Cobalt in PDB 6izy: The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5

The structure of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, PDB code: 6izy was solved by H.Shimizu, S.Sekine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.96 / 2.11
Space group	I 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	237.350, 237.350, 237.350, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.1

The structure of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Cobalt atom in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5 (pdb code 6izy). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, PDB code: 6izy:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co901 b:0.6 occ:1.00 O A:HOH1179 2.4 71.8 1.0 CG2 A:THR290 3.4 72.3 1.0 N A:GLU289 3.5 62.9 1.0 CA A:HIS288 3.8 64.3 1.0 O A:GLU287 3.8 56.7 1.0 N A:THR290 3.8 53.0 1.0 C A:HIS288 3.9 61.1 1.0 OG1 A:THR290 4.2 84.7 1.0 N A:HIS288 4.2 54.2 1.0 C A:GLU287 4.3 50.8 1.0 CB A:THR290 4.3 69.7 1.0 CA A:GLU289 4.5 63.5 1.0 C A:GLU289 4.7 58.5 1.0 CA A:THR290 4.7 63.0 1.0 O A:HIS288 4.8 55.3 1.0 CB A:GLU289 4.8 75.0 1.0

Cobalt binding site 2 out of 4 in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co902 b:91.8 occ:1.00 CE A:MET761 3.6 49.3 1.0 OG A:SER757 3.7 50.4 1.0 NE1 A:TRP803 3.8 43.5 1.0 CE1 A:TYR758 4.1 38.3 1.0 CZ A:TYR758 4.3 50.6 1.0 CD1 A:TYR758 4.3 39.1 1.0 CE2 A:TRP803 4.5 46.2 1.0 CE2 A:TYR758 4.6 43.2 1.0 NH2 A:ARG737 4.6 79.1 1.0 CB A:SER757 4.6 36.4 1.0 CG A:TYR758 4.6 37.4 1.0 CZ2 A:TRP803 4.7 46.0 1.0 O A:SER757 4.7 31.6 1.0 OH A:TYR758 4.7 46.7 1.0 CD1 A:TRP803 4.7 44.2 1.0 C A:SER757 4.7 38.3 1.0 CD2 A:TYR758 4.7 36.2 1.0 N A:TYR758 4.8 30.8 1.0 SD A:MET761 4.8 56.2 1.0 CA A:TYR758 4.9 33.8 1.0

Cobalt binding site 3 out of 4 in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co903 b:0.1 occ:1.00 O A:HOH1126 3.4 67.1 1.0 O A:HOH1091 3.8 48.8 1.0 CD1 A:TYR882 3.9 71.7 1.0 OD1 A:ASN777 3.9 46.7 1.0 SG A:CYS780 4.1 46.1 1.0 CE1 A:TYR882 4.2 72.0 1.0 CB A:CYS780 4.2 36.3 1.0 CG A:TYR882 4.3 70.5 1.0 CB A:MET809 4.4 37.4 1.0 O A:HOH1183 4.4 54.4 1.0 CG A:MET809 4.5 43.1 1.0 CB A:TYR882 4.7 60.6 1.0 CZ A:TYR882 4.8 67.8 1.0 CD2 A:TYR882 4.8 57.0 1.0 O A:HOH1116 4.9 50.1 1.0 CB A:SER763 5.0 33.9 1.0

Cobalt binding site 4 out of 4 in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co904 b:0.8 occ:1.00 NE1 A:TRP823 3.5 47.8 1.0 CD1 A:TRP823 3.8 47.2 1.0 CE2 A:TRP823 3.9 45.6 1.0 O A:PRO822 4.1 48.8 1.0 CB A:PRO822 4.3 45.3 1.0 CZ2 A:TRP823 4.4 38.0 1.0 CG A:TRP823 4.4 47.0 1.0 CD2 A:TRP823 4.4 39.8 1.0 C A:PRO822 4.5 50.0 1.0 O A:HOH1122 4.5 60.0 1.0 CG A:PRO822 4.8 46.1 1.0 OD2 A:ASP521 4.9 49.1 1.0 N A:TRP823 4.9 46.0 1.0

H.Shimizu, S.Sekine. Apo Form of DENV2 Rdrp To Be Published.