Magnesium in PDB 1dpn: B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine

The structure of B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine, PDB code: 1dpn was solved by M.Egli, V.Tereshko, M.Teplova, G.Minasov, A.Joachimiak, R.Sanishvili, C.M.Weeks, R.Miller, M.A.Maier, H.An, P.Dan Cook, M.Manoharan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 0.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.623, 39.732, 65.737, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 15.9

The structure of B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Magnesium atom in the B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine (pdb code 1dpn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine, PDB code: 1dpn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg25 b:13.9 occ:1.00 O A:HOH28 2.0 14.4 1.0 O B:HOH27 2.0 15.5 1.0 O B:HOH30 2.1 16.3 1.0 O B:HOH31 2.1 15.2 1.0 O A:HOH26 2.1 15.3 1.0 O B:HOH29 2.1 15.8 1.0 O B:HOH105 4.2 16.0 1.0 O6 B:DG22 4.2 13.8 1.0 O A:HOH57 4.2 24.2 1.0 C5 A:DC1 4.3 15.2 1.0 O B:HOH119 4.3 20.0 1.0 O B:HOH109 4.3 16.4 1.0 O B:HOH128 4.4 23.1 1.0 O A:HOH108 4.4 15.9 1.0 O6 A:DG2 4.4 12.7 1.0 N7 A:DG2 4.4 14.7 1.0 C6 A:DC1 4.7 15.4 1.0

Magnesium binding site 2 out of 4 in the B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg32 b:21.2 occ:1.00 O B:HOH33 2.0 27.2 1.0 O B:HOH37 2.0 23.1 1.0 O B:HOH35 2.1 22.3 1.0 O B:HOH36 2.1 21.2 1.0 O B:HOH34 2.1 21.5 1.0 OP1 B:DG24 3.9 17.6 0.7 OP1 B:DG24 4.2 23.9 0.3 O3' B:DC23 4.6 15.7 0.7 O3' B:DC23 4.6 15.4 0.3 P B:DG24 4.9 17.6 0.7

Magnesium binding site 3 out of 4 in the B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg38 b:24.8 occ:1.00 O A:HOH43 1.9 21.8 0.5 O A:HOH44 2.0 23.2 1.0 O B:HOH42 2.0 37.0 1.0 O B:HOH41 2.1 34.7 1.0 O A:HOH40 2.1 23.3 1.0 O B:HOH39 2.1 32.0 1.0 O A:HOH168 3.9 40.2 1.0 O A:HOH247 4.1 31.0 0.5 OP1 B:DA18 4.1 22.1 1.0 O B:HOH56 4.2 25.9 1.0 O A:HOH133 4.3 31.3 1.0 O B:HOH116 4.5 20.0 1.0 C5' A:DC11 4.8 17.4 0.7 O3' B:DA17 5.0 17.9 1.0

Magnesium binding site 4 out of 4 in the B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of B-Dodecamer Cgcgaa(Taf)Tcgcg with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg45 b:27.7 occ:0.50 O B:HOH48 2.0 25.9 0.5 OP1 B:DA17 2.1 24.3 1.0 O B:HOH47 2.4 30.4 0.5 O B:HOH50 2.4 29.8 0.5 O B:HOH49 2.7 32.2 0.5 P B:DA17 3.5 19.8 1.0 O B:HOH301 3.9 27.6 0.5 O B:HOH228 3.9 33.9 0.5 O5' B:DA17 4.2 18.5 1.0 OP2 B:DA17 4.3 20.8 1.0 O3' B:DG16 4.5 19.0 1.0 C5' B:DA17 4.6 16.6 1.0

M.Egli, V.Tereshko, M.Teplova, G.Minasov, A.Joachimiak, R.Sanishvili, C.M.Weeks, R.Miller, M.A.Maier, H.An, P.Dan Cook, M.Manoharan. X-Ray Crystallographic Analysis of the Hydration of A- and B-Form Dna at Atomic Resolution. Biopolymers V. 48 234 1998.
ISSN: ISSN 0006-3525
PubMed: 10699842
DOI: 10.1002/(SICI)1097-0282(1998)48:4<234::AID-BIP4>3.0.CO;2-H