Closeup views of amino acid-nucleotide interactions between GRE nucleotides and selected GR DBD amino acids from the right monomer of the GR DBD/29 bp GRE model at various time steps during solvated molecular dynamics. Interactions involving amino acids from the exon 3 encoded DNA recognition alpha helix, the exon 4 encoded beta strand and the exon 5 encoded predicted alpha helix are shown. Atoms on amino acids, nucleotides, and water molecules which form direct and water mediated DNA/protein H-bonds are highlighted with VDW surfaces. Hydrogen bonds are indicated with white dashed lines. Water molecules are colored light blue; amino acids and nucleotides are colored as described in figure 1.

A. Water mediated hydrogen bonds between amino acid K 461 and codon nucleotide A 36 at the N7 base site, and anticodon nucleotide C 21 at H41 Watson-Crick H-bond site are shown.
B. The Van der Waals interaction between V 462 and its codon nucleotide T 19 is shown.

C. Direct H-bonds between amino acid K 465 and anticodon (reading 3'to 5') nucleotide T 20 at O4 Watson-Crick H-bond site, codon nucleotide G 38 at N7 site and O6 Watson-Crick H-bond site, and codon nucleotide A 37 at the N7 site are shown.
D. Direct hydrogen bonds between R 466 and its codon nucleotide A 39 at the phosphate backbone O1P atom and codon nucleotide G 38 at phosphate backbone O1P atom and the sugar atom O5' are shown.

E. A water mediated H-bond between E 469 and its codon nucleotide G 38 phosphate backbone O2P atom is shown.
F. A direct H-bond between Q 471 and its anticodon nucleotide G 18 at the O6 Watson-Crick H-bond site, a direct H-bond at codon (reading 3'to 5') nucleotide A 40 at the H61 site and water mediated H- bonds with codon nucleotide C 41 at H41 site, anticodon nucleotide G 18 at the N7 site and at codon (reading 3'to 5') nucleotide A 40 at the N7 site are shown.

G. Direct H-bond between N 473 and the phosphate backbone O1P of its anticodon nucleotide T 17 (reading 3' to 5') is shown. In addition, water mediated H-bonds to N 473 and the T 17 phosphate backbone O2P atom, and anticodon nucleotide G 18 at the N7 site are shown.
H. Water mediated H-bonds between R 510 and codon nucleotide A 37 at the phosphate backbone O2P atom and non-codon nucleotide A 26 at at the phosphate backbone O2P atom are shown.

I. Direct H-bond between K 513 and the phosphate backbone O2P of its codon nucleotide A 36 is shown. In addition, water mediated H-bonds to codon nucleotide A 37 at the phosphate backbone O2P atom, codon nucleotide A 36 at sugar O3' and codon nucleotide A 26 at phosphate backbone O2P site are shown.
J. Direct H-bonds between K 517 and its codon nucleotide A 36 at the phosphate backbone O2P atom, anticodon nucleotide T35 at the sugar atom O3' and codon nucleotide A 27 at the phosphate backbone O2P atom are shown.