SON

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
PB	O1B	doub	1.48Å	1.48Å
PB	O2B	sing	1.61Å	1.48Å
PB	O3B	sing	1.61Å	1.59Å
PB	CB	sing	1.82Å	1.73Å
O2B	H2B	sing	0.97Å	0.95Å
O3B	H3B	sing	0.97Å	0.95Å
CB	CA	sing	1.51Å	1.51Å
CB	HB1	sing	1.09Å	1.12Å
CB	HB2	sing	1.09Å	1.11Å
CA	OA	doub	1.21Å	1.23Å
CA	O5'	sing	1.34Å	1.43Å
O5'	C5'	sing	1.45Å	1.43Å
C5'	C4'	sing	1.53Å	1.51Å
C5'	H5'1	sing	1.09Å	1.11Å
C5'	H5'2	sing	1.09Å	1.12Å
C4'	O4'	sing	1.44Å	1.45Å
C4'	C3'	sing	1.55Å	1.52Å
C4'	H4'	sing	1.09Å	1.12Å
O4'	C1'	sing	1.44Å	1.42Å
C1'	N9	sing	1.46Å	1.46Å
C1'	C2'	sing	1.55Å	1.53Å
C1'	H1'	sing	1.09Å	1.12Å
N9	C4	sing	1.37Å	1.37Å	Aromatic
N9	C8	sing	1.36Å	1.37Å	Aromatic
C4	N3	doub	1.33Å	1.34Å	Aromatic
C4	C5	sing	1.40Å	1.38Å	Aromatic
N3	C2	sing	1.32Å	1.33Å	Aromatic
C2	N1	doub	1.32Å	1.34Å	Aromatic
C2	H2	sing	1.08Å	1.10Å
N1	C6	sing	1.33Å	1.35Å	Aromatic
C6	N6	sing	1.38Å	1.34Å
C6	C5	doub	1.41Å	1.40Å	Aromatic
N6	HN61	sing	0.97Å	1.02Å
N6	HN62	sing	0.97Å	1.02Å
C5	N7	sing	1.35Å	1.39Å	Aromatic
N7	C8	doub	1.30Å	1.31Å	Aromatic
C8	H8	sing	1.08Å	1.10Å
C2'	O2'	sing	1.43Å	1.41Å
C2'	C3'	sing	1.55Å	1.53Å
C2'	H2'	sing	1.09Å	1.11Å
O2'	H3	sing	0.97Å	0.95Å
C3'	O3'	sing	1.43Å	1.42Å
C3'	H3'	sing	1.09Å	1.12Å
O3'	H1	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O1B	PB	O2B	110.8°	109.5°
O1B	PB	O3B	106.0°	109.5°
O1B	PB	CB	110.5°	109.5°
O2B	PB	O3B	105.9°	109.4°
O2B	PB	CB	110.9°	109.5°
PB	O2B	H2B	110.8°	106.8°
O3B	PB	CB	112.6°	109.5°
PB	O3B	H3B	106.0°	106.8°
PB	CB	CA	122.2°	109.5°
PB	CB	HB1	107.7°	109.5°
PB	CB	HB2	107.7°	109.5°
CA	CB	HB1	107.7°	109.5°
CA	CB	HB2	107.7°	109.5°
CB	CA	OA	119.2°	120.0°
CB	CA	O5'	114.6°	120.0°
HB1	CB	HB2	102.1°	109.5°
OA	CA	O5'	122.7°	120.0°
CA	O5'	C5'	109.9°	120.0°
O5'	C5'	C4'	110.2°	109.4°
O5'	C5'	H5'1	112.0°	109.5°
O5'	C5'	H5'2	111.9°	109.5°
C4'	C5'	H5'1	111.9°	109.5°
C4'	C5'	H5'2	112.0°	109.4°
C5'	C4'	O4'	110.2°	110.4°
C5'	C4'	C3'	114.7°	110.5°
C5'	C4'	H4'	103.7°	110.3°
H5'1	C5'	H5'2	98.5°	109.5°
O4'	C4'	C3'	103.7°	104.8°
O4'	C4'	H4'	114.8°	110.4°
C4'	O4'	C1'	109.7°	105.3°
C3'	C4'	H4'	110.2°	110.4°
C4'	C3'	C2'	102.4°	104.1°
C4'	C3'	O3'	110.8°	110.5°
C4'	C3'	H3'	114.3°	110.5°
O4'	C1'	N9	108.4°	110.4°
O4'	C1'	C2'	107.6°	104.9°
O4'	C1'	H1'	112.6°	110.4°
N9	C1'	C2'	113.0°	110.4°
N9	C1'	H1'	107.2°	110.3°
C1'	N9	C4	126.2°	126.3°
C1'	N9	C8	127.9°	126.3°
C2'	C1'	H1'	108.0°	110.3°
C1'	C2'	O2'	109.7°	110.8°
C1'	C2'	C3'	101.7°	104.0°
C1'	C2'	H2'	115.9°	110.4°
C4	N9	C8	105.8°	107.4°
N9	C4	N3	127.3°	134.9°
N9	C4	C5	105.8°	106.0°
N9	C8	N7	113.8°	110.0°
N9	C8	H8	125.1°	125.0°
N3	C4	C5	126.9°	119.1°
C4	N3	C2	110.5°	120.6°
C4	C5	C6	117.1°	118.1°
C4	C5	N7	110.7°	107.2°
N3	C2	N1	129.3°	122.5°
N3	C2	H2	115.0°	118.8°
N1	C2	H2	115.8°	118.8°
C2	N1	C6	118.5°	121.2°
N1	C6	N6	118.7°	120.8°
N1	C6	C5	117.7°	118.5°
N6	C6	C5	123.6°	120.8°
C6	N6	HN61	108.9°	120.0°
C6	N6	HN62	118.7°	120.0°
C6	C5	N7	132.2°	134.7°
HN61	N6	HN62	108.9°	120.0°
C5	N7	C8	103.9°	109.4°
N7	C8	H8	121.0°	125.0°
O2'	C2'	C3'	113.9°	110.6°
O2'	C2'	H2'	104.1°	110.4°
C2'	O2'	H3	109.7°	106.8°
C3'	C2'	H2'	111.9°	110.5°
C2'	C3'	O3'	112.6°	110.5°
C2'	C3'	H3'	112.6°	110.6°
O3'	C3'	H3'	104.4°	110.4°
C3'	O3'	H1	110.8°	106.8°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O1B	PB	O2B	O3B	114.5°	120.0°
O1B	PB	O2B	CB	123.1°	120.0°
O1B	PB	O3B	CB	120.9°	120.0°
O1B	PB	O2B	H2B	180.0°	180.0°
O1B	PB	O3B	H3B	180.0°	60.0°
O1B	PB	CB	CA	94.1°	55.0°
O1B	PB	CB	HB1	31.2°	175.0°
O1B	PB	CB	HB2	140.6°	65.0°
O2B	PB	O3B	CB	121.4°	120.0°
O2B	PB	O3B	H3B	62.2°	60.0°
O2B	PB	CB	CA	29.2°	65.0°
O2B	PB	CB	HB1	154.4°	55.0°
O2B	PB	CB	HB2	96.1°	175.0°
O3B	PB	O2B	H2B	65.5°	60.1°
O3B	PB	CB	CA	147.6°	175.0°
O3B	PB	CB	HB1	87.1°	65.0°
O3B	PB	CB	HB2	22.3°	55.0°
CB	PB	O2B	H2B	56.9°	59.9°
CB	PB	O3B	H3B	59.1°	180.0°
PB	CB	CA	HB1	125.3°	120.0°
PB	CB	CA	HB2	125.3°	120.0°
PB	CB	HB1	HB2	113.2°	120.0°
PB	CB	CA	OA	98.6°	80.0°
PB	CB	CA	O5'	61.0°	100.0°
CA	CB	HB1	HB2	113.2°	120.0°
CB	CA	OA	O5'	157.9°	180.0°
CB	CA	O5'	C5'	57.6°	180.0°
HB1	CB	CA	OA	26.6°	160.0°
HB1	CB	CA	O5'	173.7°	20.0°
HB2	CB	CA	OA	136.1°	40.0°
HB2	CB	CA	O5'	64.3°	140.0°
OA	CA	O5'	C5'	143.5°	0.0°
CA	O5'	C5'	C4'	156.2°	180.0°
CA	O5'	C5'	H5'1	78.6°	60.0°
CA	O5'	C5'	H5'2	30.9°	60.1°
O5'	C5'	C4'	H5'1	125.3°	120.0°
O5'	C5'	C4'	H5'2	125.2°	119.9°
O5'	C5'	H5'1	H5'2	117.8°	120.0°
O5'	C5'	C4'	O4'	68.2°	66.5°
O5'	C5'	C4'	C3'	48.3°	178.1°
O5'	C5'	C4'	H4'	168.5°	55.8°
C4'	C5'	H5'1	H5'2	117.9°	120.0°
C5'	C4'	O4'	C3'	123.2°	118.9°
C5'	C4'	O4'	H4'	116.6°	122.3°
C5'	C4'	C3'	H4'	116.5°	122.3°
C5'	C4'	O4'	C1'	148.3°	159.4°
C5'	C4'	C3'	C2'	157.8°	142.9°
C5'	C4'	C3'	O3'	81.9°	98.3°
C5'	C4'	C3'	H3'	35.8°	24.2°
H5'1	C5'	C4'	O4'	57.1°	173.5°
H5'1	C5'	C4'	C3'	173.6°	58.1°
H5'1	C5'	C4'	H4'	66.2°	64.2°
H5'2	C5'	C4'	O4'	166.5°	53.4°
H5'2	C5'	C4'	C3'	77.0°	61.9°
H5'2	C5'	C4'	H4'	43.2°	175.8°
O4'	C4'	C3'	H4'	123.3°	118.9°
C4'	O4'	C1'	N9	124.6°	159.4°
C4'	O4'	C1'	C2'	2.1°	40.5°
C4'	O4'	C1'	H1'	116.9°	78.4°
O4'	C4'	C3'	C2'	37.7°	24.1°
O4'	C4'	C3'	O3'	158.0°	142.8°
O4'	C4'	C3'	H3'	84.4°	94.7°
C3'	C4'	O4'	C1'	25.1°	40.5°
C4'	C3'	C2'	C1'	35.5°	0.2°
C4'	C3'	C2'	O2'	82.4°	118.8°
C4'	C3'	C2'	O3'	119.0°	118.7°
C4'	C3'	C2'	H3'	123.2°	118.7°
C4'	C3'	C2'	H2'	159.9°	118.7°
C4'	C3'	O3'	H3'	123.5°	122.6°
C4'	C3'	O3'	H1	180.0°	180.0°
H4'	C4'	O4'	C1'	95.1°	78.3°
H4'	C4'	C3'	C2'	85.6°	94.8°
H4'	C4'	C3'	O3'	34.7°	23.9°
H4'	C4'	C3'	H3'	152.3°	146.5°
O4'	C1'	N9	C2'	119.2°	115.5°
O4'	C1'	N9	H1'	121.9°	122.3°
O4'	C1'	C2'	H1'	121.9°	118.9°
O4'	C1'	N9	C4	133.5°	157.9°
O4'	C1'	N9	C8	46.9°	22.0°
O4'	C1'	C2'	O2'	99.4°	142.6°
O4'	C1'	C2'	C3'	21.5°	23.9°
O4'	C1'	C2'	H2'	143.0°	94.7°
N9	C1'	C2'	H1'	118.4°	122.2°
C1'	N9	C4	C8	179.7°	179.9°
C1'	N9	C4	N3	0.5°	0.1°
C1'	N9	C4	C5	179.6°	179.8°
C1'	N9	C8	N7	179.5°	180.0°
C1'	N9	C8	H8	0.5°	0.0°
N9	C1'	C2'	O2'	140.9°	98.5°
N9	C1'	C2'	C3'	98.2°	142.8°
N9	C1'	C2'	H2'	23.4°	24.2°
C2'	C1'	N9	C4	107.3°	86.6°
C2'	C1'	N9	C8	72.3°	93.5°
C1'	C2'	O2'	C3'	113.2°	114.7°
C1'	C2'	O2'	H2'	124.7°	122.7°
C1'	C2'	C3'	H2'	124.3°	118.5°
C1'	C2'	O2'	H3	180.0°	176.1°
C1'	C2'	C3'	O3'	154.6°	118.9°
C1'	C2'	C3'	H3'	87.7°	118.5°
H1'	C1'	N9	C4	11.6°	35.6°
H1'	C1'	N9	C8	168.8°	144.3°
H1'	C1'	C2'	O2'	22.5°	23.7°
H1'	C1'	C2'	C3'	143.4°	95.1°
H1'	C1'	C2'	H2'	95.1°	146.3°
N9	C4	N3	C5	179.9°	179.7°
N9	C4	N3	C2	179.9°	180.0°
N9	C4	C5	C6	179.9°	179.7°
N9	C4	C5	N7	0.0°	0.4°
C4	N9	C8	N7	0.1°	0.0°
C4	N9	C8	H8	179.9°	179.9°
C8	N9	C4	N3	179.8°	180.0°
C8	N9	C4	C5	0.1°	0.3°
N9	C8	N7	C5	0.1°	0.2°
N9	C8	N7	H8	180.0°	179.9°
C4	N3	C2	N1	0.0°	0.1°
C4	N3	C2	H2	180.0°	180.0°
N3	C4	C5	C6	0.0°	0.6°
N3	C4	C5	N7	179.8°	179.8°
C5	C4	N3	C2	0.0°	0.3°
C4	C5	C6	N1	0.0°	0.5°
C4	C5	C6	N6	179.9°	179.8°
C4	C5	C6	N7	179.8°	179.0°
C4	C5	N7	C8	0.0°	0.4°
N3	C2	N1	H2	180.0°	179.9°
N3	C2	N1	C6	0.0°	0.1°
C2	N1	C6	N6	179.9°	180.0°
C2	N1	C6	C5	0.0°	0.3°
H2	C2	N1	C6	180.0°	180.0°
N1	C6	N6	C5	179.9°	179.7°
N1	C6	N6	HN61	54.7°	0.1°
N1	C6	N6	HN62	180.0°	179.7°
N1	C6	C5	N7	179.8°	179.6°
C6	N6	HN61	HN62	130.8°	179.6°
N6	C6	C5	N7	0.3°	0.7°
C5	C6	N6	HN61	125.4°	179.7°
C5	C6	N6	HN62	0.1°	0.6°
C6	C5	N7	C8	179.8°	179.5°
C5	N7	C8	H8	179.9°	179.8°
O2'	C2'	C3'	H2'	117.8°	122.6°
O2'	C2'	C3'	O3'	36.6°	0.1°
O2'	C2'	C3'	H3'	154.4°	122.5°
C3'	C2'	O2'	H3	66.8°	61.4°
C2'	C3'	O3'	H3'	122.5°	122.7°
C2'	C3'	O3'	H1	66.0°	65.3°
H2'	C2'	O2'	H3	55.3°	61.2°
H2'	C2'	C3'	O3'	81.1°	122.6°
H2'	C2'	C3'	H3'	36.6°	0.0°
H3'	C3'	O3'	H1	56.4°	57.4°

Definition date:	2004-01-26
Last modified:	2011-06-04
Release status:	REL
Processing site:	RCSB
Derived from:	1S5Z