Iodine in PDB 6kr3: Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2)

The structure of Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2), PDB code: 6kr3 was solved by J.Wu, G.Lu, H.Q.Ye, P.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.81 / 2.93
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	178.845, 209.975, 157.873, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 26.8

The structure of Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2) also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2) (pdb code 6kr3). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 15 binding sites of Iodine where determined in the Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2), PDB code: 6kr3:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 15 in the Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1001 b:76.7 occ:0.95 N A:GLY58 3.8 36.0 1.0 CB A:SAH1013 3.9 41.2 0.9 CA A:GLY58 4.1 40.0 1.0 NZ A:LYS61 4.2 51.5 1.0 CB A:ARG57 4.4 43.0 1.0 OG A:SER56 4.4 37.7 1.0 C A:ARG57 4.5 38.0 1.0 C A:SAH1013 4.6 41.1 0.9 CB A:SER56 4.6 42.1 1.0 N A:ARG57 4.7 40.7 1.0 CA A:SAH1013 4.7 44.0 0.9 O A:SAH1013 4.7 41.2 0.9 CA A:ARG57 4.8 37.6 1.0 OXT A:SAH1013 4.8 41.7 0.9 OD2 A:ASP146 4.9 42.6 1.0

Iodine binding site 2 out of 15 in the Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1002 b:76.7 occ:1.00 N A:GLY148 3.7 32.5 1.0 N A:GLU149 3.8 39.1 1.0 C8 A:SAH1013 3.9 46.6 0.9 C A:GLY148 4.0 35.4 1.0 C2' A:SAH1013 4.1 41.4 0.9 CA A:GLU149 4.1 35.8 1.0 CG A:GLU149 4.2 40.5 1.0 O A:GLY148 4.3 30.2 1.0 C3' A:SAH1013 4.4 44.3 0.9 CB A:GLU149 4.4 37.2 1.0 CA A:GLY148 4.4 35.1 1.0 CA A:ILE147 4.6 32.3 1.0 C A:ILE147 4.6 32.2 1.0 C5' A:SAH1013 4.6 45.6 0.9 CG2 A:ILE147 4.7 37.7 1.0 N9 A:SAH1013 4.7 51.6 0.9 O4' A:SAH1013 4.7 41.1 0.9 C1' A:SAH1013 4.7 41.9 0.9 C4' A:SAH1013 4.9 41.6 0.9 N7 A:SAH1013 4.9 46.4 0.9

Iodine binding site 3 out of 15 in the Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1003 b:76.7 occ:0.97 CB A:LYS249 4.0 56.3 1.0 CA A:HIS247 4.0 68.0 1.0 CD B:PRO336 4.1 62.2 1.0 CD2 A:HIS247 4.1 58.6 1.0 N A:LYS249 4.3 62.6 1.0 CG1 B:ILE335 4.3 46.9 1.0 C A:HIS247 4.4 69.2 1.0 CB A:HIS247 4.4 63.9 1.0 N A:LYS248 4.5 67.0 1.0 CG A:HIS247 4.6 63.7 1.0 CA B:ILE335 4.7 60.3 1.0 SD B:MET337 4.7 73.6 1.0 CA A:LYS249 4.7 60.6 1.0 CE B:MET337 4.9 58.9 1.0 CB B:ILE335 4.9 57.8 1.0 O A:HIS247 4.9 75.5 1.0 CD1 B:ILE335 5.0 49.1 1.0

Iodine binding site 4 out of 15 in the Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1004 b:76.7 occ:1.00 NH2 B:ARG326 3.7 48.8 1.0 CA A:GLY323 3.9 39.7 1.0 NE B:ARG326 3.9 49.8 1.0 CA B:GLY323 4.0 41.5 1.0 NH1 A:ARG326 4.2 41.2 1.0 CG B:LEU327 4.3 41.8 1.0 CG A:LEU327 4.3 34.8 1.0 CZ B:ARG326 4.3 50.0 1.0 CD2 B:LEU327 4.3 39.4 1.0 CZ A:ARG326 4.4 42.6 1.0 O B:GLY323 4.4 37.3 1.0 NE A:ARG326 4.5 41.7 1.0 O A:GLY323 4.5 36.4 1.0 CD A:ARG326 4.5 40.6 1.0 CD2 A:LEU327 4.5 42.0 1.0 CD1 A:LEU327 4.6 35.8 1.0 CG A:ARG326 4.6 35.9 1.0 C B:GLY323 4.7 41.8 1.0 C A:GLY323 4.7 42.8 1.0 CB A:ARG326 4.7 37.7 1.0 CD1 B:LEU327 4.7 37.6 1.0 CB B:ARG326 4.9 46.7 1.0 NH2 A:ARG326 4.9 52.8 1.0 N A:GLY323 4.9 37.1 1.0

Iodine binding site 5 out of 15 in the Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1005 b:76.7 occ:0.91 CD A:PRO336 3.9 55.0 1.0 CD2 B:HIS247 4.1 57.9 1.0 CG1 A:ILE335 4.2 43.2 1.0 CB B:HIS247 4.5 62.9 1.0 CA B:HIS247 4.5 77.3 1.0 CE A:MET337 4.5 50.7 1.0 CA A:ILE335 4.5 53.0 1.0 CG B:HIS247 4.6 59.6 1.0 SD A:MET337 4.7 64.0 1.0 N B:LYS248 4.7 82.6 1.0 CB B:LYS249 4.8 70.4 1.0 CG2 A:ILE335 4.8 49.0 1.0 CB A:ILE335 4.8 51.0 1.0 CG A:PRO336 4.9 54.5 1.0 CD1 A:ILE335 4.9 37.3 1.0 N B:LYS249 4.9 78.5 1.0 C B:HIS247 4.9 78.4 1.0 N A:PRO336 5.0 53.0 1.0

Iodine binding site 6 out of 15 in the Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1006 b:94.2 occ:0.82 O A:HOH1126 3.2 39.4 1.0 N A:VAL723 3.6 53.0 1.0 O A:TRP823 3.8 60.5 1.0 CA A:ARG722 4.1 43.5 1.0 O A:VAL723 4.1 46.9 1.0 CB A:ARG722 4.2 45.5 1.0 CA A:MET824 4.3 55.8 1.0 C A:ARG722 4.3 49.8 1.0 CA A:VAL723 4.4 45.0 1.0 CB A:VAL723 4.5 31.0 1.0 CG A:ARG722 4.5 46.4 1.0 CB A:MET824 4.7 54.5 1.0 SD A:MET824 4.7 51.9 1.0 C A:VAL723 4.8 51.1 1.0 C A:TRP823 4.8 49.8 1.0

Iodine binding site 7 out of 15 in the Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1007 b:0.0 occ:0.80 CD2 A:LEU571 3.5 69.9 1.0 CA A:ALA567 4.0 64.6 1.0 N A:ALA567 4.1 66.9 1.0 C A:GLU566 4.2 66.2 1.0 O A:GLU566 4.2 68.7 1.0 CB A:ALA567 4.4 71.4 1.0 CB A:GLU566 4.5 61.6 1.0 CB A:LYS570 4.6 60.7 1.0 CA A:GLY445 4.6 81.1 1.0 CG A:LEU571 4.7 70.7 1.0 O A:HIS442 4.8 77.5 1.0 O A:LYS563 4.9 68.1 1.0

Iodine binding site 8 out of 15 in the Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1008 b:0.6 occ:0.70 ND2 A:ASN610 3.8 47.9 1.0 CA A:GLY662 4.1 40.5 1.0 N A:ASP663 4.3 40.0 1.0 OD1 A:ASP663 4.3 41.9 1.0 CB A:ASN610 4.5 44.3 1.0 CA A:TYR607 4.5 50.2 1.0 CG A:ASN610 4.6 45.5 1.0 CD1 A:TYR607 4.6 46.2 1.0 OG1 A:THR606 4.7 59.9 1.0 C A:GLY662 4.8 42.0 1.0 CG A:ASP663 4.8 41.7 1.0 N A:TYR607 4.9 53.7 1.0 CB A:TYR607 4.9 51.0 1.0

Iodine binding site 9 out of 15 in the Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1009 b:0.2 occ:0.71 ND2 A:ASN777 3.4 55.2 1.0 CD A:PRO884 3.7 69.6 1.0 CG A:PRO884 3.8 75.5 1.0 CA A:LEU774 4.0 32.3 1.0 OH A:TYR838 4.1 52.9 1.0 O A:ARG773 4.2 46.7 1.0 N A:LEU774 4.2 34.3 1.0 CD A:ARG773 4.3 38.6 1.0 C A:ARG773 4.4 40.1 1.0 CB A:LEU774 4.5 33.1 1.0 CG A:LEU774 4.5 31.9 1.0 CG A:ASN777 4.5 50.0 1.0 CG A:ARG773 4.7 43.4 1.0 CE A:MET883 4.8 37.2 1.0 CB A:ASN777 4.8 45.1 1.0 CB A:PRO884 4.9 79.5 1.0 CB A:ARG773 5.0 39.2 1.0

Iodine binding site 10 out of 15 in the Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1010 b:91.2 occ:0.58 CB A:ASN241 4.0 45.8 1.0 CB A:MET245 4.0 58.6 1.0 CE A:MET245 4.0 71.9 1.0 O A:ASN241 4.2 57.4 1.0 C A:ASN241 4.2 50.8 1.0 N A:ARG242 4.3 49.9 1.0 CG A:ARG242 4.3 48.1 1.0 CA A:ARG242 4.4 51.3 1.0 OE1 B:GLN845 4.5 58.3 1.0 CG A:MET245 4.6 66.5 1.0 CA A:MET245 4.6 60.8 1.0 CA A:ASN241 4.7 48.7 1.0 SD A:MET245 4.9 97.4 1.0 CD B:GLN845 4.9 55.3 1.0

J.Wu, G.Lu, H.Q.Ye, P.Gong. Crystal Structure of Dengue Virus Nonstructural Protein NS5 To Be Published.