Cobalt in PDB 4zkk: The Novel Double-Fold Structure of D(Gcatgcatgc)

The structure of The Novel Double-Fold Structure of D(Gcatgcatgc), PDB code: 4zkk was solved by A.Thirugnanasambandam, S.Karthik, P.K.Mandal, N.Gautham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.93 / 1.80
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	34.640, 34.640, 89.601, 90.00, 90.00, 120.00
R / Rfree (%)	22.9 / 24.6

The binding sites of Cobalt atom in the The Novel Double-Fold Structure of D(Gcatgcatgc) (pdb code 4zkk). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the The Novel Double-Fold Structure of D(Gcatgcatgc), PDB code: 4zkk:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the The Novel Double-Fold Structure of D(Gcatgcatgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of The Novel Double-Fold Structure of D(Gcatgcatgc) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:27.5 occ:1.00 O A:HOH209 2.0 28.2 1.0 O A:HOH204 2.1 22.0 1.0 N7 A:DG1 2.2 20.4 1.0 N7 A:DG9 2.3 26.3 1.0 O A:HOH211 2.3 25.2 1.0 C8 A:DG1 3.1 32.9 1.0 C8 A:DG9 3.2 26.6 1.0 C5 A:DG1 3.3 32.7 1.0 C5 A:DG9 3.4 28.5 1.0 O6 A:DG1 3.7 28.4 1.0 O6 A:DG9 3.7 29.2 1.0 C6 A:DG1 3.9 29.7 1.0 N4 A:DC2 3.9 22.5 1.0 C6 A:DG9 3.9 28.5 1.0 OP1 A:DT8 4.1 31.7 1.0 O A:HOH221 4.2 39.8 1.0 O A:HOH206 4.3 28.5 1.0 N9 A:DG1 4.3 26.1 1.0 O3' A:DA7 4.4 33.3 1.0 N9 A:DG9 4.4 26.8 1.0 C4 A:DG1 4.4 26.2 1.0 O A:HOH208 4.5 26.6 1.0 C4 A:DG9 4.5 24.9 1.0 C4 A:DC2 4.7 27.9 1.0 C1' A:DA7 4.8 39.9 1.0 C5 A:DC2 4.8 27.2 1.0 P A:DT8 4.9 35.7 1.0 O4' A:DA7 4.9 37.4 1.0

Cobalt binding site 2 out of 4 in the The Novel Double-Fold Structure of D(Gcatgcatgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of The Novel Double-Fold Structure of D(Gcatgcatgc) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:27.1 occ:0.51 CO A:CO102 0.0 27.1 0.5 CO A:CO102 1.5 26.6 0.5 O A:HOH202 1.6 49.1 1.0 O A:HOH223 2.2 35.4 0.5 O A:HOH215 2.3 41.5 1.0 O A:HOH223 2.4 33.9 0.5 N7 A:DG5 2.4 33.6 1.0 O A:HOH218 2.8 47.2 1.0 O6 A:DG5 3.0 39.8 1.0 O A:HOH203 3.2 45.3 1.0 C5 A:DG5 3.2 37.5 1.0 C6 A:DG5 3.5 37.9 1.0 C8 A:DG5 3.5 38.7 1.0 N4 A:DC6 3.6 35.9 1.0 O A:HOH222 3.7 71.3 1.0 O A:HOH216 4.1 35.5 1.0 C4 A:DC6 4.5 36.9 1.0 C4 A:DG5 4.5 39.9 1.0 N9 A:DG5 4.7 42.2 1.0 C5 A:DC6 4.8 35.1 1.0 O3' A:DA3 4.8 46.6 1.0 N1 A:DG5 4.9 34.3 1.0 C1' A:DA3 4.9 39.9 1.0 O4' A:DA3 4.9 39.2 1.0

Cobalt binding site 3 out of 4 in the The Novel Double-Fold Structure of D(Gcatgcatgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of The Novel Double-Fold Structure of D(Gcatgcatgc) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:26.6 occ:0.49 CO A:CO102 0.0 26.6 0.5 CO A:CO102 1.5 27.1 0.5 O A:HOH203 1.7 45.3 1.0 O A:HOH223 2.0 33.9 0.5 N7 A:DG5 2.2 33.6 1.0 O A:HOH218 2.3 47.2 1.0 O A:HOH215 2.4 41.5 1.0 O A:HOH223 2.5 35.4 0.5 C8 A:DG5 2.9 38.7 1.0 O A:HOH202 3.2 49.1 1.0 C5 A:DG5 3.5 37.5 1.0 OP2 A:DG5 4.0 50.0 1.0 O A:HOH222 4.1 71.3 1.0 O6 A:DG5 4.2 39.8 1.0 O3' A:DA3 4.2 46.6 1.0 N9 A:DG5 4.2 42.2 1.0 C6 A:DG5 4.2 37.9 1.0 N4 A:DC6 4.4 35.9 1.0 C4 A:DG5 4.5 39.9 1.0 O5' A:DT4 4.6 92.7 1.0 O4' A:DA3 4.7 39.2 1.0 C4' A:DA3 4.8 36.4 1.0 O A:HOH216 4.9 35.5 1.0 O5' A:DG5 4.9 47.0 1.0 C5 A:DC6 4.9 35.1 1.0 C1' A:DA3 5.0 39.9 1.0

Cobalt binding site 4 out of 4 in the The Novel Double-Fold Structure of D(Gcatgcatgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of The Novel Double-Fold Structure of D(Gcatgcatgc) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co103 b:71.3 occ:0.50 O A:HOH217 1.7 75.2 1.0 O A:HOH219 2.5 65.7 1.0 N6 A:DA7 4.2 45.1 1.0 N3 A:DC10 4.8 38.3 1.0

A.Thirugnanasambandam, S.Karthik, P.K.Mandal, N.Gautham. The Novel Double-Folded Structure of D(Gcatgcatgc): A Possible Model For Triplet-Repeat Sequences Acta Crystallogr.,Sect.D V. 71 2119 2015.
ISSN: ESSN 1399-0047
PubMed: 26457435
DOI: 10.1107/S1399004715013930