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. Author manuscript; available in PMC: 2010 Oct 1.
Published in final edited form as: J Phys Chem B. 2009 Oct 1;113(39):13035–13047. doi: 10.1021/jp903172x

Table 1.

Predominant Active-site Protein Residue Side-chain Orientations Assumed During Pol λ smatch Dynamicsa

System Protein Residue
Tyr505 Phe506 IIe492 Asn513 Arg514 Arg517
A:C inactive active active active active active
A:G inactive active active new inactive active
A(syn):G inactive active active new active active
T:G mainly
nactive		 mainly
active, but
briefly
inactive		 inactive &
new		 new active mainly active
with small
conformational
changes
A(syn):A inactive inactive inactive &
new		 active active mainly active
with small
conformational
changes
A:A inactive,
ctive, &
new		 active and
sideways
variant		 active active intermediate active
a

Table Definitions: inactive, refers to side-chain orientation in binary pol λ /DNA complex (PDB entry 1XSL)

active, refers to side-chain orientation in ternary pol λ/DNA/dTTP complex (PDB entry 1XSN)

new, refers to side-chain orientation not captured crystallographically

intermediate, refers to side-chain orientation lying between the active and inactive positions