#1 HBAT CUSTOMIZATION FOR RNA STRUCTURAL STUDIES

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RNA Related (1)
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2008-11-05
2008-11-05
Abhishek Tiwari
No

CRITERIA FOR RNA :

1. Atoms nomenclature: (Since RNA can form bonds between bases, backbone, sugar etc.)

Base atoms : N1,N3,N4,N6,N7,N9,O2,O4,O6,C5,C6,C2,C8 (in terms of atoms which will participate in hbonding in A,G,C,U nucleotides)

Sugar atoms : C1', C2', O2',O4'

Backbone atoms: OP1, OP2, O5',C5',C4',C3',O3'

Donor atoms: O of HOH,O2',C1',C2',C3',C4',C5', (O3',O5' -> Only if present in terminal/end residues)

Adenine (A) -> C2,N6, N9, C8

Guanine (G) -> N1, N2, C8, N9

Cytosine (C) -> N1,N4,C5,C6

Uracil (U) -> N1,N3, C5,C6

Acceptor atoms: O of HOH,OP1,OP2, O2', O3', O4' , O5'

Adenine (A) -> N1, N3, N7,N6,N9

Guanine (G) -> N3, O6, N7,N1,N2,N9

Cytosine (C) -> O2, N3,N1,N4

Uracil (U) -> O2,O4,N1,N3

If bond is base-base , then we have to sub classify those atoms are from which edge i.e. Watson -crick (WC), Hoogsteen (H) or Sugar (S)

WC -> A -> N6, N1, C2

G -> O6, N1, N2

C-> N4, N3, O2

U-> O4, N3, O2

H-> A-> N6, N7, [ A(N6) can be of both WC or H type]

G-> O6, N7

C-> N4, C5

U-> O4, C5

S-> A-> C2, N3, O2'

G-> N2,N3, O2'

C-> O2, O2' (ribose sugar's Oxygen)

U->O2, O2'

2. All types of strong and weak hbonds is required.

3. Kindly include Water (HOH, DOD) in the donor. We would like to study what bonds water forms with other nucleotides .

4. Also, in nomenclature of donor/acceptor atoms, kindly mention if atoms is not from a nucleotide but from a HETATOM -> HOH, Metal ligands, peptides.

5. Proper annotation in HBAT hbond list of RNA atoms- eg. atoms involved in hbond are from a Base/Backbone/Sugar. (Please add more details on the same)

Discussion