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Table 3 Hydrogen bond interactions between DNA and HMG box of SOX2 protein determined through molecular docking experiments

From: Evolutionary relevance of single nucleotide variants within the forebrain exclusive human accelerated enhancer regions

Derived A-allele DNA

Ancestral T-allele DNA

S.No

Interacting residues of SOX2

D…A Distance Ȧ

D-H…A Distance Ȧ

Interacting nucleotides

Interacting residues of SOX2

D…A Distance Ȧ

D-H…A Distance Ȧ

Interacting nucleotides

1

ARG43NH1

3.02

2.64

DT37O2

ARG43NH1

3.68

2.02

DT39O2

2

ARG43NH1

2.95

2.09

DG38O4

ARG43NH1

3.5

2.18

DT39O4

3

ARG43NH2

3.07

1.94

DT16O2

ARG43NH2

2.97

2.14

DA14O3

4

ARG43NH2

2.95

2.32

DT16O4

ARG56NH1

3.75

2.31

DT42O4

5

ASN46ND2

3.8

2.13

DA15O4

ASN68ND2

3

2.21

DC10O2

6

ALA47N

3.68

2.34

DA14O3

ASN68ND2

3.74

2.31

DC10O4

7

ARG56NH1

2.88

2.07

DT40O3

ASN68OD1

2.43

2.05

DG41H21

8

ASN68ND2

2.97

2.47

DG41O3

-

-

-

-

9

LYS73HZ1

2.15

2.22

DA11O3

-

-

-

-

10

ARG113N

3.01

2.09

DT37O3

-

-

-

-

11

ARG114NH2

3

1.85

DG18O3

-

-

-

-

12

LYS115HZ2

2.26

1.76

DA9O5

-

-

-

-

  1. Amino acid numbering is based on position of HMG box domain (39–115) within SOX2 protein. The sequence of bases in one strand of DNA (chain b) are numbered from 1–25 and in the other strand (chain a) are numbered as 26–50. D (A, C, T, G) denotes Deoxyribonucleotides, D…A, denotes distances between donor atom and acceptor atom, while D-H…A illustrates distance between the hydrogen bonded to donor atom and acceptor atom
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BMC Molecular and Cell Biology

ISSN: 2661-8850

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