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Cobalt in PDB 2p8d: The Structure of the Dickerson Sequence with An Incorporated Cena Residue

Protein crystallography data

The structure of The Structure of the Dickerson Sequence with An Incorporated Cena Residue, PDB code: 2p8d was solved by K.Robeyns, L.Van Meervelt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.76 / 1.90
Space group P 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 24.915, 38.780, 66.923, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 30.8

Cobalt Binding Sites:

The binding sites of Cobalt atom in the The Structure of the Dickerson Sequence with An Incorporated Cena Residue (pdb code 2p8d). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the The Structure of the Dickerson Sequence with An Incorporated Cena Residue, PDB code: 2p8d:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 2p8d

Go back to Cobalt Binding Sites List in 2p8d
Cobalt binding site 1 out of 3 in the The Structure of the Dickerson Sequence with An Incorporated Cena Residue


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of The Structure of the Dickerson Sequence with An Incorporated Cena Residue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co101

b:39.3
occ:1.00
CO B:NCO101 0.0 39.3 1.0
N6 B:NCO101 2.0 38.6 1.0
N5 B:NCO101 2.0 40.7 1.0
N3 B:NCO101 2.0 39.4 1.0
N1 B:NCO101 2.0 38.8 1.0
N4 B:NCO101 2.0 38.2 1.0
N2 B:NCO101 2.0 39.0 1.0
O B:HOH111 4.0 40.3 1.0
O B:HOH109 4.1 43.9 1.0
O B:HOH112 4.2 41.7 1.0
OP1 B:DT7 4.4 35.7 1.0
O B:HOH133 4.8 50.6 1.0

Cobalt binding site 2 out of 3 in 2p8d

Go back to Cobalt Binding Sites List in 2p8d
Cobalt binding site 2 out of 3 in the The Structure of the Dickerson Sequence with An Incorporated Cena Residue


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of The Structure of the Dickerson Sequence with An Incorporated Cena Residue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co102

b:54.0
occ:1.00
CO B:NCO102 0.0 54.0 1.0
N4 B:NCO102 2.0 53.4 1.0
N1 B:NCO102 2.0 53.4 1.0
N5 B:NCO102 2.0 54.6 1.0
N2 B:NCO102 2.0 51.9 1.0
N6 B:NCO102 2.0 53.8 1.0
N3 B:NCO102 2.0 54.1 1.0
OP2 B:DT7 3.9 38.4 1.0
O B:HOH127 4.1 45.3 1.0
O B:HOH113 4.2 44.3 1.0
O B:HOH121 4.6 48.0 1.0
O B:HOH120 4.6 55.6 1.0
O B:HOH132 4.7 50.7 1.0

Cobalt binding site 3 out of 3 in 2p8d

Go back to Cobalt Binding Sites List in 2p8d
Cobalt binding site 3 out of 3 in the The Structure of the Dickerson Sequence with An Incorporated Cena Residue


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of The Structure of the Dickerson Sequence with An Incorporated Cena Residue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co103

b:46.2
occ:0.50
CO B:NCO103 0.0 46.2 0.5
N2 B:NCO103 2.0 46.1 0.5
N1 B:NCO103 2.0 44.8 0.5
N3 B:NCO103 2.0 45.0 0.5
N6 B:NCO103 2.0 46.1 0.5
N4 B:NCO103 2.0 45.4 0.5
N5 B:NCO103 2.0 46.0 0.5
O6 B:DG12 4.0 50.9 1.0
N7 B:DG12 4.3 51.1 1.0
C6 B:DG12 4.8 50.8 1.0
C5 B:DG12 4.9 51.8 1.0

Reference:

K.Robeyns, P.Herdewijn, L.Van Meervelt. Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Cgcgaattcgcg). Nucleic Acids Res. V. 36 1407 2008.
ISSN: ISSN 0305-1048
PubMed: 18160414
DOI: 10.1093/NAR/GKM1132
Page generated: Sun Dec 13 10:38:35 2020

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