Iodine in PDB 3sex: Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)

The structure of Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II), PDB code: 3sex was solved by M.Zhao, A.B.Soriaga, A.Laganowsky, M.R.Sawaya, D.Cascio, T.O.Yeates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.66 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.560, 67.500, 191.440, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.8

The structure of Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Iodine atom in the Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) (pdb code 3sex). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 26 binding sites of Iodine where determined in the Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II), PDB code: 3sex:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 26 in the Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range: probe atom residue distance (Å) B Occ A:I373 b:24.4 occ:1.00 O A:HOH502 3.4 35.0 1.0 N A:VAL245 3.6 8.8 1.0 CG A:ARG317 4.0 13.5 1.0 O A:VAL245 4.1 6.3 1.0 CG A:PRO316 4.1 20.5 1.0 CA A:GLY244 4.1 11.5 1.0 CB A:PRO316 4.2 19.4 1.0 C A:GLY244 4.4 11.3 1.0 N A:ARG317 4.4 9.4 1.0 C A:PRO316 4.5 11.5 1.0 CB A:VAL245 4.5 6.7 1.0 CA A:VAL245 4.6 7.5 1.0 O A:PRO316 4.7 9.5 1.0 CA A:ARG317 4.7 11.1 1.0 C A:VAL245 4.8 6.6 1.0 O A:HOH552 4.8 36.0 1.0 CG2 A:VAL245 4.8 8.1 1.0 O A:TYR243 5.0 10.0 1.0 CA A:PRO316 5.0 13.6 1.0 CB A:ARG317 5.0 10.3 1.0

Iodine binding site 2 out of 26 in the Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range: probe atom residue distance (Å) B Occ A:I374 b:27.1 occ:1.00 ND2 A:ASN151 3.6 7.8 1.0 N A:TYR211 3.9 2.8 1.0 OD1 A:ASN151 4.0 8.8 1.0 CB A:ASP210 4.0 12.9 1.0 CB A:TYR211 4.1 9.6 1.0 CG A:ASN151 4.1 9.5 1.0 CB A:GLN153 4.3 11.9 1.0 OD2 C:ASP210 4.6 17.9 1.0 CG A:GLN153 4.6 10.0 1.0 CG A:GLU154 4.6 7.8 1.0 CA A:TYR211 4.6 5.9 1.0 O A:HOH542 4.7 16.5 1.0 CA A:ASP210 4.8 9.1 1.0 C A:ASP210 4.8 5.7 1.0 CG A:ASP210 4.9 17.0 1.0 CD1 C:ILE213 4.9 15.8 1.0 O C:HOH631 5.0 34.9 1.0

Iodine binding site 3 out of 26 in the Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range: probe atom residue distance (Å) B Occ A:I375 b:26.9 occ:1.00 O C:HOH558 3.3 37.3 1.0 O A:HOH462 3.7 35.5 1.0 N A:GLY57 3.8 8.4 1.0 O A:HOH652 3.8 36.2 1.0 CA A:GLY57 4.0 8.0 1.0 CZ2 A:TRP11 4.3 8.5 1.0 CG1 A:VAL51 4.3 14.5 1.0 CB A:VAL51 4.4 11.5 1.0 CA C:GLY144 4.4 20.8 1.0 CG2 A:VAL51 4.5 11.7 1.0 CB A:ASP56 4.6 8.9 1.0 CH2 A:TRP11 4.7 11.1 1.0 O A:HOH491 4.8 37.3 1.0 C A:GLY57 4.9 7.1 1.0 C A:ASP56 4.9 8.5 1.0 N C:GLY144 5.0 21.5 1.0

Iodine binding site 4 out of 26 in the Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range: probe atom residue distance (Å) B Occ A:I376 b:25.1 occ:1.00 O A:HOH535 3.5 24.3 1.0 N A:ALA169 3.7 13.0 1.0 O A:HOH601 3.7 19.9 1.0 CE1 A:PHE259 3.8 13.2 1.0 CZ A:PHE259 3.9 17.1 1.0 CB A:ALA169 4.1 11.6 1.0 CG A:GLU329 4.2 27.0 1.0 CB A:TYR168 4.3 11.2 1.0 O A:PHE170 4.4 16.0 1.0 O A:HOH609 4.4 27.3 1.0 CA A:ALA169 4.4 12.8 1.0 N A:PHE170 4.5 11.6 1.0 O A:HOH544 4.6 14.6 1.0 CA A:TYR168 4.6 11.1 1.0 C A:TYR168 4.6 12.5 1.0 CD A:PRO332 4.7 10.8 1.0 CG A:PRO332 4.7 11.0 1.0 CB A:GLU329 4.7 19.6 1.0 C A:ALA169 5.0 12.8 1.0

Iodine binding site 5 out of 26 in the Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range: probe atom residue distance (Å) B Occ A:I377 b:31.8 occ:1.00 O C:HOH405 3.3 8.0 1.0 O C:HOH647 3.6 39.3 1.0 CG C:GLU222 3.7 12.5 1.0 O C:HOH628 4.0 29.8 1.0 O C:GLY144 4.1 22.9 1.0 CB C:GLU222 4.3 8.1 1.0 CB A:GLU39 4.4 15.9 1.0 CD C:GLU222 4.4 12.2 1.0 CA A:PRO41 4.5 9.6 1.0 CA C:GLU222 4.5 5.4 1.0 OE1 A:GLU39 4.5 21.6 1.0 CG A:PRO41 4.5 14.1 1.0 O C:HOH428 4.5 29.2 1.0 CD A:GLU39 4.6 22.7 1.0 N A:PRO41 4.6 8.7 1.0 NZ C:LYS145 4.7 30.2 1.0 CB A:PRO41 4.7 9.1 1.0 CG A:GLU39 4.7 20.0 1.0 OE2 C:GLU222 4.7 13.1 1.0 O C:HOH611 4.9 22.5 1.0 CD C:LYS145 4.9 28.0 1.0 CD A:PRO41 5.0 11.8 1.0 N A:HIS40 5.0 8.9 1.0

Iodine binding site 6 out of 26 in the Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range: probe atom residue distance (Å) B Occ A:I378 b:51.6 occ:1.00 O A:HOH576 3.5 24.1 1.0 CA A:LYS27 3.9 15.3 1.0 N A:LYS27 4.1 18.2 1.0 CB A:LYS27 4.1 17.3 1.0 CD A:LYS27 4.2 17.9 1.0 C A:LYS26 4.4 17.9 1.0 O A:LYS26 4.5 16.5 1.0 CG A:LYS27 4.7 18.3 1.0 CB A:LYS26 4.8 24.5 1.0 CB A:LYS30 5.0 23.6 1.0

Iodine binding site 7 out of 26 in the Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range: probe atom residue distance (Å) B Occ A:I379 b:47.8 occ:1.00 O A:HOH448 3.6 21.6 1.0 ND2 A:ASN219 3.7 10.7 1.0 O A:HOH630 4.0 40.6 1.0 CB A:ASN219 4.0 8.3 1.0 CE1 A:HIS220 4.2 15.2 1.0 CG A:GLU215 4.2 9.8 1.0 CA A:HIS216 4.3 7.7 1.0 CG A:ASN219 4.3 11.3 1.0 O A:GLU215 4.3 6.7 1.0 N A:HIS216 4.5 9.0 1.0 CD A:GLU215 4.5 12.3 1.0 C A:GLU215 4.5 7.0 1.0 OE1 A:GLU215 4.7 13.8 1.0 ND1 A:HIS220 4.7 19.4 1.0 OE2 A:GLU215 5.0 13.3 1.0 CB A:HIS216 5.0 6.9 1.0

Iodine binding site 8 out of 26 in the Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range: probe atom residue distance (Å) B Occ A:I380 b:51.8 occ:1.00 O A:HOH640 3.2 24.6 1.0 O A:ALA363 3.7 11.5 1.0 OG1 A:THR367 3.9 25.9 1.0 C A:ALA363 4.1 12.6 1.0 CB A:ALA363 4.4 15.9 1.0 N A:ALA364 4.7 10.2 1.0 CA A:ALA363 4.8 15.9 1.0 CB A:THR367 4.8 19.8 1.0 CA A:ALA364 4.9 9.7 1.0

Iodine binding site 9 out of 26 in the Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range: probe atom residue distance (Å) B Occ A:I381 b:42.6 occ:1.00 O A:HOH557 2.9 42.2 1.0 ND2 A:ASN13 3.2 18.1 1.0 O A:HOH393 3.5 11.3 1.0 N A:LYS43 3.5 8.9 1.0 CA A:LYS43 4.0 15.1 1.0 OE1 A:GLU45 4.0 15.0 1.0 CZ3 A:TRP63 4.1 12.9 1.0 CH2 A:TRP63 4.1 12.9 1.0 O A:PRO41 4.1 11.2 1.0 N A:LEU44 4.2 8.0 1.0 CG A:ASN13 4.4 18.9 1.0 C A:ASP42 4.4 10.6 1.0 C A:LYS43 4.6 13.2 1.0 CA A:ASP42 4.6 10.1 1.0 O A:HOH419 4.7 20.7 1.0 OD1 A:ASP42 4.8 21.4 1.0 CB A:ASN13 4.8 11.1 1.0 O A:HOH631 4.8 35.8 1.0 CD2 A:LEU44 4.8 13.1 1.0 CG A:LEU44 4.9 10.2 1.0

Iodine binding site 10 out of 26 in the Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Ni-Mediated Dimer of Maltose-Binding Protein A216H/K220H By Synthetic Symmetrization (Form II) within 5.0Å range: probe atom residue distance (Å) B Occ A:I382 b:50.5 occ:1.00 I C:IOD382 3.4 45.8 1.0 O A:HOH423 3.4 27.2 1.0 CD C:ARG355 3.6 21.7 1.0 ND2 A:ASN350 3.9 15.8 1.0 CD A:ARG355 4.0 26.8 1.0 CG C:ARG355 4.1 15.5 1.0 CB A:ARG355 4.2 20.4 1.0 OD1 A:ASN350 4.2 13.6 1.0 CG A:ASN350 4.2 14.2 1.0 CB C:ARG355 4.6 14.0 1.0 CG A:ARG355 4.7 24.4 1.0 CG A:GLN356 4.8 20.9 1.0 NE C:ARG355 4.9 29.8 1.0

A.Laganowsky, M.Zhao, A.B.Soriaga, M.R.Sawaya, D.Cascio, T.O.Yeates. An Approach to Crystallizing Proteins By Metal-Mediated Synthetic Symmetrization. Protein Sci. V. 20 1876 2011.
ISSN: ISSN 0961-8368
PubMed: 21898649
DOI: 10.1002/PRO.727