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Table 1 Hydrogen bonds between DHNP, the catalytic water, and DHNA revealed by molecular dynamics simulation

From: Crystallographic and molecular dynamics simulation analysis of Escherichia coli dihydroneopterin aldolase

 

occurrence

distance

EcDHNP:NPa

(%)

(Ã…)

(Ã…)

Leu72 - NH…O = C4

99.73

2.91 ± 0.14

2.94

WAT - OH… O = C4

82.2

2.94 ± 0.20

2.79

Glu73 - OE1…H - N3

100

2.79 ± 0.09

2.76

Glu73 - OE2…H - NC2

99.74

2.84 ± 0.13

2.73

Leu51′ - O…H - NC2

95.94

2.93 ± 0.15

2.85

Tyr53′ - NH…N1

16.04

3.33 ± 0.12

2.98

WAT - OH…N5

70.61

3.18 ± 0.19

3.31

Ser52′-OG…H - N8

88.82

3.03 ± 0.17

NAb

Glu21 - OE1…H - OC1′

80.59

2.69 ± 0.24

2.64

Val17 - NH…OC1′

80.15

2.98 ± 0.20

2.88

Lys98 - NZ… H - OC2′

76.54

2.95 ± 0.16

2.75

Tyr53′ - OH…OC2′

63.96

3.10 ± 0.19

2.61

Ala101 - O…H - OC3′

7.33

3.00 ± 0.24

2.90

Lys98 - NZH…WAT

91.5

2.98 ± 0.17

2.87

  1. aThe corresponding hydrogen bonds in the crystal structure of EcDHNP:NP are listed for comparison. bNA, not applicable.