Cobalt 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:

Potassium	(K)	4 atoms
Copper	(Cu)	12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Cobalt 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 Cobalt atom.
In total 18 binding sites of Cobalt where determined in the Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs, PDB code: 7eay:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 18 in the Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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:Co103 b:78.0 occ:1.00 CO A:NCO103 0.0 78.0 1.0 N6 A:NCO103 2.0 66.1 1.0 N5 A:NCO103 2.0 61.1 1.0 N3 A:NCO103 2.0 51.4 1.0 N1 A:NCO103 2.0 51.1 1.0 N2 A:NCO103 2.0 64.1 1.0 N4 A:NCO103 2.0 52.0 1.0 O6 A:DG2 4.3 37.5 1.0 N7 A:DG2 4.3 36.3 1.0 O6 A:DG1 4.8 33.7 1.0

Cobalt binding site 2 out of 18 in the Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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 A:Co104 b:105.9 occ:1.00 CO A:NCO104 0.0 105.9 1.0 N2 A:NCO104 2.0 45.7 1.0 N6 A:NCO104 2.0 67.8 1.0 N1 A:NCO104 2.0 61.7 1.0 N5 A:NCO104 2.0 60.4 1.0 N3 A:NCO104 2.0 66.1 1.0 N4 A:NCO104 2.0 53.5 1.0 O2 B:J0X7 3.7 39.2 1.0 O8 A:J0X6 4.3 42.0 1.0 O A:HOH203 4.5 48.2 1.0 O B:HOH101 4.5 41.5 1.0 O B:HOH102 4.5 48.4 1.0 C2 B:J0X7 4.9 41.8 1.0

Cobalt binding site 3 out of 18 in the Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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 C:Co103 b:76.8 occ:1.00 CO C:NCO103 0.0 76.8 1.0 N3 C:NCO103 2.0 49.3 1.0 N1 C:NCO103 2.0 52.8 1.0 N4 C:NCO103 2.0 45.4 1.0 N2 C:NCO103 2.0 54.2 1.0 N6 C:NCO103 2.0 61.2 1.0 N5 C:NCO103 2.0 57.8 1.0 N7 A:DG9 4.4 43.5 1.0 N7 C:DG9 4.4 38.2 1.0 O6 C:DG9 4.5 42.0 1.0 O6 A:DG9 4.7 42.5 1.0 O4 A:DT10 4.7 50.6 1.0 O4 C:DT10 4.8 47.3 1.0

Cobalt binding site 4 out of 18 in the Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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 C:Co104 b:81.4 occ:1.00 CO C:NCO104 0.0 81.4 1.0 N5 C:NCO104 2.0 66.7 1.0 N4 C:NCO104 2.0 66.3 1.0 N2 C:NCO104 2.0 63.2 1.0 N1 C:NCO104 2.0 54.4 1.0 N3 C:NCO104 2.0 49.1 1.0 N6 C:NCO104 2.0 53.2 1.0 O C:HOH206 4.1 46.5 1.0 N7 C:DG2 4.4 37.0 1.0 O6 C:DG2 4.4 36.5 1.0 O6 C:DG1 4.9 39.2 1.0

Cobalt binding site 5 out of 18 in the Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ C:Co105 b:109.6 occ:1.00 CO C:NCO105 0.0 109.6 1.0 N4 C:NCO105 2.0 84.9 1.0 N1 C:NCO105 2.0 100.2 1.0 N3 C:NCO105 2.0 84.5 1.0 N2 C:NCO105 2.0 68.3 1.0 N5 C:NCO105 2.0 71.2 1.0 N6 C:NCO105 2.0 80.7 1.0 OP1 C:DG8 4.3 42.3 1.0 OP1 G:DA3 4.4 48.8 1.0 OP2 A:J0X6 4.4 40.0 1.0

Cobalt binding site 6 out of 18 in the Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ D:Co101 b:55.9 occ:0.50 O6 D:DG1 4.7 48.3 1.0 N7 D:DG1 4.9 57.9 1.0 O6 B:DG1 5.0 48.1 1.0

Cobalt binding site 7 out of 18 in the Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ E:Co103 b:96.9 occ:1.00 CO E:NCO103 0.0 96.9 1.0 N4 E:NCO103 2.0 64.3 1.0 N3 E:NCO103 2.0 63.1 1.0 N1 E:NCO103 2.0 65.5 1.0 N5 E:NCO103 2.0 66.3 1.0 N2 E:NCO103 2.0 70.1 1.0 N6 E:NCO103 2.0 67.3 1.0 O6 H:DG1 4.3 59.5 1.0 O6 F:DG1 4.7 48.1 1.0 N4 E:DC12 4.8 60.7 1.0 N4 G:DC12 4.9 52.3 1.0

Cobalt binding site 8 out of 18 in the Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ E:Co104 b:74.7 occ:1.00 CO E:NCO104 0.0 74.7 1.0 N5 E:NCO104 2.0 57.5 1.0 N2 E:NCO104 2.0 58.0 1.0 N1 E:NCO104 2.0 55.9 1.0 N6 E:NCO104 2.0 60.6 1.0 N4 E:NCO104 2.0 61.0 1.0 N3 E:NCO104 2.0 61.6 1.0 N7 E:DG9 4.2 50.1 1.0 N7 G:DG9 4.6 43.4 1.0 O6 E:DG9 4.6 43.2 1.0 O4 E:DT10 4.7 53.2 1.0 O6 G:DG9 4.7 43.5 1.0 N6 H:DA3 4.9 54.2 1.0 N7 E:DG8 5.0 46.6 1.0

Cobalt binding site 9 out of 18 in the Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ E:Co105 b:87.4 occ:1.00 CO E:NCO105 0.0 87.4 1.0 N3 E:NCO105 2.0 68.6 1.0 N5 E:NCO105 2.0 55.5 1.0 N2 E:NCO105 2.0 52.5 1.0 N6 E:NCO105 2.0 54.9 1.0 N4 E:NCO105 2.0 56.0 1.0 N1 E:NCO105 2.0 61.2 1.0 O6 E:DG2 4.0 41.1 1.0 N7 E:DG2 4.3 39.7 1.0 O6 E:DG1 4.5 38.5 1.0 C6 E:DG2 4.8 38.5 1.0 N7 E:DG1 4.9 39.4 1.0 C5 E:DG2 4.9 38.2 1.0

Cobalt binding site 10 out of 18 in the Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Dna Containing Cu(II)-Mediated 4-N-Carboxymethylcytosine Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ E:Co106 b:106.2 occ:1.00 CO E:NCO106 0.0 106.2 1.0 N5 E:NCO106 2.0 73.9 1.0 N1 E:NCO106 2.0 89.4 1.0 N6 E:NCO106 2.0 77.2 1.0 N3 E:NCO106 2.0 76.2 1.0 N2 E:NCO106 2.0 75.3 1.0 N4 E:NCO106 2.0 66.5 1.0 OP1 E:DA3 4.6 53.4 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.