Iodine in PDB 2pvi: Pvuii Endonuclease Complexed to An Iodinated Cognate Dna

All present enzymatic activity of Pvuii Endonuclease Complexed to An Iodinated Cognate Dna:
3.1.21.4;

The structure of Pvuii Endonuclease Complexed to An Iodinated Cognate Dna, PDB code: 2pvi was solved by J.Horton, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.50 / 1.76
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	95.800, 86.300, 48.500, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 25.5

The binding sites of Iodine atom in the Pvuii Endonuclease Complexed to An Iodinated Cognate Dna (pdb code 2pvi). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Pvuii Endonuclease Complexed to An Iodinated Cognate Dna, PDB code: 2pvi:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in the Pvuii Endonuclease Complexed to An Iodinated Cognate Dna


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Pvuii Endonuclease Complexed to An Iodinated Cognate Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:I9 b:26.4 occ:1.00 I C:C389 0.0 26.4 1.0 C5 C:C389 2.2 22.1 1.0 C6 C:C389 3.1 21.9 1.0 C4 C:C389 3.2 22.6 1.0 N4 C:C389 3.3 21.1 1.0 O B:HOH169 3.5 40.8 1.0 CD2 B:HIS83 3.8 23.7 1.0 NE2 B:HIS83 3.8 21.8 1.0 O1P C:C389 4.0 24.2 1.0 CG B:HIS83 4.1 22.9 1.0 CE1 B:HIS83 4.1 19.2 1.0 C7 C:DT10 4.2 21.6 1.0 C8 C:DG8 4.2 22.8 1.0 ND1 B:HIS83 4.3 22.8 1.0 N7 C:DG8 4.3 25.8 1.0 CE1 B:HIS84 4.4 41.2 0.5 C3' C:DG8 4.4 27.2 1.0 N1 C:C389 4.4 24.5 1.0 N3 C:C389 4.4 22.0 1.0 ND1 B:HIS84 4.4 41.6 0.5 N9 C:DG8 4.5 23.3 1.0 CA B:HIS83 4.5 21.6 1.0 NE2 B:HIS84 4.5 43.3 0.5 C5 C:DG8 4.6 22.8 1.0 N B:HIS84 4.6 28.1 1.0 CG B:HIS84 4.6 38.7 0.5 C4 C:DG8 4.7 22.1 1.0 CD2 B:HIS84 4.7 42.3 0.5 C2' C:DG8 4.7 23.7 1.0 O B:THR82 4.7 24.1 1.0 O5' C:C389 4.8 25.0 1.0 CB B:HIS83 4.8 20.6 1.0 O5' C:DG8 4.9 31.3 1.0 P C:C389 4.9 23.4 1.0 C2 C:C389 4.9 21.7 1.0

Iodine binding site 2 out of 2 in the Pvuii Endonuclease Complexed to An Iodinated Cognate Dna


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Pvuii Endonuclease Complexed to An Iodinated Cognate Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:I9 b:20.6 occ:1.00 I D:C389 0.0 20.6 1.0 C5 D:C389 2.1 18.5 1.0 C6 D:C389 3.1 18.6 1.0 C4 D:C389 3.2 20.4 1.0 N4 D:C389 3.4 15.4 1.0 O A:HOH212 3.5 47.2 1.0 NE2 A:HIS83 3.7 18.6 1.0 CD2 A:HIS83 3.7 17.1 1.0 CE1 A:HIS83 4.0 21.4 1.0 CG A:HIS83 4.1 18.0 1.0 O1P D:C389 4.1 18.5 1.0 C8 D:DG8 4.1 17.1 1.0 N7 D:DG8 4.2 15.8 1.0 C7 D:DT10 4.2 14.8 1.0 ND1 A:HIS83 4.3 20.0 1.0 N1 D:C389 4.4 19.8 1.0 N3 D:C389 4.4 20.7 1.0 N9 D:DG8 4.4 16.6 1.0 C3' D:DG8 4.5 16.8 1.0 C5 D:DG8 4.5 18.4 1.0 CE1 A:HIS84 4.5 38.6 0.5 N A:HIS84 4.5 25.4 1.0 ND1 A:HIS84 4.5 39.2 0.5 CA A:HIS83 4.5 19.2 1.0 NE2 A:HIS84 4.6 39.4 0.5 CG A:HIS84 4.6 35.5 0.5 CD2 A:HIS84 4.6 38.8 0.5 C4 D:DG8 4.7 16.7 1.0 C2' D:DG8 4.8 17.8 1.0 O5' D:DG8 4.8 20.1 1.0 O A:THR82 4.8 15.4 1.0 O D:HOH67 4.8 26.4 1.0 CB A:HIS83 4.9 17.5 1.0 OP2 D:DG8 4.9 19.1 1.0 C2 D:C389 4.9 21.2 1.0 O5' D:C389 4.9 16.8 1.0

J.R.Horton, J.Bonventre, X.Cheng. How Is Modification of the Dna Substrate Recognized By the Pvuii Restriction Endonuclease? J.Biol.Chem. V. 379 451 1998.
ISSN: ISSN 0021-9258
PubMed: 9628337