Magnesium in PDB 1dpl: A-Dna Decamer Gcgta(T23)Tacgc with Incorporated 2'-Methoxy- 3'-Methylenephosphate-Thymidine

The structure of A-Dna Decamer Gcgta(T23)Tacgc with Incorporated 2'-Methoxy- 3'-Methylenephosphate-Thymidine, PDB code: 1dpl 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 / 0.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.627, 42.717, 46.906, 90.00, 90.00, 90.00
R / Rfree (%)	11.7 / 12.1

The binding sites of Magnesium atom in the A-Dna Decamer Gcgta(T23)Tacgc with Incorporated 2'-Methoxy- 3'-Methylenephosphate-Thymidine (pdb code 1dpl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the A-Dna Decamer Gcgta(T23)Tacgc with Incorporated 2'-Methoxy- 3'-Methylenephosphate-Thymidine, PDB code: 1dpl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the A-Dna Decamer Gcgta(T23)Tacgc with Incorporated 2'-Methoxy- 3'-Methylenephosphate-Thymidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A-Dna Decamer Gcgta(T23)Tacgc with Incorporated 2'-Methoxy- 3'-Methylenephosphate-Thymidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:7.6 occ:1.00 O A:HOH306 2.0 12.1 1.0 O B:HOH304 2.1 8.9 1.0 O A:HOH302 2.1 7.8 1.0 O A:HOH307 2.1 9.8 1.0 O B:HOH303 2.1 8.8 1.0 O A:HOH305 2.1 8.9 1.0 O B:HOH330 3.9 7.5 1.0 O6 A:DG3 4.0 6.4 1.0 O B:HOH337 4.0 8.4 1.0 O A:HOH373 4.1 9.3 1.0 O A:HOH365 4.1 11.3 1.0 N7 A:DG3 4.2 5.9 1.0 O A:HOH427 4.3 10.4 0.5 O A:HOH313 4.3 7.7 1.0 O4 B:T2316 4.3 5.5 1.0 O B:HOH312 4.4 9.9 1.0 O A:HOH319 4.6 10.6 1.0 N4 A:DC2 4.7 6.3 1.0 C6 A:DG3 4.8 5.3 1.0 O4 A:DT4 4.8 5.2 1.0 N6 B:DA15 4.8 5.8 1.0 C5 A:DG3 4.9 5.5 1.0 N6 A:DA5 5.0 5.3 1.0

Magnesium binding site 2 out of 2 in the A-Dna Decamer Gcgta(T23)Tacgc with Incorporated 2'-Methoxy- 3'-Methylenephosphate-Thymidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A-Dna Decamer Gcgta(T23)Tacgc with Incorporated 2'-Methoxy- 3'-Methylenephosphate-Thymidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1301 b:17.7 occ:0.50 O B:HOH1304 1.8 12.4 0.5 O B:HOH1305 2.0 14.1 0.5 O B:HOH1303 2.1 14.1 0.5 O B:HOH1302 2.1 15.2 0.5 O B:HOH1306 2.1 19.6 0.5 O B:HOH1307 2.1 21.8 0.5 OP1 B:DA17 4.1 9.8 1.0 OP2 B:DA17 4.2 9.1 1.0 OP1 B:T2316 4.5 8.9 1.0 P B:DA17 4.5 7.5 1.0 O B:HOH429 4.6 17.6 0.5 C3M B:T2316 4.8 7.6 1.0 O B:HOH481 4.8 73.4 0.5

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