Nickel in PDB 5m68: At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination

The structure of At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination, PDB code: 5m68 was solved by J.L.Campos, N.Saperas, F.J.Acosta-Reyes, M.Pagan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.78 / 2.64
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	44.780, 44.780, 99.010, 90.00, 90.00, 120.00
R / Rfree (%)	22.7 / 24.7

Pages:

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

Binding sites:

The binding sites of Nickel atom in the At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination (pdb code 5m68). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 11 binding sites of Nickel where determined in the At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination, PDB code: 5m68:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 11 in the At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni101 b:56.3 occ:1.00 O A:HOH204 2.1 54.0 1.0 N7 A:DG24 2.1 54.5 1.0 O A:HOH205 2.1 54.5 1.0 O A:HOH201 2.1 55.6 1.0 O A:HOH208 2.1 55.4 1.0 C8 A:DG24 2.8 53.9 1.0 C5 A:DG24 3.2 54.2 1.0 O6 A:DG24 3.8 55.7 1.0 C6 A:DG24 3.8 54.7 1.0 N9 A:DG24 4.0 53.2 1.0 C4 A:DG24 4.2 53.8 1.0 OP2 A:DG24 4.4 48.7 1.0 C2' A:DC23 4.9 45.4 1.0 O5' A:DG24 5.0 48.4 1.0

Nickel binding site 2 out of 11 in the At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni102 b:66.7 occ:1.00 O A:HOH206 2.1 61.9 1.0 O A:HOH202 2.1 63.5 1.0 N7 A:DG14 2.1 54.9 1.0 O A:HOH203 2.1 65.7 1.0 O A:HOH207 2.1 68.9 1.0 O A:HOH210 2.1 69.7 1.0 C8 A:DG14 2.9 52.0 1.0 C5 A:DG14 3.2 50.9 1.0 O6 A:DG14 3.7 49.3 1.0 C6 A:DG14 3.8 50.1 1.0 N9 A:DG14 4.2 51.9 1.0 C4 A:DG14 4.3 51.3 1.0 O4 B:DT22 4.9 42.5 1.0 OP2 A:DG14 5.0 59.2 1.0

Nickel binding site 3 out of 11 in the At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni101 b:55.6 occ:1.00 O B:HOH205 2.1 53.5 1.0 O B:HOH202 2.1 51.7 1.0 O B:HOH204 2.1 56.5 1.0 O B:HOH206 2.1 55.0 1.0 N7 B:DG14 2.1 50.1 1.0 O B:HOH207 2.1 58.5 1.0 C8 B:DG14 3.0 48.5 1.0 C5 B:DG14 3.1 48.7 1.0 O6 B:DG14 3.5 48.8 1.0 C6 B:DG14 3.7 48.4 1.0 N9 B:DG14 4.2 47.7 1.0 C4 B:DG14 4.3 48.3 1.0 N6 B:DA15 4.9 39.6 1.0

Nickel binding site 4 out of 11 in the At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni101 b:50.5 occ:1.00 O C:HOH201 2.1 49.9 1.0 O C:HOH206 2.1 50.3 1.0 N7 C:DG24 2.1 48.6 1.0 O C:HOH202 2.1 49.3 1.0 O C:HOH208 2.1 51.6 1.0 O C:HOH203 2.1 51.2 1.0 C8 C:DG24 3.0 47.9 1.0 C5 C:DG24 3.2 47.8 1.0 O6 C:DG24 3.6 49.1 1.0 C6 C:DG24 3.8 48.0 1.0 OP2 C:DG24 4.1 47.0 1.0 N9 C:DG24 4.2 47.5 1.0 C4 C:DG24 4.3 47.2 1.0

Nickel binding site 5 out of 11 in the At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni102 b:66.7 occ:1.00 O D:HOH204 2.1 66.1 1.0 O C:HOH209 2.1 65.0 1.0 O C:HOH205 2.1 66.3 1.0 O C:HOH204 2.1 64.2 1.0 O C:HOH207 2.1 61.4 1.0 N7 C:DG14 2.1 55.5 1.0 C8 C:DG14 2.7 52.0 1.0 C5 C:DG14 3.3 50.7 1.0 N9 C:DG14 4.0 50.8 1.0 C6 C:DG14 4.0 49.8 1.0 O6 C:DG14 4.0 49.1 1.0 C4 C:DG14 4.2 50.4 1.0 O4 D:DT22 4.5 40.9 1.0 N6 C:DA15 4.8 40.9 1.0

Nickel binding site 6 out of 11 in the At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni101 b:39.3 occ:1.00 O D:HOH201 2.1 38.9 1.0 O D:HOH202 2.1 39.3 1.0 N7 D:DG24 2.1 38.6 1.0 C5 D:DG24 3.0 38.4 1.0 C8 D:DG24 3.1 38.8 1.0 O6 D:DG24 3.2 39.2 1.0 C6 D:DG24 3.5 38.7 1.0 OP2 D:DG24 3.9 39.2 1.0 C4 D:DG24 4.3 38.3 1.0 N9 D:DG24 4.3 38.6 1.0 N1 D:DG24 4.8 38.7 1.0 O5' D:DG24 4.9 39.0 1.0 P D:DG24 4.9 38.5 1.0

Nickel binding site 7 out of 11 in the At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni102 b:57.1 occ:1.00 O D:HOH205 2.1 53.2 1.0 O D:HOH203 2.1 54.5 1.0 N7 D:DG14 2.1 49.7 1.0 O D:HOH207 2.1 56.3 1.0 O D:HOH206 2.1 56.7 1.0 O D:HOH208 2.1 60.0 1.0 C8 D:DG14 2.9 47.6 1.0 C5 D:DG14 3.3 46.6 1.0 O6 D:DG14 3.8 46.4 1.0 C6 D:DG14 3.9 46.2 1.0 OP2 D:DG14 4.0 50.7 1.0 N9 D:DG14 4.1 46.5 1.0 C4 D:DG14 4.3 46.3 1.0 P D:DG14 4.9 50.3 1.0 N6 D:DA15 4.9 43.8 1.0

Nickel binding site 8 out of 11 in the At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni101 b:60.6 occ:1.00 O E:HOH206 2.1 60.0 1.0 N7 E:DG24 2.1 58.4 1.0 O E:HOH203 2.1 59.6 1.0 O A:HOH209 2.1 60.4 1.0 O E:HOH202 2.1 60.0 1.0 O E:HOH205 2.1 58.1 1.0 C8 E:DG24 2.8 57.3 1.0 C5 E:DG24 3.3 57.6 1.0 O6 E:DG24 3.9 59.5 1.0 C6 E:DG24 4.0 58.1 1.0 N9 E:DG24 4.1 56.4 1.0 C4 E:DG24 4.3 56.9 1.0 OP2 E:DG24 4.8 51.5 1.0

Nickel binding site 9 out of 11 in the At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni102 b:66.4 occ:1.00 O E:HOH201 2.1 60.0 1.0 O E:HOH204 2.1 64.4 1.0 N7 E:DG14 2.1 57.3 1.0 O F:HOH203 2.1 64.1 1.0 O E:HOH207 2.1 65.9 1.0 C8 E:DG14 3.0 54.7 1.0 C5 E:DG14 3.2 54.5 1.0 O6 E:DG14 3.6 56.2 1.0 C6 E:DG14 3.7 54.5 1.0 N9 E:DG14 4.2 54.5 1.0 C4 E:DG14 4.3 54.5 1.0 O4 F:DT22 4.5 51.0 1.0 N6 E:DA15 4.8 50.5 1.0

Nickel binding site 10 out of 11 in the At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of At-Rich Dna Dodecamer with Extra Helical Guanine-Nickel Coordination within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni101 b:65.6 occ:1.00 N7 F:DG14 2.1 60.8 1.0 O F:HOH205 2.1 64.5 1.0 O F:HOH202 2.1 62.7 1.0 O F:HOH206 2.1 65.5 1.0 O F:HOH211 2.1 66.1 1.0 O F:HOH209 2.1 64.0 1.0 C8 F:DG14 2.9 59.8 1.0 C5 F:DG14 3.2 58.2 1.0 O6 F:DG14 3.7 59.4 1.0 C6 F:DG14 3.8 57.7 1.0 N9 F:DG14 4.1 58.9 1.0 C4 F:DG14 4.3 57.8 1.0 OP2 F:DG14 4.9 63.5 1.0

J.L.Campos, N.Saperas, F.J.Acosta-Reyes, M.Pagan. At-Rich Dna with Extra Helical Guanine-Nickel Coordination To Be Published.