Iodine in PDB 3r2v: Crystal Structure of Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2

The structure of Crystal Structure of Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2, PDB code: 3r2v was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	52.810, 106.540, 33.490, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2 (pdb code 3r2v). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Crystal Structure of Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2, PDB code: 3r2v:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in the Crystal Structure of Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2


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 Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1 b:19.2 occ:0.60 O A:HOH89 3.6 23.4 1.0 CB A:GLN566 3.9 15.9 1.0 CA A:GLN563 4.0 11.3 1.0 O A:HOH42 4.1 15.0 1.0 CG A:GLN563 4.1 17.4 1.0 CB A:ASN567 4.2 12.5 1.0 CB A:GLN563 4.4 12.5 1.0 N A:ASN567 4.5 11.4 1.0 N A:GLN563 4.5 11.2 1.0 CG2 A:ILE562 4.6 14.0 1.0 O A:ILE562 4.7 12.2 1.0 CG A:GLN566 4.7 20.7 1.0 NE2 A:GLN563 4.8 24.7 1.0 C A:ILE562 4.8 11.9 1.0 C A:GLN566 4.8 13.1 1.0 CD A:GLN563 4.9 20.4 1.0 CA A:GLN566 4.9 14.7 1.0

Iodine binding site 2 out of 12 in the Crystal Structure of Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2


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 Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I2 b:18.4 occ:0.42 ND2 A:ASN573 3.8 14.0 1.0 CB A:ASN573 3.9 12.9 1.0 CG A:ASN573 4.0 13.8 1.0 CA A:MET570 4.1 12.6 1.0 O A:ALA569 4.1 12.5 1.0 N A:MET570 4.4 12.0 1.0 C A:ALA569 4.4 11.4 1.0 O A:HOH763 4.5 20.1 1.0 CB A:MET570 4.7 14.0 1.0 OD1 A:ASN573 4.8 15.2 1.0 CG A:MET570 5.0 16.1 1.0 O A:MET570 5.0 13.5 1.0

Iodine binding site 3 out of 12 in the Crystal Structure of Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2


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 Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I3 b:23.5 occ:0.60 O A:HOH61 3.3 21.2 1.0 NE2 A:GLN628 3.5 32.8 1.0 O A:HOH146 3.9 25.2 1.0 CB A:PRO626 4.0 13.1 1.0 O A:PRO626 4.1 17.9 1.0 CG A:PRO626 4.1 14.1 1.0 C A:PRO626 4.2 16.2 1.0 N A:GLN628 4.3 22.4 1.0 N A:LYS627 4.5 17.4 1.0 O A:HOH62 4.5 19.0 1.0 C A:LYS627 4.5 20.3 1.0 CA A:LYS627 4.5 19.3 1.0 O A:HOH106 4.5 22.0 1.0 CB A:GLN628 4.6 25.6 1.0 CD A:GLN628 4.7 30.2 1.0 CA A:PRO626 4.8 14.8 1.0 CA A:GLN628 4.9 24.2 1.0

Iodine binding site 4 out of 12 in the Crystal Structure of Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2


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 Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I4 b:20.4 occ:0.44 O A:HOH60 3.1 15.5 1.0 O A:HOH764 3.4 7.1 1.0 CE2 A:TYR572 3.8 9.4 1.0 O A:HOH181 4.5 33.9 1.0 CD A:ARG597 4.5 9.9 1.0 CD2 A:TYR572 4.6 10.1 1.0 CB A:ARG597 4.7 8.4 1.0 O A:HOH62 4.7 19.0 1.0 OH A:TYR572 4.7 9.5 1.0 CZ A:TYR572 4.8 8.8 1.0 CG A:PRO568 4.9 11.2 1.0 NH1 A:ARG597 4.9 10.4 1.0 O A:HOH61 5.0 21.2 1.0 CG A:ARG597 5.0 8.3 1.0

Iodine binding site 5 out of 12 in the Crystal Structure of Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2


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 Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I5 b:20.3 occ:0.15 I A:IOD5 0.0 20.3 0.1 I A:IOD5 2.6 26.0 0.1 O A:HOH80 3.2 13.8 1.0 NE2 A:GLN632 3.4 13.5 1.0 CA A:SER714 3.7 25.0 1.0 O A:HOH163 3.8 31.3 1.0 CB A:SER714 3.9 26.1 1.0 N A:SER714 3.9 21.8 1.0 O A:ARG630 4.0 25.8 1.0 CE2 A:PHE694 4.0 15.5 1.0 C A:LEU713 4.2 19.1 1.0 CG A:GLN632 4.3 13.4 1.0 CD A:GLN632 4.3 11.9 1.0 O A:HOH66 4.3 17.8 1.0 CB A:LEU713 4.4 16.1 1.0 CZ A:PHE694 4.5 17.0 1.0 O A:LEU713 4.5 18.9 1.0 CA A:LEU713 4.8 16.7 1.0 O A:ARG692 4.9 11.9 1.0

Iodine binding site 6 out of 12 in the Crystal Structure of Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2


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 Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I5 b:26.0 occ:0.14 I A:IOD5 0.0 26.0 0.1 I A:IOD5 2.6 20.3 0.1 O A:HOH163 2.8 31.3 1.0 CA A:SER714 3.7 25.0 1.0 NZ A:LYS736 3.7 30.8 1.0 O A:SER714 4.0 28.9 1.0 CB A:SER714 4.0 26.1 1.0 CE A:LYS736 4.2 28.1 1.0 C A:SER714 4.3 27.1 1.0 CE2 A:PHE694 4.4 15.5 1.0 N A:SER714 4.6 21.8 1.0 O A:LEU713 4.6 18.9 1.0 CZ A:PHE694 4.7 17.0 1.0 C A:LEU713 4.9 19.1 1.0

Iodine binding site 7 out of 12 in the Crystal Structure of Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2


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 Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I6 b:28.3 occ:0.40 O A:HOH85 3.1 21.8 1.0 O A:HOH138 3.3 23.2 1.0 O A:HOH82 3.3 27.3 1.0 CD1 A:ILE676 4.1 32.3 1.0 CB A:GLU558 4.2 16.2 1.0 CA A:GLU558 4.2 14.7 1.0 CG2 A:ILE676 4.2 29.3 1.0 N A:GLU558 4.2 14.1 1.0 CD1 A:TRP557 4.2 13.7 1.0 CB A:ILE676 4.3 29.0 1.0 O A:HOH87 4.4 20.3 1.0 CG1 A:ILE676 4.8 29.9 1.0 CG A:GLU558 4.8 16.4 1.0 C A:TRP557 4.9 13.0 1.0 O A:HOH757 4.9 16.2 1.0 O A:HOH758 4.9 12.8 1.0

Iodine binding site 8 out of 12 in the Crystal Structure of Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2


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 Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I7 b:26.9 occ:0.28 O A:HOH83 3.6 19.1 1.0 O A:HOH88 3.9 22.7 1.0 CB A:SER565 4.1 13.5 1.0 CA A:ILE562 4.2 12.3 1.0 CG1 A:ILE562 4.3 14.6 1.0 CG2 A:ILE562 4.3 14.0 1.0 OE1 A:GLN566 4.3 29.7 1.0 OG A:SER565 4.4 17.3 1.0 CB A:ILE562 4.5 13.6 1.0 O A:ILE562 4.6 12.2 1.0 CG A:GLN566 4.6 20.7 1.0 O A:HOH185 4.8 30.9 1.0 CD A:GLN566 4.8 27.3 1.0 C A:ILE562 4.9 11.9 1.0 O A:LYS561 5.0 11.8 1.0

Iodine binding site 9 out of 12 in the Crystal Structure of Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2


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 Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I8 b:40.3 occ:0.29 O A:HOH135 3.2 19.3 1.0 N A:GLN632 3.2 15.8 1.0 CA A:MET631 3.6 20.1 1.0 SD A:MET631 3.6 21.9 0.4 CB A:ASN711 3.7 18.9 1.0 CA A:ASN711 3.8 16.9 1.0 C A:MET631 3.9 17.9 1.0 CB A:MET631 4.1 20.8 1.0 CA A:GLN632 4.3 14.1 1.0 CB A:GLN632 4.3 14.1 1.0 O A:GLN632 4.3 17.4 1.0 O A:ARG630 4.3 25.8 1.0 O A:HOH80 4.4 13.8 1.0 CG A:GLN632 4.4 13.4 1.0 CG A:MET631 4.5 22.2 1.0 O A:ILE710 4.5 15.9 1.0 CE A:MET631 4.6 24.8 1.0 N A:MET631 4.7 22.3 1.0 N A:ASN711 4.7 15.4 1.0 C A:GLN632 4.8 13.8 1.0 C A:ASN711 4.8 16.7 1.0 O A:ASN711 4.8 17.4 1.0 C A:ARG630 4.9 24.7 1.0 C A:ILE710 5.0 15.0 1.0

Iodine binding site 10 out of 12 in the Crystal Structure of Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2


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 Polymerase Basic Protein 2 E538-R753 From Influenza A Virus A/Yokohama/2017/03 H3N2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I9 b:22.2 occ:0.13 O A:HOH122 3.1 29.0 1.0 O A:HOH137 3.4 26.8 1.0 CD1 A:TRP552 4.1 14.6 1.0 CG A:GLU576 4.6 16.3 1.0 NE1 A:TRP552 4.6 15.2 1.0 CG A:TRP552 4.6 14.1 1.0 O A:HOH114 4.9 18.2 1.0 CB A:TRP552 4.9 13.2 1.0 CB A:GLU576 5.0 16.0 1.0

E.R.Smith, D.W.Begley, V.Anderson, A.C.Raymond, T.E.Haffner, J.I.Robinson, T.E.Edwards, N.Duncan, C.J.Gerdts, M.B.Mixon, P.Nollert, B.L.Staker, L.J.Stewart. The Protein Maker: An Automated System For High-Throughput Parallel Purification. Acta Crystallogr.,Sect.F V. 67 1015 2011.
ISSN: ESSN 1744-3091
PubMed: 21904043
DOI: 10.1107/S1744309111028776