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 20.7 75.2 -55.0 46.0 40.1 75.8  VAL-345   ASP-346  20.1 19.1 69.6 6.9 18.9 32.6 209.4  ASP-346   PHE-347  19.8 19.8 27.6 -20.0 47.9 53.4 -0.1  PHE-347   SER-348  19.4 19.6 3.5 8.8 100.7 111.4 -3.0 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

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  18.5 18.5 -1.9 -8.2 56.5 57.5 8.3  SER-1383   VAL-1384  19.7 20.0 -14.0 35.8 38.8 43.3 -25.5  VAL-1384   THR-1385  18.9 19.2 102.4 -84.6 88.4 70.0 6.9  THR-1385   ARG-1386  20.1 18.1 95.5 -108.0 61.1 79.9 -15.9  ARG-1386   HIS-1387  16.8 15.2 -102.0 -7.1 164.9 142.0 -323.9  HIS-1387   GLY-1388  15.0 15.0 24.3 -0.8 79.4 106.8 -3.6  GLY-1388   PHE-1389  11.6 15.8 108.7 26.9 107.4 127.6 556.6  PHE-1389   ASN-1390  11.8 14.0 -16.3 68.1 48.1 91.1 27.5  ASN-1390   ARG-1391  8.6 11.5 -119.0 174.8 70.1 135.2 -16.6  ARG-1391   SER-1392  7.9 9.9 142.3 155.6 98.9 106.5 27.0  SER-1392   ASN-1393  10.2 9.4 -157.1 98.8 55.1 76.5 9.3  ASN-1393   THR-1394  8.0 6.2 -42.4 80.7 46.7 16.7 -101.3 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  GLN-1432   MET-1433  3.4 4.0 6.9 8.9 85.8 71.1 20.5  MET-1433   ALA-1434  1.3 2.2 -27.3 11.0 45.9 47.1 36.0  ALA-1434   PRO-1435  3.0 3.8 2.5 -6.0 72.9 72.1 12.1  PRO-1435   ILE-1436  5.6 5.6 24.8 -14.1 88.3 83.4 49.7 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