Iodine in PDB 5mk5: Structures of Dhbn Domain of Human Blm Helicase

All present enzymatic activity of Structures of Dhbn Domain of Human Blm Helicase:
3.6.4.12;

The structure of Structures of Dhbn Domain of Human Blm Helicase, PDB code: 5mk5 was solved by J.Shi, W.-F.Chen, B.Zhang, S.-H.Fan, X.Ai, N.-N.Liu, S.Rety, X.-G.Xi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.84 / 2.16
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	34.082, 144.729, 96.767, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 29.7

The structure of Structures of Dhbn Domain of Human Blm Helicase also contains other interesting chemical elements:

Potassium

(K)

3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Iodine atom in the Structures of Dhbn Domain of Human Blm Helicase (pdb code 5mk5). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 20 binding sites of Iodine where determined in the Structures of Dhbn Domain of Human Blm Helicase, PDB code: 5mk5:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 20 in the Structures of Dhbn Domain of Human Blm Helicase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structures of Dhbn Domain of Human Blm Helicase within 5.0Å range: probe atom residue distance (Å) B Occ A:I501 b:39.6 occ:0.77 HA A:HIS378 3.4 12.6 1.0 HE2 A:HIS374 3.5 34.9 1.0 HB2 A:HIS378 3.6 19.1 1.0 HD2 A:LYS381 3.6 65.6 1.0 NE2 A:HIS374 3.9 29.0 1.0 CG A:HIS378 4.0 34.4 1.0 CB A:HIS378 4.0 15.8 1.0 CA A:HIS378 4.1 10.9 1.0 CD2 A:HIS378 4.2 21.0 1.0 HD2 A:HIS378 4.3 25.2 1.0 HE3 A:LYS381 4.4 72.5 1.0 CD2 A:HIS374 4.4 13.4 1.0 HD2 A:HIS374 4.4 16.2 1.0 CD A:LYS381 4.5 54.6 1.0 N A:HIS378 4.5 11.1 1.0 ND1 A:HIS378 4.5 35.4 1.0 H A:HIS378 4.6 12.9 1.0 HE2 A:LYS381 4.7 72.5 1.0 CE1 A:HIS374 4.7 18.0 1.0 CE A:LYS381 4.7 60.3 1.0 NE2 A:HIS378 4.8 28.2 1.0 HD1 A:HIS378 4.8 42.6 1.0 HE1 A:HIS374 4.9 21.7 1.0 HD3 A:LYS381 4.9 65.6 1.0 CE1 A:HIS378 4.9 22.4 1.0 HB3 A:HIS378 5.0 19.1 1.0 O A:HIS374 5.0 11.9 1.0

Iodine binding site 2 out of 20 in the Structures of Dhbn Domain of Human Blm Helicase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structures of Dhbn Domain of Human Blm Helicase within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:57.0 occ:0.68 HH21 A:ARG407 3.0 36.7 1.0 O A:HOH620 3.1 15.9 1.0 HZ1 A:LYS381 3.2 73.3 1.0 HG2 A:GLU377 3.3 39.5 1.0 HZ3 A:LYS381 3.4 73.3 1.0 HE2 A:LYS381 3.5 72.5 1.0 HD21 A:LEU411 3.5 38.7 1.0 NZ A:LYS381 3.6 61.0 1.0 HB3 A:GLU377 3.6 26.1 1.0 O A:HOH639 3.7 48.1 1.0 NH2 A:ARG407 3.7 30.5 1.0 HD22 A:LEU411 3.8 38.7 1.0 CD A:GLU377 3.9 23.7 1.0 OE1 A:GLU377 3.9 88.5 1.0 CG A:GLU377 3.9 32.9 1.0 O A:HOH605 4.0 37.2 1.0 HH22 A:ARG407 4.0 36.7 1.0 O A:HOH634 4.1 45.9 1.0 CE A:LYS381 4.1 60.3 1.0 CD2 A:LEU411 4.1 32.2 1.0 CB A:GLU377 4.3 21.6 1.0 HE A:ARG407 4.3 24.2 1.0 OE2 A:GLU377 4.4 47.1 1.0 HZ2 A:LYS381 4.4 73.3 1.0 HA A:GLU377 4.5 13.1 1.0 HD21 B:LEU372 4.5 41.6 1.0 HE3 A:LYS381 4.6 72.5 1.0 HD23 A:LEU411 4.6 38.7 1.0 HD11 A:LEU411 4.7 46.8 1.0 HG3 A:LYS381 4.7 79.2 1.0 CZ A:ARG407 4.8 30.4 1.0 HG3 A:GLU377 4.8 39.5 1.0 O A:HOH601 4.9 54.2 1.0 NE A:ARG407 4.9 20.6 1.0 O A:HOH603 4.9 51.8 1.0 HG2 A:LYS381 4.9 79.2 1.0 CA A:GLU377 4.9 11.3 1.0 HD13 A:LEU411 5.0 46.8 1.0

Iodine binding site 3 out of 20 in the Structures of Dhbn Domain of Human Blm Helicase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structures of Dhbn Domain of Human Blm Helicase within 5.0Å range: probe atom residue distance (Å) B Occ A:I503 b:43.6 occ:1.00 H A:ASP395 2.9 60.2 1.0 HZ3 B:LYS390 3.2 50.9 1.0 HB3 A:LEU394 3.3 33.4 1.0 OD1 A:ASP395 3.3 0.2 1.0 HD3 B:LYS390 3.4 69.0 1.0 HD2 B:PRO387 3.5 37.9 1.0 HA A:LEU394 3.5 47.0 1.0 HG23 B:ILE386 3.7 44.5 1.0 HD22 A:LEU394 3.7 51.9 1.0 N A:ASP395 3.7 50.1 1.0 HA B:ILE386 3.8 75.9 1.0 HD3 B:PRO387 3.8 37.9 1.0 HB2 A:ASP395 3.8 42.3 1.0 HE2 B:LYS390 3.9 0.1 1.0 NZ B:LYS390 4.0 42.3 1.0 HG12 B:ILE386 4.1 76.4 1.0 CD B:PRO387 4.1 31.5 1.0 CB A:LEU394 4.1 27.8 1.0 CA A:LEU394 4.1 39.1 1.0 CD B:LYS390 4.2 57.5 1.0 CG A:ASP395 4.2 48.5 1.0 CE B:LYS390 4.2 86.7 1.0 CB A:ASP395 4.4 35.2 1.0 HZ1 B:LYS390 4.4 50.9 1.0 C A:LEU394 4.5 56.6 1.0 CD2 A:LEU394 4.5 43.2 1.0 HD23 A:LEU394 4.5 51.9 1.0 H A:CYS396 4.5 44.5 1.0 HZ2 B:LYS390 4.6 50.9 1.0 CG2 B:ILE386 4.6 37.0 1.0 CA A:ASP395 4.7 31.1 1.0 CA B:ILE386 4.7 63.2 1.0 HD2 B:LYS390 4.7 69.0 1.0 HB2 A:LEU394 4.8 33.4 1.0 HD13 A:LEU394 4.8 62.8 1.0 HG2 B:PRO387 4.8 49.6 1.0 CG A:LEU394 4.8 66.7 1.0 CG1 B:ILE386 4.9 63.6 1.0 HG2 B:LYS390 5.0 70.8 1.0

Iodine binding site 4 out of 20 in the Structures of Dhbn Domain of Human Blm Helicase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structures of Dhbn Domain of Human Blm Helicase within 5.0Å range: probe atom residue distance (Å) B Occ A:I504 b:86.6 occ:0.76 OE1 A:GLU377 3.2 88.5 1.0 HE21 A:GLN370 3.2 18.1 1.0 HE22 A:GLN370 3.4 18.1 1.0 OE2 A:GLU377 3.5 47.1 1.0 HA A:HIS374 3.5 30.1 1.0 CD A:GLU377 3.6 23.7 1.0 HD2 A:HIS374 3.6 16.2 1.0 HG22 A:ILE373 3.6 45.1 1.0 NE2 A:GLN370 3.6 15.0 1.0 O A:HOH631 3.7 13.2 0.5 K A:K506 3.7 65.3 1.0 HB2 A:HIS374 3.8 20.6 1.0 OD1 C:ASP362 4.1 27.6 1.0 CA A:HIS374 4.2 25.0 1.0 HG21 A:ILE373 4.4 45.1 1.0 CD2 A:HIS374 4.4 13.4 1.0 CB A:HIS374 4.4 17.0 1.0 CG2 A:ILE373 4.4 37.5 1.0 N A:HIS374 4.6 12.9 1.0 HB2 A:GLU377 4.7 26.1 1.0 CG A:HIS374 4.8 12.7 1.0 CG A:GLU377 4.8 32.9 1.0 H A:HIS374 4.8 15.0 1.0 HG3 A:GLU377 4.8 39.5 1.0 HB A:ILE373 4.9 26.1 1.0 CD A:GLN370 4.9 14.6 1.0

Iodine binding site 5 out of 20 in the Structures of Dhbn Domain of Human Blm Helicase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structures of Dhbn Domain of Human Blm Helicase within 5.0Å range: probe atom residue distance (Å) B Occ A:I505 b:87.8 occ:0.69 HD23 A:LEU382 3.1 44.4 1.0 O B:HOH601 3.3 39.1 1.0 HB3 A:LYS381 3.3 19.3 1.0 HD21 A:LEU382 3.5 44.4 1.0 HB2 A:LYS381 3.6 19.3 1.0 CD2 A:LEU382 3.7 36.9 1.0 HG A:LEU382 3.8 32.2 1.0 CB A:LYS381 3.9 16.0 1.0 HA A:LEU382 4.2 24.5 1.0 CG A:LEU382 4.3 26.8 1.0 N A:LEU382 4.3 22.0 1.0 HD3 A:LYS381 4.3 65.6 1.0 H A:LEU382 4.4 26.5 1.0 C A:LYS381 4.5 16.6 1.0 HD2 A:LYS381 4.5 65.6 1.0 HE1 A:HIS378 4.5 27.0 1.0 HD22 A:LEU382 4.5 44.4 1.0 HD1 A:HIS378 4.6 42.6 1.0 CA A:LEU382 4.7 20.3 1.0 CD A:LYS381 4.8 54.6 1.0 O A:LYS381 4.8 24.5 1.0 CA A:LYS381 4.9 46.0 1.0 CE1 A:HIS378 4.9 22.4 1.0 ND1 A:HIS378 4.9 35.4 1.0 HG21 A:THR385 4.9 40.2 1.0 CG A:LYS381 5.0 66.0 1.0 O A:HIS378 5.0 10.3 1.0

Iodine binding site 6 out of 20 in the Structures of Dhbn Domain of Human Blm Helicase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structures of Dhbn Domain of Human Blm Helicase within 5.0Å range: probe atom residue distance (Å) B Occ B:I501 b:58.6 occ:1.00 HZ3 A:LYS390 3.0 91.9 1.0 HD13 A:ILE386 3.0 69.5 1.0 H B:ASP395 3.2 45.4 1.0 HB2 B:ASP395 3.3 84.2 1.0 HB3 B:LEU394 3.3 30.7 1.0 HD12 A:ILE386 3.4 69.5 1.0 H B:CYS396 3.5 35.9 1.0 HZ1 A:LYS390 3.6 91.9 1.0 HD22 B:LEU394 3.6 51.7 1.0 CD1 A:ILE386 3.6 57.8 1.0 NZ A:LYS390 3.7 76.5 1.0 N B:ASP395 3.8 37.7 1.0 HA A:ILE386 3.8 37.6 1.0 HD3 A:PRO387 3.9 61.5 1.0 HD11 A:ILE386 4.0 69.5 1.0 HE2 A:LYS390 4.0 48.6 1.0 CB B:ASP395 4.1 70.1 1.0 HD2 A:PRO387 4.1 61.5 1.0 HG23 A:ILE386 4.2 46.7 1.0 CB B:LEU394 4.2 25.5 1.0 N B:CYS396 4.3 29.8 1.0 SG B:CYS396 4.3 35.1 1.0 CG B:ASP395 4.3 42.0 1.0 HA B:LEU394 4.3 40.2 1.0 HZ2 A:LYS390 4.3 91.9 1.0 CE A:LYS390 4.4 40.4 1.0 CD2 B:LEU394 4.4 43.0 1.0 CA B:ASP395 4.4 32.4 1.0 CD A:PRO387 4.4 51.2 1.0 HD23 B:LEU394 4.5 51.7 1.0 HB3 B:CYS396 4.5 42.1 1.0 HG B:CYS396 4.6 42.2 1.0 C B:LEU394 4.6 30.1 1.0 HD3 A:LYS390 4.6 75.2 1.0 CA B:LEU394 4.6 33.5 1.0 OD1 B:ASP395 4.7 63.6 1.0 OD2 B:ASP395 4.7 57.7 1.0 HD13 B:LEU394 4.7 29.8 1.0 CA A:ILE386 4.8 31.3 1.0 O B:HOH623 4.8 33.0 1.0 HB2 B:LEU394 4.9 30.7 1.0 C B:ASP395 4.9 27.3 1.0 HB3 B:ASP395 4.9 84.2 1.0 CG B:LEU394 4.9 30.9 1.0 CB B:CYS396 4.9 35.0 1.0 CG1 A:ILE386 4.9 35.3 1.0

Iodine binding site 7 out of 20 in the Structures of Dhbn Domain of Human Blm Helicase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structures of Dhbn Domain of Human Blm Helicase within 5.0Å range: probe atom residue distance (Å) B Occ B:I502 b:0.9 occ:0.92 HZ2 B:LYS381 2.8 82.7 1.0 HE2 B:HIS374 3.1 79.9 1.0 HB2 B:HIS378 3.1 27.2 1.0 HZ3 B:LYS381 3.2 82.7 1.0 NZ B:LYS381 3.4 68.9 1.0 HA B:HIS378 3.5 24.1 1.0 HD2 B:LYS381 3.6 86.1 1.0 NE2 B:HIS374 3.7 66.5 1.0 CB B:HIS378 3.7 22.6 1.0 CG B:HIS378 3.8 35.2 1.0 HD2 B:HIS374 3.9 0.4 1.0 HZ1 B:LYS381 4.0 82.7 1.0 CA B:HIS378 4.1 20.0 1.0 CD2 B:HIS374 4.1 93.6 1.0 CD2 B:HIS378 4.1 36.6 1.0 ND1 B:HIS378 4.2 95.0 1.0 CD B:LYS381 4.2 71.7 1.0 HD3 B:LYS381 4.3 86.1 1.0 HD2 B:HIS378 4.3 44.1 1.0 CE B:LYS381 4.4 43.2 1.0 HD1 B:HIS378 4.4 0.1 1.0 H B:HIS378 4.4 24.1 1.0 N B:HIS378 4.5 20.0 1.0 HB3 B:HIS378 4.6 27.2 1.0 NE2 B:HIS378 4.7 27.6 1.0 CE1 B:HIS378 4.7 42.9 1.0 CE1 B:HIS374 4.8 89.0 1.0 O B:HIS374 4.8 17.2 1.0 HE3 B:LYS381 4.9 51.9 1.0

Iodine binding site 8 out of 20 in the Structures of Dhbn Domain of Human Blm Helicase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structures of Dhbn Domain of Human Blm Helicase within 5.0Å range: probe atom residue distance (Å) B Occ B:I503 b:97.3 occ:0.75 HB2 B:LYS390 2.9 84.4 1.0 HB2 B:PRO387 3.2 33.4 1.0 HG2 B:PRO387 3.6 49.6 1.0 HD2 B:LYS390 3.6 69.0 1.0 HB3 B:PRO387 3.8 33.4 1.0 CB B:PRO387 3.8 27.8 1.0 CB B:LYS390 3.9 70.2 1.0 H B:LYS390 4.1 44.2 1.0 CG B:PRO387 4.2 41.2 1.0 HB2 B:ASP389 4.2 49.9 1.0 HB3 B:LYS390 4.2 84.4 1.0 N B:LYS390 4.3 36.7 1.0 CD B:LYS390 4.4 57.5 1.0 CA B:LYS390 4.6 67.0 1.0 HD3 B:LYS390 4.6 69.0 1.0 CG B:LYS390 4.7 58.9 1.0 HG3 B:PRO387 4.7 49.6 1.0 HA B:LYS390 4.8 80.5 1.0 HG3 B:LYS390 4.8 70.8 1.0 C B:ASP389 4.9 82.0 1.0

Iodine binding site 9 out of 20 in the Structures of Dhbn Domain of Human Blm Helicase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structures of Dhbn Domain of Human Blm Helicase within 5.0Å range: probe atom residue distance (Å) B Occ B:I504 b:69.8 occ:0.72 HH21 B:ARG407 2.9 33.4 1.0 O B:HOH631 2.9 45.3 1.0 O B:HOH609 3.0 45.4 1.0 HE3 B:LYS381 3.1 51.9 1.0 HH22 B:ARG407 3.2 33.4 1.0 NH2 B:ARG407 3.3 27.8 1.0 HB3 B:GLU377 3.4 19.1 1.0 HG2 B:GLU377 3.5 36.1 1.0 HE2 B:LYS381 3.6 51.9 1.0 CE B:LYS381 3.8 43.2 1.0 HZ1 B:LYS381 3.8 82.7 1.0 O B:HOH611 3.9 15.6 1.0 HD21 B:LEU411 4.0 22.9 1.0 CD B:GLU377 4.0 35.9 1.0 CG B:GLU377 4.0 30.0 1.0 OE1 B:GLU377 4.1 38.2 1.0 CB B:GLU377 4.2 16.3 1.0 NZ B:LYS381 4.3 68.9 1.0 HD22 B:LEU411 4.4 22.9 1.0 OE2 B:GLU377 4.4 37.3 1.0 HD11 B:LEU411 4.5 18.4 1.0 CZ B:ARG407 4.5 20.3 1.0 CD2 B:LEU411 4.6 19.0 1.0 HZ2 B:LYS381 4.7 82.7 1.0 HA B:GLU377 4.7 23.4 1.0 HG3 B:LYS381 4.8 47.1 1.0 HB2 B:GLU377 4.8 19.1 1.0 HE B:ARG407 4.8 28.6 1.0 HD13 B:LEU411 4.9 18.4 1.0 HG3 B:GLU377 5.0 36.1 1.0 HZ3 B:LYS381 5.0 82.7 1.0

Iodine binding site 10 out of 20 in the Structures of Dhbn Domain of Human Blm Helicase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structures of Dhbn Domain of Human Blm Helicase within 5.0Å range: probe atom residue distance (Å) B Occ C:I503 b:37.7 occ:1.00 H D:ASP395 2.8 44.1 1.0 HD2 C:LYS390 3.1 41.8 1.0 HD2 C:PRO387 3.3 56.5 1.0 HD3 C:LYS390 3.3 41.8 1.0 HA D:LEU394 3.5 44.2 1.0 HB2 D:ASP395 3.6 43.1 1.0 CD C:LYS390 3.6 34.8 1.0 N D:ASP395 3.6 36.8 1.0 HG23 C:ILE386 3.6 46.4 1.0 HA C:ILE386 3.7 33.0 1.0 HE2 C:LYS390 3.7 47.8 1.0 HB3 D:LEU394 3.7 50.1 1.0 HD22 D:LEU394 3.8 44.1 1.0 HG12 C:ILE386 3.8 30.2 1.0 CG D:ASP395 3.9 49.0 1.0 HD23 D:LEU394 3.9 44.1 1.0 HD3 C:PRO387 4.0 56.5 1.0 CD C:PRO387 4.1 47.0 1.0 OD2 D:ASP395 4.1 43.8 1.0 CB D:ASP395 4.1 36.4 1.0 OD1 D:ASP395 4.2 47.1 1.0 CE C:LYS390 4.2 39.8 1.0 CA D:LEU394 4.2 37.2 1.0 CD2 D:LEU394 4.3 37.1 1.0 CB D:LEU394 4.4 41.7 1.0 C D:LEU394 4.5 44.3 1.0 CA D:ASP395 4.5 47.9 1.0 HZ3 C:LYS390 4.5 0.4 1.0 H D:CYS396 4.5 51.4 1.0 CG2 C:ILE386 4.6 38.5 1.0 CA C:ILE386 4.6 27.5 1.0 HG23 C:THR385 4.7 24.3 1.0 HB3 C:LYS390 4.7 34.1 1.0 CG1 C:ILE386 4.7 25.1 1.0 HB2 C:LYS390 4.8 34.1 1.0 CB C:ILE386 4.9 18.9 1.0 HG3 C:PRO387 4.9 49.0 1.0 CG C:PRO387 4.9 40.8 1.0 CG C:LYS390 4.9 53.0 1.0 HG2 C:PRO387 4.9 49.0 1.0 NZ C:LYS390 4.9 0.9 1.0 HE3 C:LYS390 5.0 47.8 1.0

J.Shi, W.F.Chen, B.Zhang, S.H.Fan, X.Ai, N.N.Liu, S.Rety, X.G.Xi. A Helical Bundle in the N-Terminal Domain of the Blm Helicase Mediates Dimer and Potentially Hexamer Formation. J. Biol. Chem. V. 292 5909 2017.
ISSN: ESSN 1083-351X
PubMed: 28228481
DOI: 10.1074/JBC.M116.761510