. 2020 Dec 5;31(4):503–516. doi: 10.1007/s13337-020-00640-9

Table 2.

Interactions of RNA dependent RNA polymerase with the regulatory elements of coat protein (CP) subgenomic promoter (SGP) region in the CGMMV genome

Regulatory elements (Co-ordinates)	Interacting nucleotides: amino acids (co-ordinates) in different interacting sites*
I (− 114 to − 109)	G(− 114):ASP57; G(− 113):GLN56; U(− 112):LYS19, GLN69; C(− 111):LYS19; A(− 110):VAL14; A(− 109):SER20, LYS16
II (− 60 to − 43)	U(− 60): ILE41; U(− 59): PHE24; G(− 58):CYS88; G(− 57):SER22; A(− 56): TYR68; G(− 55):VAL75; G(− 54):VAL75, ASP7, TYR67; U(− 53):LYS51; U(− 52):LYS51; U(− 51):ARG52; A(− 50):LYS51 G(− 49):MET30,SER27; C(− 48):ASP23, PHE24; C(− 47):VAL75, SER22, SER22; U(− 46):MET45, VAL75, ARG70, CYS88; C(− 45):TRP33,TRP46; C(− 44):TYR111; A(− 43):LEU116
III (+ 09 to + 21)	G(9):LYS35; U(10):LYS35; U(11):ILE54; A(12):LYS35; G(13):SER72; G(14):ASP106; C(15):VAL14; U(16):ASP96, LYS100, SER15; A(17):ASP96, LYS97, LYS16; G(18):LYS16; U(19):GLN56, LYS16; G(20):THR64, GLN56;U(21):THR64
IV (+ 97 to 114)	C(97):GLU11; C(98):GLU8, ILE9, GLU11, LEU10; A(99):GLU8, LEU116; G(101):GLY115; C(103):CYS104; A(105):TRP33; A(106):VAL75, THR76; A(107):MET45, VAL75, TRP46; G(108):MET45; G(109):ASP74; U(110):ASP74; C(111):PHE58, LYS71; U(112):GLN56; G(113):PHE58; A(114):PHE58
V (+ 136 to + 144)	G(136):GLN59; G(138):LYS63; C(139):LEU65; U(140):TYR67,TYR68; C(141):GLN69, LYS19,GLN69,ARG52; G(143):SER72; G(144):SER72

Regulatory elements
(Co-ordinates)

Interacting nucleotides: amino acids (co-ordinates)
in different interacting sites*

(− 114 to − 109)

G(− 114):ASP57; G(− 113):GLN56; U(− 112):LYS19, GLN69; C(− 111):LYS19; A(− 110):VAL14; A(− 109):SER20, LYS16

(− 60 to − 43)

U(− 60): ILE41; U(− 59): PHE24; G(− 58):CYS88; G(− 57):SER22; A(− 56): TYR68; G(− 55):VAL75; G(− 54):VAL75, ASP7, TYR67; U(− 53):LYS51; U(− 52):LYS51; U(− 51):ARG52; A(− 50):LYS51

G(− 49):MET30,SER27; C(− 48):ASP23, PHE24; C(− 47):VAL75, SER22, SER22; U(− 46):MET45, VAL75, ARG70, CYS88; C(− 45):TRP33,TRP46; C(− 44):TYR111; A(− 43):LEU116

III

(+ 09 to + 21)

G(9):LYS35; U(10):LYS35; U(11):ILE54; A(12):LYS35; G(13):SER72; G(14):ASP106; C(15):VAL14; U(16):ASP96, LYS100, SER15; A(17):ASP96, LYS97, LYS16; G(18):LYS16; U(19):GLN56, LYS16; G(20):THR64, GLN56;U(21):THR64

(+ 97 to 114)

C(97):GLU11; C(98):GLU8, ILE9, GLU11, LEU10; A(99):GLU8, LEU116; G(101):GLY115; C(103):CYS104; A(105):TRP33; A(106):VAL75, THR76; A(107):MET45, VAL75, TRP46; G(108):MET45; G(109):ASP74; U(110):ASP74; C(111):PHE58, LYS71; U(112):GLN56; G(113):PHE58; A(114):PHE58

(+ 136 to + 144)

G(136):GLN59; G(138):LYS63; C(139):LEU65; U(140):TYR67,TYR68;

C(141):GLN69, LYS19,GLN69,ARG52; G(143):SER72; G(144):SER72

*Value in parenthesis indicating the coordinates of nucleotides in the RNA with respective to translation start site (TLSS). The nucleotides located upstream of TLSS (+ 1) have (−) markings; nucleotides located downstream of TLSS have (+) markings. The interacting partners were identified from the interaction analysis between core RdRp and RNA ligands derived from complementary sequences of CP-SGP using Patch-dock web server