Magnesium in PDB 1dcr: Crystal Structure of Dna Sheared Tandem G-A Base Pairs

The structure of Crystal Structure of Dna Sheared Tandem G-A Base Pairs, PDB code: 1dcr was solved by Y.-G.Gao, H.Robinson, R.Sanishvili, A.Joachimiak, A.H.-J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	20.950, 61.860, 68.490, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 26.6

The structure of Crystal Structure of Dna Sheared Tandem G-A Base Pairs also contains other interesting chemical elements:

Bromine	(Br)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of Dna Sheared Tandem G-A Base Pairs (pdb code 1dcr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Dna Sheared Tandem G-A Base Pairs, PDB code: 1dcr:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Dna Sheared Tandem G-A Base Pairs


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Dna Sheared Tandem G-A Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg21 b:41.1 occ:1.00 O A:HOH1079 2.1 30.0 1.0 O A:HOH1082 2.1 33.2 1.0 O A:HOH1078 2.1 44.6 1.0 O A:HOH1081 2.1 65.9 1.0 O A:HOH1080 2.1 56.3 1.0 OP1 A:DG10 2.1 46.4 1.0 P A:DG10 3.1 39.6 1.0 OP2 A:DG10 3.3 34.8 1.0 O A:HOH1054 4.1 40.3 0.5 O5' A:DG10 4.2 37.5 1.0 O3' A:DG9 4.3 40.6 1.0 C3' A:DG9 4.5 34.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Dna Sheared Tandem G-A Base Pairs


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Dna Sheared Tandem G-A Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg22 b:35.9 occ:1.00 O A:HOH1083 2.1 43.4 1.0 O A:HOH1087 2.1 28.8 1.0 O A:HOH1086 2.1 42.1 1.0 O A:HOH1085 2.1 34.7 1.0 O A:HOH1084 2.1 28.2 1.0 N7 A:DG9 2.3 27.4 1.0 C8 A:DG9 3.2 27.4 1.0 C5 A:DG9 3.4 30.1 1.0 O6 A:DG9 3.6 29.2 1.0 OP2 A:DA8 3.8 46.0 1.0 C6 A:DG9 3.9 21.4 1.0 N9 A:DG9 4.5 27.6 1.0 C4 A:DG9 4.6 19.8 1.0 O A:HOH1076 4.6 51.4 1.0 C2' A:DA8 5.0 29.8 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Dna Sheared Tandem G-A Base Pairs


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Dna Sheared Tandem G-A Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg23 b:31.8 occ:0.50 OP1 B:DG20 2.0 37.5 1.0 O B:HOH1088 2.1 46.1 0.5 O B:HOH1089 2.1 46.1 0.5 O B:HOH1090 2.1 41.8 0.5 O B:HOH1091 2.1 73.5 0.5 P B:DG20 3.4 29.0 1.0 O B:HOH1028 3.4 18.1 0.5 O3' B:DG19 3.8 27.2 1.0 O5' B:DG20 4.2 28.6 1.0 O B:HOH1028 4.3 23.1 0.5 O B:HOH1020 4.4 42.9 1.0 O B:HOH1003 4.5 28.1 1.0 OP2 B:DG20 4.6 30.7 1.0 C4' B:DG19 4.9 28.0 1.0

Y.G.Gao, H.Robinson, R.Sanishvili, A.Joachimiak, A.H.Wang. Structure and Recognition of Sheared Tandem G X A Base Pairs Associated with Human Centromere Dna Sequence at Atomic Resolution. Biochemistry V. 38 16452 1999.
ISSN: ISSN 0006-2960
PubMed: 10600106
DOI: 10.1021/BI9914614