Dna-Directed RNA Polymerase II Largest Subunit

(All numbering and residues are taken from first PDB file)

Bending Residue Dihedral Analysis

Residue i Residue i+1 Distance of hinge axis to residue i in conformer 1 (A) Distance of hinge axis to residue i in conformer 2 (A) Change in psi (i) (deg) Change in phi (i+1) (deg) Angle of psi(i) axis to hinge axis conformer 1 (deg) Angle of psi(i) axis to hinge axis conformer 2 (deg) Percentage Progress  ARG-344   VAL-345  20.6 20.6 85.8 -68.9 43.8 40.5 32.9  VAL-345   ASP-346  20.1 19.1 86.9 -12.7 21.2 32.1 210.9  ASP-346   PHE-347  19.9 19.9 23.0 -10.1 45.7 48.1 31.9  PHE-347   SER-348  19.6 19.8 10.5 4.3 99.6 110.4 -9.7 Graph shows rotational transition at bending residues and can be used to identify hinge bending residues. Probably only informative for interdomain rotations greater than 20 degrees

Residue i Residue i+1 Distance of hinge axis to residue i in conformer 1 (A) Distance of hinge axis to residue i in conformer 2 (A) Change in psi (i) (deg) Change in phi (i+1) (deg) Angle of psi(i) axis to hinge axis conformer 1 (deg) Angle of psi(i) axis to hinge axis conformer 2 (deg) Percentage Progress  THR-1382   SER-1383  18.9 18.4 0.3 -8.7 122.0 118.4 8.7  SER-1383   VAL-1384  19.9 19.3 -22.1 34.3 40.6 41.9 -22.4  VAL-1384   THR-1385  19.0 18.7 91.9 -90.4 86.1 70.2 -4.8  THR-1385   ARG-1386  20.1 17.4 100.9 -92.2 59.5 66.7 53.1  ARG-1386   HIS-1387  16.6 14.7 -122.0 4.6 163.8 141.0 -357.1  HIS-1387   GLY-1388  14.9 14.6 58.4 -53.6 77.9 103.3 13.8  GLY-1388   PHE-1389  11.4 14.3 111.5 37.4 105.1 139.4 576.2  PHE-1389   ASN-1390  11.3 13.3 12.0 37.3 131.5 100.2 -5.0  ASN-1390   ARG-1391  8.1 10.7 -81.7 125.7 67.8 134.4 -39.4  ARG-1391   SER-1392  7.7 8.7 147.7 151.5 100.1 106.8 14.3  SER-1392   ASN-1393  10.3 9.1 -154.7 142.0 53.4 70.9 -83.6  ASN-1393   THR-1394  8.2 7.2 -80.9 75.4 48.9 30.7 8.7  THR-1394   GLY-1395  5.5 6.0 -68.6 104.1 89.9 98.4 -3.2 Graph shows rotational transition at bending residues and can be used to identify hinge bending residues. Probably only informative for interdomain rotations greater than 20 degrees

Residue i Residue i+1 Distance of hinge axis to residue i in conformer 1 (A) Distance of hinge axis to residue i in conformer 2 (A) Change in psi (i) (deg) Change in phi (i+1) (deg) Angle of psi(i) axis to hinge axis conformer 1 (deg) Angle of psi(i) axis to hinge axis conformer 2 (deg) Percentage Progress  GLY-1431   GLN-1432  7.0 7.5 16.7 -3.7 60.0 58.7 34.4  GLN-1432   MET-1433  3.5 4.0 -16.9 22.9 95.1 107.8 3.1  MET-1433   ALA-1434  1.2 2.0 -27.7 -10.7 48.2 49.2 84.2  ALA-1434   PRO-1435  2.9 3.3 9.6 -1.9 70.5 68.2 13.0 Graph shows rotational transition at bending residues and can be used to identify hinge bending residues. Probably only informative for interdomain rotations greater than 20 degrees