Iodine in PDB 1xc6: Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose

All present enzymatic activity of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose:
3.2.1.23;

The structure of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose, PDB code: 1xc6 was solved by A.L.Rojas, R.A.P.Nagem, K.N.Neustroev, M.Arand, M.Adamska, E.V.Eneyskaya, A.A.Kulminskaya, R.C.Garratt, A.M.Golubev, I.Polikarpov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.40 / 2.10
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	110.960, 110.960, 161.050, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 18.6

The structure of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose also contains other interesting chemical elements:

Sodium

(Na)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 52;

Binding sites:

The binding sites of Iodine atom in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose (pdb code 1xc6). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 52 binding sites of Iodine where determined in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose, PDB code: 1xc6:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:I9021 b:28.0 occ:0.70 O A:HOH9811 2.9 44.9 1.0 O A:HOH9097 3.6 9.6 1.0 O A:HOH9197 3.7 18.4 1.0 OH A:TYR360 3.8 11.1 1.0 N A:PHE313 3.9 12.8 1.0 O A:HOH9417 4.0 16.6 1.0 CE2 A:TYR360 4.1 8.7 1.0 CA A:GLY312 4.2 12.5 1.0 CD2 A:PHE313 4.3 10.5 1.0 C8 A:NAG1992 4.4 24.4 1.0 CZ A:TYR360 4.5 8.6 1.0 CB A:GLN946 4.5 10.9 1.0 CA A:GLN946 4.6 11.3 1.0 C A:GLY312 4.6 12.8 1.0 CG A:GLN946 4.6 9.4 1.0 CB A:PHE313 4.7 12.5 1.0 O A:HOH9925 4.9 45.7 1.0 CA A:PHE313 4.9 13.8 1.0 OG A:SER362 4.9 10.4 1.0 CB A:SER362 4.9 7.8 1.0 CG A:PHE313 4.9 11.7 1.0 CD A:GLN946 5.0 10.4 1.0

Iodine binding site 2 out of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:I9022 b:27.7 occ:0.30 O A:HOH9353 2.9 23.8 1.0 N A:LYS379 3.3 13.2 1.0 CB A:ASN321 3.6 14.3 1.0 N A:HIS322 3.7 13.2 1.0 CB A:LYS379 3.7 13.3 1.0 O A:HOH9610 3.7 31.4 1.0 N A:GLU378 3.8 13.5 1.0 CA A:ASN321 3.9 14.4 1.0 CG A:LYS379 3.9 13.1 1.0 CA A:LYS379 4.0 12.9 1.0 CB A:GLU378 4.1 14.6 1.0 CD2 A:HIS322 4.1 13.9 1.0 C A:GLU378 4.2 14.3 1.0 I A:IOD9023 4.2 28.7 0.7 CA A:GLU378 4.2 13.1 1.0 C A:ASN321 4.2 13.5 1.0 CD A:LYS379 4.4 13.9 1.0 O A:ALA317 4.4 13.7 1.0 CB A:ARG377 4.5 14.3 1.0 C A:ARG377 4.5 13.0 1.0 CB A:HIS322 4.5 14.0 1.0 CG A:HIS322 4.7 14.9 1.0 CA A:HIS322 4.7 13.0 1.0 CA A:ARG377 4.8 13.4 1.0 CG A:ASN321 4.9 16.2 1.0

Iodine binding site 3 out of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:I9023 b:28.7 occ:0.70 O A:HOH9610 3.1 31.4 1.0 I A:IOD9057 3.7 69.0 0.5 O2 A:BMA3004 3.8 48.6 1.0 O A:HOH9353 3.8 23.8 1.0 N A:GLU378 3.9 13.5 1.0 CA A:ARG377 3.9 13.4 1.0 O6 A:NAG3002 3.9 32.6 1.0 C2 A:BMA3003 4.0 22.9 1.0 O4 A:NAG3002 4.0 17.9 1.0 I A:IOD9022 4.2 27.7 0.3 O2 A:BMA3003 4.3 18.7 1.0 CG A:ARG377 4.4 13.4 1.0 CB A:ARG377 4.4 14.3 1.0 C6 A:NAG3002 4.4 24.4 1.0 C A:ARG377 4.4 13.0 1.0 C1 A:BMA3003 4.5 20.6 1.0 C5 A:NAG3002 4.5 21.3 1.0 CB A:GLU378 4.8 14.6 1.0 O A:THR376 4.9 16.2 1.0 C4 A:NAG3002 4.9 18.7 1.0 N A:ARG377 4.9 14.6 1.0 CA A:GLU378 5.0 13.1 1.0

Iodine binding site 4 out of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:I9024 b:29.1 occ:0.50 O A:HOH9486 3.2 22.9 1.0 N A:ASN244 3.5 16.2 1.0 CA A:HIS243 4.0 17.4 1.0 CG A:PRO212 4.1 21.3 1.0 C A:HIS243 4.3 17.1 1.0 CB A:THR248 4.3 20.5 1.0 CG2 A:THR248 4.4 21.2 1.0 O A:HOH7027 4.4 41.2 1.0 CD2 A:HIS243 4.4 16.9 1.0 CB A:PRO212 4.4 21.4 1.0 O A:HOH9239 4.4 14.9 1.0 CA A:ASN244 4.4 16.1 1.0 O A:HOH9884 4.5 47.3 1.0 O A:GLY242 4.6 18.1 1.0 OG1 A:THR248 4.6 19.1 1.0 CB A:HIS243 4.7 17.4 1.0 ND2 A:ASN244 4.8 16.5 1.0 CG A:HIS243 4.9 17.3 1.0 N A:HIS243 5.0 17.2 1.0

Iodine binding site 5 out of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:I9025 b:32.9 occ:0.30 O A:HOH9424 3.0 25.6 1.0 N A:LEU713 3.4 18.9 1.0 CB A:LEU713 3.9 20.2 1.0 CA A:SER712 4.0 20.9 1.0 CG A:LEU713 4.1 21.2 1.0 CB A:SER712 4.1 22.0 1.0 CG2 A:THR706 4.2 12.4 1.0 C A:SER712 4.2 19.8 1.0 CA A:LEU713 4.2 19.2 1.0 CD1 A:LEU713 4.6 18.8 1.0 O A:LEU713 4.8 17.8 1.0 N A:THR706 4.9 17.9 1.0 O A:HOH9463 5.0 26.6 1.0

Iodine binding site 6 out of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:I9026 b:32.2 occ:0.50 OG A:SER260 3.3 15.6 1.0 O A:HOH9522 3.5 32.3 1.0 O A:HOH9301 3.8 21.7 1.0 O A:HOH9864 4.1 48.6 1.0 CA A:PRO262 4.1 18.1 1.0 N A:PRO262 4.1 17.5 1.0 CB A:SER260 4.2 14.5 1.0 CB A:PRO262 4.3 19.3 1.0 N A:TYR261 4.4 13.2 1.0 CZ A:PHE282 4.4 17.2 1.0 CD A:PRO262 4.4 19.1 1.0 CA A:SER260 4.5 13.3 1.0 C A:TYR261 4.6 15.0 1.0 C A:SER260 4.8 13.5 1.0 CB A:PRO279 4.9 21.7 1.0 OH A:TYR281 4.9 25.5 1.0 CG A:PRO279 4.9 22.3 1.0 O A:TYR261 5.0 14.1 1.0 CG A:PRO262 5.0 20.0 1.0

Iodine binding site 7 out of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:I9027 b:37.8 occ:0.65 OG A:SER465 3.1 36.0 1.0 ND2 A:ASN411 3.5 28.1 1.0 CB A:SER465 4.0 28.7 1.0 CA A:TYR446 4.0 22.8 1.0 N A:TYR446 4.1 23.1 1.0 CG A:LYS447 4.1 28.6 1.0 C A:TYR446 4.1 22.8 1.0 C A:GLU445 4.4 25.3 1.0 O A:TYR446 4.4 24.7 1.0 CE A:LYS447 4.4 34.7 1.0 CB A:GLU445 4.5 32.3 1.0 O A:GLU445 4.5 24.4 1.0 CG A:ASN411 4.5 29.4 1.0 N A:LYS447 4.5 23.2 1.0 OD1 A:ASN411 4.6 28.6 1.0 CD A:LYS447 4.7 32.3 1.0

Iodine binding site 8 out of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:I9028 b:47.9 occ:0.30 OG1 A:THR692 3.3 30.9 1.0 O A:HOH9585 3.6 35.2 1.0 N A:TYR693 4.0 25.1 1.0 O A:HOH9532 4.0 28.9 1.0 CA A:TYR693 4.0 23.3 1.0 C A:THR692 4.1 27.6 1.0 O A:THR692 4.2 27.6 1.0 CB A:THR692 4.3 30.2 1.0 CD1 A:TYR693 4.3 18.7 1.0 CD A:LYS690 4.3 40.1 1.0 O A:PRO687 4.4 16.5 1.0 CB A:PRO687 4.4 17.0 1.0 CB A:TYR693 4.4 21.0 1.0 CB A:LYS690 4.7 31.4 1.0 CA A:THR692 4.8 28.5 1.0 CG A:TYR693 4.9 20.4 1.0

Iodine binding site 9 out of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:I9029 b:29.5 occ:0.39 I A:IOD9065 3.6 56.8 0.3 N A:THR888 3.7 17.8 1.0 CA A:LEU887 3.8 19.8 1.0 OG1 A:THR888 4.0 20.6 1.0 CB A:LEU887 4.0 21.3 1.0 C A:LEU887 4.3 19.0 1.0 CE A:LYS889 4.3 36.6 1.0 CG A:LYS889 4.4 27.4 1.0 CG A:LEU887 4.4 23.8 1.0 NZ A:LYS889 4.4 42.2 1.0 O A:GLY886 4.7 18.7 1.0 CD A:ARG893 4.7 24.3 1.0 CA A:THR888 4.8 19.2 1.0 O A:HOH9831 4.8 66.3 1.0 N A:LYS889 4.8 17.6 1.0 CD A:LYS889 4.9 32.3 1.0 CB A:THR888 4.9 21.4 1.0 CD2 A:LEU887 5.0 25.2 1.0

Iodine binding site 10 out of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:I9030 b:38.5 occ:0.65 O A:HOH9370 3.4 33.2 1.0 O A:VAL551 3.9 19.8 1.0 N A:GLY513 4.0 23.5 1.0 CA A:PRO512 4.0 23.3 1.0 CA A:SER552 4.1 20.8 1.0 CG1 A:VAL551 4.3 19.0 1.0 C A:VAL551 4.3 19.9 1.0 N A:THR553 4.3 20.4 1.0 CB A:PRO512 4.3 24.8 1.0 CG2 A:THR553 4.4 24.6 1.0 C A:SER552 4.4 20.3 1.0 N A:SER552 4.5 20.1 1.0 C A:PRO512 4.6 23.6 1.0 CB A:VAL551 4.9 19.6 1.0 O A:HOH9783 5.0 44.2 1.0 O A:HOH9527 5.0 32.2 1.0

A.L.Rojas, R.A.P.Nagem, K.N.Neustroev, M.Arand, M.Adamska, E.V.Eneyskaya, A.A.Kulminskaya, R.C.Garratt, A.M.Golubev, I.Polikarpov. Crystal Structures of Beta-Galactosidase From Penicillium Sp. and Its Complex with Galactose J.Mol.Biol. V. 343 1281 2004.
ISSN: ISSN 0022-2836
PubMed: 15491613
DOI: 10.1016/J.JMB.2004.09.012