Magnesium in PDB 4zym: Structural Implications of Homo-Pyrimidine Base Pairs on the Parallel- Stranded D(Gay) Motif.

The structure of Structural Implications of Homo-Pyrimidine Base Pairs on the Parallel- Stranded D(Gay) Motif., PDB code: 4zym was solved by S.K.Tripathi, P.Paukstelis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.06 / 2.53
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.954, 29.354, 74.731, 90.00, 112.47, 90.00
R / Rfree (%)	23 / 24.3

The binding sites of Magnesium atom in the Structural Implications of Homo-Pyrimidine Base Pairs on the Parallel- Stranded D(Gay) Motif. (pdb code 4zym). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structural Implications of Homo-Pyrimidine Base Pairs on the Parallel- Stranded D(Gay) Motif., PDB code: 4zym:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structural Implications of Homo-Pyrimidine Base Pairs on the Parallel- Stranded D(Gay) Motif.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Implications of Homo-Pyrimidine Base Pairs on the Parallel- Stranded D(Gay) Motif. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:46.7 occ:1.00 OP2 A:DA10 3.9 28.6 1.0 OP1 A:DA10 4.1 40.9 1.0 OP1 D:DC4 4.5 30.0 1.0 P A:DA10 4.5 33.0 1.0 OP2 D:DC4 4.7 28.9 1.0

Magnesium binding site 2 out of 4 in the Structural Implications of Homo-Pyrimidine Base Pairs on the Parallel- Stranded D(Gay) Motif.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Implications of Homo-Pyrimidine Base Pairs on the Parallel- Stranded D(Gay) Motif. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:51.7 occ:1.00 OP1 B:DA10 3.5 68.2 1.0 OP2 B:DA10 4.0 47.8 1.0 P B:DA10 4.2 54.6 1.0

Magnesium binding site 3 out of 4 in the Structural Implications of Homo-Pyrimidine Base Pairs on the Parallel- Stranded D(Gay) Motif.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Implications of Homo-Pyrimidine Base Pairs on the Parallel- Stranded D(Gay) Motif. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:45.8 occ:1.00 OP2 C:DC4 2.6 25.9 1.0 N7 C:DG5 2.7 21.6 1.0 C8 C:DG5 3.6 20.2 1.0 C5 C:DG5 3.8 19.2 1.0 P C:DC4 3.8 32.5 1.0 O3' C:DT3 3.9 30.0 1.0 O6 C:DG5 3.9 26.4 1.0 C6 C:DG5 4.3 23.1 1.0 C2' C:DT3 4.4 31.5 1.0 C4' C:DT3 4.5 27.7 1.0 C3' C:DT3 4.5 30.9 1.0 O5' C:DC4 4.6 35.8 1.0 N9 C:DG5 4.8 19.5 1.0 C4 C:DG5 5.0 18.8 1.0 C1' C:DT3 5.0 28.5 1.0

Magnesium binding site 4 out of 4 in the Structural Implications of Homo-Pyrimidine Base Pairs on the Parallel- Stranded D(Gay) Motif.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Implications of Homo-Pyrimidine Base Pairs on the Parallel- Stranded D(Gay) Motif. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg102 b:61.1 occ:1.00 OP1 C:DA7 2.4 44.3 1.0 O D:HOH103 3.5 62.3 1.0 P C:DA7 3.6 47.3 1.0 C5' C:DA7 3.7 43.9 1.0 O5' C:DA7 3.8 40.9 1.0 OP2 C:DA7 4.5 43.5 1.0 O3' C:DG6 4.8 32.8 1.0

S.Tripathi, P.J.Paukstelis. Structural Implications of Homopyrimidine Base Pairs in the Parallel-Stranded D(Yga) Motif. Chembiochem V. 17 1177 2016.
ISSN: ESSN 1439-7633
PubMed: 26629965
DOI: 10.1002/CBIC.201500491