TABLE 3.

Average active site interatomic distances for pol λ as observed during the last 1-ns of simulations and from x-ray crystal structure (PDB entry 1XSN)

Distance (Å)	Sim. 1	Sim. 2	Sim. 3	Sim. 4	Ternary (1XSN)
Nucleotidyl transfer distance
dTTP (Pα) : P6 (O3′)	7.86	4.76	4.68	6.14	n/a
Distance between magnesium ions
Mg2+(A) : Mg2+(B)	n/a	4.16	n/a	4.35	n/a
Catalytic magnesium ion coordination
Mg2+(A) : Asp427 (Oδ1)	n/a	3.17	n/a	1.82	n/a
Mg2+(A) : Asp427 (Oδ2)	n/a	1.86	n/a	3.50	n/a
Mg2+(A) : Asp429 (Oδ1)	n/a	1.83	n/a	1.85	n/a
Mg2+(A) : Asp490 (Oδ1)	n/a	6.05	n/a	1.92	n/a
Mg2+(A) : Asp490 (Oδ2)	n/a	4.15	n/a	1.91	n/a
Mg2+(A) : Wat2 (OH2)	n/a	2.03	n/a	2.10	n/a
Mg2+(A) : Wat3 (OH2)	n/a	n/a	n/a	1.98	n/a
Mg2+(A) : Wat4 (OH2)	n/a	2.05	n/a	n/a	n/a
Mg2+(A) : Wat5 (OH2)	n/a	2.08	n/a	22.7	n/a
Mg2+(A) : dTTP (O1α)	n/a	1.84	n/a	3.85	n/a
Mg2+(A) : P6 (O3′)	n/a	4.92	n/a	4.73	n/a
Nucleotide magnesium ion coordination
Mg2+(B) : Asp427 (Oδ1)	1.85	1.83	3.36	3.55	3.62
Mg2+(B) : Asp427 (Oδ2)	3.50	3.79	1.86	1.84	2.00
Mg2+(B) : Asp427 (O)	4.02	2.20	4.07	4.03	3.94
Mg2+(B) : Asp429 (Oδ2)	1.89	1.86	1.86	1.88	2.13
Mg2+(B) : Wat1 (OH2)	2.05	2.05	2.04	2.07	n/a
Mg2+(B) : Wat6 (OH2)	n/a	n/a	n/a	n/a	2.15
Mg2+(B) : dTTP (O1β)	1.91	1.83	1.91	1.92	1.88
Mg2+(B) : dTTP (O1α)	1.90	3.74	1.92	1.90	1.98
Mg2+(B) : dTTP (O3γ)	1.84	1.82	1.86	1.85	2.20

Key: Mg²⁺(A), catalytic ion; Mg²⁺(B), nucleotide-binding ion; dTTP, 2′-deoxythymidine 5′-triphosphate; P6, primer terminus; Wat1, Wat2, Wat3, Wat4, Wat5, Wat6, water molecules; n/a, not available.