Calcium in PDB 5i4s: Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine

The structure of Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine, PDB code: 5i4s was solved by A.F.Ahmad Sobri, R.L.Brady, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.91 / 2.46
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	41.487, 41.487, 101.738, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 26.8

The binding sites of Calcium atom in the Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine (pdb code 5i4s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine, PDB code: 5i4s:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:88.8 occ:1.00 O2 A:DT8 2.7 59.7 1.0 N3 B:DA18 3.1 41.2 1.0 O4' A:1W59 3.3 62.3 1.0 C2 B:DA18 3.4 38.6 1.0 O4' B:DT19 3.6 66.1 1.0 C4' A:1W59 3.7 64.0 1.0 C2 A:DT8 3.9 51.9 1.0 C5' A:1W59 4.0 68.9 1.0 C1' A:DT8 4.0 61.3 1.0 C4' B:DT19 4.1 62.8 1.0 C1' A:1W59 4.2 67.8 1.0 C4 B:DA18 4.3 36.4 1.0 C1' B:DT19 4.5 64.4 1.0 N1 A:DT8 4.5 57.3 1.0 N1 B:DA18 4.6 39.9 1.0 C5' B:DT19 4.7 56.4 1.0 C2' A:DT8 4.7 59.2 1.0 C1 A:1W59 4.8 71.3 1.0 C1' B:DA18 4.8 50.7 1.0 O2 B:DT19 4.8 49.8 1.0 O B:HOH202 4.8 41.8 1.0 C2 B:DA17 4.9 50.9 1.0 O3' A:DT8 4.9 61.0 1.0 O4' A:DT8 4.9 60.1 1.0 O5' A:1W59 4.9 66.2 1.0 N1 B:DT19 5.0 54.7 1.0 N3 A:DT8 5.0 46.1 1.0 N9 B:DA18 5.0 42.7 1.0

Calcium binding site 2 out of 8 in the Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:74.4 occ:1.00 OP2 A:DG12 2.7 43.1 1.0 O A:HOH203 3.2 71.6 1.0 P A:DG12 3.8 45.7 1.0 O3' A:DC11 4.1 39.9 1.0 OP1 A:DG12 4.2 42.6 1.0 C3' A:DC11 4.4 40.6 1.0 C4' A:DC11 4.7 45.9 1.0 C5' A:DC11 4.9 47.1 1.0

Calcium binding site 3 out of 8 in the Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:76.2 occ:1.00 OP2 A:DT8 3.0 78.6 1.0 O A:HOH205 3.1 54.3 1.0 C2' A:DT7 3.6 62.7 1.0 C3' A:DT7 3.9 69.1 1.0 C7 A:DT8 4.3 54.2 1.0 P A:DT8 4.4 84.2 1.0 O5' A:DT7 4.6 89.2 1.0 O3' A:DT7 4.7 71.7 1.0 OP2 A:DT7 4.8 0.2 1.0 OP1 A:DT7 4.9 97.4 1.0 P A:DT7 5.0 98.7 1.0

Calcium binding site 4 out of 8 in the Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca104 b:0.8 occ:1.00 OP2 A:DG10 2.7 75.8 1.0 C2' A:1W59 3.7 70.2 1.0 C3' A:1W59 3.8 62.0 1.0 P A:DG10 3.9 73.1 1.0 O5' A:DG10 4.1 63.5 1.0 C8 A:DG10 4.2 50.2 1.0 O3' A:1W59 4.4 68.8 1.0 N7 A:DG10 4.8 47.8 1.0 O5' A:1W59 4.9 66.2 1.0

Calcium binding site 5 out of 8 in the Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:58.8 occ:1.00 OP1 B:DG24 2.0 49.2 1.0 O B:HOH208 2.5 39.7 1.0 P B:DG24 3.3 46.6 1.0 O3' B:DC23 3.8 44.3 1.0 OP2 B:DG24 4.1 48.8 1.0 O5' B:DG24 4.4 45.7 1.0 C5' B:DG24 4.9 44.7 1.0

Calcium binding site 6 out of 8 in the Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine within 5.0Å range:

Calcium binding site 7 out of 8 in the Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca103 b:0.1 occ:1.00 OP1 B:DT20 3.7 67.5 1.0 P B:DT20 5.0 76.4 1.0

Calcium binding site 8 out of 8 in the Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)- Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca104 b:0.5 occ:1.00 OP2 B:1W521 2.9 83.9 1.0 OP1 B:1W521 3.3 78.1 1.0 P B:1W521 3.6 79.6 1.0 O3' B:DT20 4.6 76.1 1.0 C3' B:DT20 4.8 66.2 1.0 O5' B:1W521 4.9 77.0 1.0

A.F.Ahmad Sobri, R.L.Brady. Non-Natural Dna Pair Z (6-Amino-5-Nitro-2[1H] Pyridone Heterocycle)-Guanosine To Be Published.