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Cobalt in PDB 2fij: Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Au-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and Arabino- Uridine (Au)

Protein crystallography data

The structure of Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Au-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and Arabino- Uridine (Au), PDB code: 2fij was solved by M.Egli, F.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.37 / 1.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 32.277, 32.469, 66.749, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 16.9

Other elements in 2fij:

The structure of Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Au-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and Arabino- Uridine (Au) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Au-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and Arabino- Uridine (Au) (pdb code 2fij). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Au-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and Arabino- Uridine (Au), PDB code: 2fij:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 2fij

Go back to Cobalt Binding Sites List in 2fij
Cobalt binding site 1 out of 3 in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Au-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and Arabino- Uridine (Au)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Au-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and Arabino- Uridine (Au) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co2211

b:10.4
occ:1.00
CO A:NCO2211 0.0 10.4 1.0
N6 A:NCO2211 2.0 16.6 1.0
N4 A:NCO2211 2.0 17.8 1.0
N5 A:NCO2211 2.0 17.0 1.0
N2 A:NCO2211 2.0 16.7 1.0
N1 A:NCO2211 2.0 14.1 1.0
N3 A:NCO2211 2.0 13.5 1.0
OP1 A:DC2 3.9 14.7 1.0
OP1 B:DC12 3.9 14.8 1.0
O A:HOH186 4.1 27.5 1.0
O B:HOH170 4.1 36.6 1.0
O A:HOH123 4.2 28.9 1.0
O A:HOH183 4.2 34.7 1.0
OP2 B:DG13 4.5 15.7 1.0
OP1 B:DG13 4.5 17.1 1.0
OP1 A:DG3 4.5 17.7 1.0
OP2 A:DG3 4.5 15.6 1.0
P B:DG13 4.9 15.1 1.0
P A:DG3 5.0 14.5 1.0

Cobalt binding site 2 out of 3 in 2fij

Go back to Cobalt Binding Sites List in 2fij
Cobalt binding site 2 out of 3 in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Au-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and Arabino- Uridine (Au)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Au-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and Arabino- Uridine (Au) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co2213

b:14.2
occ:1.00
CO A:NCO2213 0.0 14.2 1.0
N6 A:NCO2213 2.0 17.4 1.0
N3 A:NCO2213 2.0 18.9 1.0
N2 A:NCO2213 2.0 15.7 1.0
N4 A:NCO2213 2.0 19.4 1.0
N1 A:NCO2213 2.0 17.7 1.0
N5 A:NCO2213 2.0 17.6 1.0
O B:HOH174 3.7 31.8 0.5
O A:HOH102 4.0 22.1 1.0
O B:HOH228 4.1 58.8 1.0
CL A:CL101 4.2 13.2 1.0
O A:HOH110 4.2 27.1 1.0
O B:HOH111 4.2 23.7 1.0
O6 A:DG3 4.3 13.0 1.0
O A:HOH182 4.3 33.1 1.0
N7 A:DG3 4.3 11.9 1.0
O B:HOH148 4.4 22.6 1.0
O A:HOH146 4.6 43.2 1.0
O A:HOH140 4.7 35.8 1.0
O4 A:DT4 4.7 12.4 1.0
O4 B:UAR16 4.8 13.2 1.0
O B:HOH169 4.9 28.9 0.5
C6 A:DG3 5.0 12.5 1.0

Cobalt binding site 3 out of 3 in 2fij

Go back to Cobalt Binding Sites List in 2fij
Cobalt binding site 3 out of 3 in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Au-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and Arabino- Uridine (Au)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Au-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and Arabino- Uridine (Au) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co2212

b:14.9
occ:1.00
CO B:NCO2212 0.0 14.9 1.0
N1 B:NCO2212 2.0 17.5 1.0
N2 B:NCO2212 2.0 19.4 1.0
N4 B:NCO2212 2.0 15.3 1.0
N6 B:NCO2212 2.0 17.4 1.0
N5 B:NCO2212 2.0 19.0 1.0
N3 B:NCO2212 2.0 16.9 1.0
O A:HOH160 3.9 29.8 1.0
O B:HOH104 4.0 19.8 1.0
O A:HOH218 4.1 33.6 1.0
CL A:CL101 4.2 13.2 1.0
O A:HOH106 4.2 22.2 1.0
O6 B:DG13 4.3 12.7 1.0
N7 B:DG13 4.3 12.1 1.0
O B:HOH158 4.3 38.4 1.0
O B:HOH159 4.4 28.3 1.0
O A:HOH129 4.4 24.0 1.0
O B:HOH130 4.4 29.4 1.0
O4 B:DT14 4.6 12.2 1.0
O4 A:UAR6 4.9 13.0 1.0
O B:HOH205 4.9 35.1 1.0
O A:HOH140 4.9 35.8 1.0
C6 B:DG13 5.0 11.9 1.0
C5 B:DG13 5.0 11.8 1.0

Reference:

F.Li, S.Sarkhel, C.J.Wilds, Z.Wawrzak, T.P.Prakash, M.Manoharan, M.Egli. 2'-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating Rna Affinities and Processing of Their Heteroduplexes with Rna By Rnase H. Biochemistry V. 45 4141 2006.
ISSN: ISSN 0006-2960
PubMed: 16566588
DOI: 10.1021/BI052322R
Page generated: Sun Dec 13 10:37:48 2020

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