Potassium in PDB 7eay: Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs

The structure of Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs, PDB code: 7eay was solved by J.Kondo, A.Terashima, A.Yoshimura, Y.Tada, A.Ono, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.27 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	89.923, 155.333, 80.627, 90, 90, 90
R / Rfree (%)	21.4 / 25.3

The structure of Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs also contains other interesting chemical elements:

Cobalt	(Co)	18 atoms
Copper	(Cu)	12 atoms

The binding sites of Potassium atom in the Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs (pdb code 7eay). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs, PDB code: 7eay:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:K105 b:48.9 occ:1.00 OP1 C:J0X7 2.3 35.6 1.0 OP1 A:J0X7 2.4 32.1 1.0 O C:HOH201 2.5 34.9 1.0 O C:HOH212 2.6 52.8 1.0 O A:HOH202 2.6 36.4 1.0 O A:HOH209 2.7 48.5 1.0 P C:J0X7 3.7 34.3 1.0 P A:J0X7 3.8 34.4 1.0 OP1 C:DC5 3.8 38.4 1.0 OP1 A:DC5 4.0 31.9 1.0 C3' C:J0X6 4.1 33.8 1.0 C3' A:J0X6 4.3 31.8 1.0 O3' C:J0X6 4.3 37.6 1.0 O3' A:J0X6 4.4 34.5 1.0 O5' C:J0X7 4.5 38.6 1.0 O5' A:J0X7 4.6 40.3 1.0 C4' C:J0X6 4.7 34.3 1.0 OP2 C:J0X7 4.7 43.8 1.0 C5' C:J0X6 4.7 32.9 1.0 OP2 A:J0X7 4.7 41.2 1.0 C4' A:J0X6 4.7 36.2 1.0 C5' A:J0X6 4.9 34.0 1.0

Potassium binding site 2 out of 4 in the Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ E:K107 b:53.3 occ:1.00 OP1 E:J0X7 2.5 40.5 1.0 OP1 G:J0X7 2.5 39.3 1.0 O E:HOH206 2.6 45.4 1.0 O G:HOH201 2.6 42.5 1.0 O G:HOH207 2.7 40.6 1.0 O E:HOH201 2.7 40.4 1.0 OP1 E:DC5 3.5 35.0 1.0 O G:HOH202 3.8 46.1 1.0 P E:J0X7 3.8 40.0 1.0 P G:J0X7 3.9 36.6 1.0 C3' E:J0X6 4.1 37.5 1.0 O3' E:J0X6 4.1 38.8 1.0 OP1 G:DC5 4.2 36.1 1.0 C3' G:J0X6 4.5 37.3 1.0 O3' G:J0X6 4.6 41.4 1.0 C4' E:J0X6 4.6 41.0 1.0 C5' E:J0X6 4.6 39.0 1.0 OP2 E:J0X7 4.7 43.0 1.0 OP2 G:J0X7 4.8 39.2 1.0 P E:DC5 4.8 32.5 1.0 O5' G:J0X7 4.8 43.0 1.0 O5' E:J0X7 4.9 42.2 1.0 C4' G:J0X6 5.0 42.4 1.0

Potassium binding site 3 out of 4 in the Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ H:K101 b:66.7 occ:1.00 OP2 H:DC11 2.6 40.5 1.0 O H:HOH206 2.8 38.9 1.0 O H:HOH208 2.8 59.6 1.0 C6 H:DC11 3.3 31.6 1.0 C5' H:DC11 3.5 35.2 1.0 C5 H:DC11 3.6 32.9 1.0 P H:DC11 3.8 38.0 1.0 O5' H:DC11 3.9 35.3 1.0 C3' H:DT10 4.0 35.8 1.0 O4' H:DC11 4.0 42.8 1.0 C4' H:DC11 4.3 42.1 1.0 C6 H:DT10 4.4 36.5 1.0 O3' H:DT10 4.4 35.5 1.0 O5' H:DT10 4.5 42.4 1.0 C5 H:DT10 4.5 38.5 1.0 N1 H:DC11 4.5 33.9 1.0 C2' H:DT10 4.6 34.1 1.0 N1 H:DT10 4.7 37.8 1.0 C7 H:DT10 4.8 36.2 1.0 OP2 H:DT10 4.9 39.3 1.0 C3' H:DC11 4.9 36.9 1.0 C1' H:DC11 4.9 32.5 1.0

Potassium binding site 4 out of 4 in the Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ I:K106 b:52.5 occ:1.00 OP1 I:J0X7 2.4 36.1 1.0 OP1 K:J0X7 2.4 35.4 1.0 O I:HOH204 2.6 36.8 1.0 O K:HOH206 2.7 45.0 1.0 OP1 I:DC5 3.7 37.9 1.0 P I:J0X7 3.8 35.3 1.0 P K:J0X7 3.8 36.2 1.0 OP1 K:DC5 4.0 36.5 1.0 C3' I:J0X6 4.2 35.9 1.0 C3' K:J0X6 4.2 36.3 1.0 O3' I:J0X6 4.3 38.9 1.0 O3' K:J0X6 4.5 37.3 1.0 O5' K:J0X7 4.6 42.9 1.0 C5' I:J0X6 4.6 33.4 1.0 OP2 I:J0X7 4.7 45.1 1.0 C4' I:J0X6 4.7 37.6 1.0 O5' I:J0X7 4.7 44.0 1.0 C4' K:J0X6 4.8 37.8 1.0 OP2 K:J0X7 4.8 40.1 1.0 C5' K:J0X6 4.9 32.8 1.0

J.Kondo, A.Terashima, A.Yoshimura, Y.Tada, A.Ono. Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs To Be Published.