Cobalt in PDB 2fil: Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat)

The structure of Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat), PDB code: 2fil 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)	30.00 / 1.69
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	32.733, 69.180, 32.831, 90.00, 92.21, 90.00
R / Rfree (%)	20.3 / 21.5

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

Fluorine

(F)

4 atoms

The binding sites of Cobalt atom in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat) (pdb code 2fil). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat), PDB code: 2fil:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat)


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-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co3212 b:63.5 occ:1.00 CO A:NCO3212 0.0 63.5 1.0 N6 A:NCO3212 2.0 60.2 1.0 N3 A:NCO3212 2.0 65.0 1.0 N4 A:NCO3212 2.0 56.9 1.0 N1 A:NCO3212 2.0 62.9 1.0 N5 A:NCO3212 2.0 64.3 1.0 N2 A:NCO3212 2.0 63.3 1.0 O A:HOH1082 3.9 48.4 1.0 N1 B:NCO3217 4.1 0.6 1.0 N7 A:DG103 4.2 41.1 1.0 O A:HOH1081 4.5 47.7 1.0 O4 A:DT104 4.5 46.5 1.0 O A:HOH1001 4.6 52.3 1.0 O6 A:DG103 4.6 44.1 1.0 O B:HOH1072 4.7 63.4 1.0 O A:HOH1283 4.8 81.5 1.0 O A:HOH1009 4.8 51.9 1.0 N5 B:NCO3217 4.8 0.9 1.0

Cobalt binding site 2 out of 7 in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat)


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-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co3213 b:78.5 occ:1.00 CO A:NCO3213 0.0 78.5 1.0 N2 A:NCO3213 2.0 68.4 1.0 N6 A:NCO3213 2.0 72.8 1.0 N1 A:NCO3213 2.0 76.1 1.0 N5 A:NCO3213 2.0 74.4 1.0 N4 A:NCO3213 2.0 69.6 1.0 N3 A:NCO3213 2.0 75.2 1.0 OP1 A:DC102 3.6 53.1 1.0 OP1 B:DC202 4.1 45.5 1.0 O B:HOH1027 4.4 70.2 1.0 P A:DC102 4.9 46.0 1.0

Cobalt binding site 3 out of 7 in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat)


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-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co3211 b:65.9 occ:1.00 CO B:NCO3211 0.0 65.9 1.0 N6 B:NCO3211 2.0 60.9 1.0 N5 B:NCO3211 2.0 57.1 1.0 N4 B:NCO3211 2.0 63.9 1.0 N1 B:NCO3211 2.0 64.0 1.0 N2 B:NCO3211 2.0 67.2 1.0 N3 B:NCO3211 2.0 54.5 1.0 O B:HOH1072 4.2 63.4 1.0 N7 B:DG203 4.2 36.9 1.0 O A:HOH1001 4.4 52.3 1.0 O4 B:DT204 4.8 36.8 1.0 O6 B:DG203 4.8 36.4 1.0 O B:HOH1132 4.8 43.2 1.0

Cobalt binding site 4 out of 7 in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co3217 b:1.0 occ:1.00 CO B:NCO3217 0.0 1.0 1.0 N2 B:NCO3217 2.0 0.7 1.0 N5 B:NCO3217 2.0 0.9 1.0 N4 B:NCO3217 2.0 0.8 1.0 N1 B:NCO3217 2.0 0.6 1.0 N3 B:NCO3217 2.0 0.9 1.0 N6 B:NCO3217 2.0 0.9 1.0 O B:HOH1010 3.6 46.8 1.0 OP2 B:DT204 3.9 60.4 1.0 OP2 B:A2M205 4.3 51.4 1.0 N4 A:NCO3212 4.3 56.9 1.0 OP1 B:DT204 4.3 59.8 1.0 P B:DT204 4.6 61.3 1.0 N6 A:NCO3212 4.9 60.2 1.0 N1 A:NCO3212 5.0 62.9 1.0

Cobalt binding site 5 out of 7 in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat) within 5.0Å range: probe atom residue distance (Å) B Occ C:Co3214 b:56.7 occ:1.00 CO C:NCO3214 0.0 56.7 1.0 N4 C:NCO3214 2.0 42.3 1.0 N6 C:NCO3214 2.0 51.4 1.0 N1 C:NCO3214 2.0 53.3 1.0 N5 C:NCO3214 2.0 55.7 1.0 N3 C:NCO3214 2.0 56.7 1.0 N2 C:NCO3214 2.0 55.5 1.0 O C:HOH1089 3.5 58.1 1.0 O C:HOH1113 4.2 54.3 1.0 O D:HOH1015 4.3 27.8 1.0 O D:HOH1202 4.4 83.8 1.0 O C:HOH1070 4.4 50.0 1.0 O D:HOH1017 4.5 39.3 0.5 O C:HOH1122 4.5 62.5 1.0 N7 C:DG303 4.6 32.7 1.0 O C:HOH1100 4.6 67.8 1.0 O6 C:DG303 4.7 36.6 1.0 O4 D:TAF406 4.7 51.5 1.0 O4 C:DT304 4.8 35.3 1.0

Cobalt binding site 6 out of 7 in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat) within 5.0Å range: probe atom residue distance (Å) B Occ D:Co3215 b:26.6 occ:1.00 CO D:NCO3215 0.0 26.6 1.0 N4 D:NCO3215 1.9 24.8 1.0 N6 D:NCO3215 2.0 28.2 1.0 N1 D:NCO3215 2.0 25.2 1.0 N5 D:NCO3215 2.0 22.5 1.0 N2 D:NCO3215 2.0 24.6 1.0 N3 D:NCO3215 2.0 20.7 1.0 O D:HOH1159 3.3 71.0 1.0 O D:HOH1086 4.1 34.9 1.0 O D:HOH1034 4.2 53.6 1.0 O D:HOH1021 4.2 32.0 1.0 O D:HOH1015 4.2 27.8 1.0 O D:HOH1088 4.3 46.2 1.0 O D:HOH1031 4.4 44.1 0.5 O6 D:DG403 4.5 31.0 1.0 N7 D:DG403 4.6 27.4 1.0 O D:HOH1224 4.7 53.7 1.0 O4 D:DT404 4.7 19.8 1.0 O4 C:TAF306 4.8 46.8 1.0

Cobalt binding site 7 out of 7 in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat) within 5.0Å range: probe atom residue distance (Å) B Occ D:Co3216 b:74.0 occ:1.00 CO D:NCO3216 0.0 74.0 1.0 N6 D:NCO3216 2.0 73.5 1.0 N4 D:NCO3216 2.0 67.3 1.0 N3 D:NCO3216 2.0 69.1 1.0 N5 D:NCO3216 2.0 72.1 1.0 N1 D:NCO3216 2.0 70.3 1.0 N2 D:NCO3216 2.0 68.2 1.0 OP1 D:DC402 3.5 44.1 1.0 O D:HOH1221 4.4 57.2 1.0 P D:DC402 4.7 45.8 1.0

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