.9 0.1 1.0 N3 B:G27 4.1 0.7 1.0 O2 B:U28 4.2 0.6 1.0 C2 B:U28 4.4 1.0 1.0 C1' B:U28 4.4 0.6 1.0 N1 B:U28 4.5 0.1 1.0 C6 B:C51 4.6 1.0 1.0 C2' B:C51 4.6 0.5 1.0 O2' B:C51 4.7 0.1 1.0 N3 B:C51 4.7 0.4 1.0 O4' B:U28 4.8 0.6 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of In Vitro Evolved Glms Ribozyme Triple Mutant, Calcium Ion Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca208 b:0.3 occ:1.00 OP1 B:G54 2.8 0.8 1.0 OP1 B:C66 4.1 0.6 1.0 P B:G54 4.1 0.2 1.0 O5' B:G54 4.7 0.5 1.0 OP2 B:G54 4.7 0.5 1.0 OP2 B:C55 4.9 0.3 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