Iodine in PDB 5u4t: Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin

The structure of Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin, PDB code: 5u4t was solved by P.Bury, F.Huang, P.Leadlay, M.V.B.Dias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.03 / 2.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.620, 66.782, 69.123, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 21.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin (pdb code 5u4t). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 13 binding sites of Iodine where determined in the Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin, PDB code: 5u4t:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 13 in the Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin


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 A Methyltransferase Involved in the Biosynthesis of Gentamicin within 5.0Å range: probe atom residue distance (Å) B Occ A:I401 b:27.3 occ:0.73 HB2 A:PHE181 2.9 32.3 1.0 H A:PHE181 3.0 28.1 1.0 O A:HOH645 3.2 34.8 1.0 HD1 A:PHE181 3.4 20.4 1.0 HB2 A:MET180 3.6 17.4 1.0 HH21 A:ARG224 3.6 40.8 1.0 HD21 A:ASN221 3.7 29.5 1.0 ND2 A:ASN221 3.7 24.6 1.0 O A:HOH530 3.7 39.5 1.0 HB3 A:MET180 3.8 17.4 1.0 N A:PHE181 3.8 23.4 1.0 CG A:ASN221 3.8 20.8 1.0 CB A:PHE181 3.8 26.9 1.0 HG22 A:THR217 3.9 21.6 1.0 OD1 A:ASN221 4.0 36.1 1.0 HH22 A:ARG224 4.0 40.8 1.0 HD22 A:ASN221 4.0 29.5 1.0 HG23 A:THR217 4.1 21.6 1.0 CB A:MET180 4.1 14.5 1.0 NH2 A:ARG224 4.2 34.0 1.0 CD1 A:PHE181 4.2 17.0 1.0 H A:GLU182 4.3 22.7 1.0 CA A:PHE181 4.3 18.5 1.0 HB2 A:ASN221 4.3 29.3 1.0 CG2 A:THR217 4.4 18.0 1.0 HG21 A:THR217 4.4 21.6 1.0 HB3 A:ASN221 4.4 29.3 1.0 HB3 A:PHE181 4.4 32.3 1.0 N A:GLU182 4.5 18.9 1.0 HG3 A:GLU182 4.5 57.4 1.0 CB A:ASN221 4.5 24.4 1.0 CG A:PHE181 4.5 17.5 1.0 C A:PHE181 4.6 23.9 1.0 O A:ASP179 4.8 21.5 1.0 C A:MET180 4.9 18.0 1.0 HG3 A:MET180 4.9 35.1 1.0 HA A:GLU182 5.0 26.1 1.0

Iodine binding site 2 out of 13 in the Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin


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 A Methyltransferase Involved in the Biosynthesis of Gentamicin within 5.0Å range: probe atom residue distance (Å) B Occ A:I402 b:27.8 occ:0.39 H A:ILE8 2.8 26.5 1.0 HG3 A:ARG156 3.0 21.5 1.0 HA A:THR7 3.2 27.6 1.0 HA A:ARG156 3.4 23.7 1.0 N A:ILE8 3.7 22.1 1.0 CG A:ARG156 3.8 17.9 1.0 HB A:ILE8 3.9 15.9 1.0 HB2 A:ARG156 3.9 18.4 1.0 O A:ILE8 4.0 16.3 1.0 HD2 A:ARG156 4.0 19.2 1.0 HG23 A:THR7 4.0 31.6 1.0 O A:SER6 4.1 22.0 1.0 CA A:THR7 4.1 23.0 1.0 CB A:ARG156 4.2 15.3 1.0 HB3 A:ALA159 4.2 21.7 1.0 CA A:ARG156 4.2 19.8 1.0 HG13 A:ILE8 4.3 26.4 1.0 HB2 A:ALA159 4.4 21.7 1.0 C A:THR7 4.4 17.3 1.0 CD A:ARG156 4.5 16.0 1.0 HG2 A:ARG156 4.5 21.5 1.0 CA A:ILE8 4.5 17.0 1.0 CB A:ILE8 4.6 13.2 1.0 CB A:ALA159 4.7 18.1 1.0 C A:ILE8 4.7 24.1 1.0 CG2 A:THR7 4.7 26.4 1.0 HB1 A:ALA159 4.8 21.7 1.0 HG22 A:THR7 4.8 31.6 1.0 N A:ARG156 4.9 16.4 1.0 C A:SER6 4.9 18.3 1.0 CG1 A:ILE8 4.9 22.0 1.0 HE A:ARG156 5.0 23.5 1.0 CB A:THR7 5.0 26.3 1.0

Iodine binding site 3 out of 13 in the Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin


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 A Methyltransferase Involved in the Biosynthesis of Gentamicin within 5.0Å range: probe atom residue distance (Å) B Occ A:I403 b:44.3 occ:0.35 O A:HOH674 3.1 35.9 1.0 HG2 A:PRO10 3.2 22.3 1.0 HA A:GLU11 3.2 24.0 1.0 HB2 A:PRO10 3.4 16.3 1.0 HB3 A:GLU11 3.5 26.7 1.0 HD3 A:ARG162 3.5 27.4 1.0 N A:GLU11 3.7 22.1 1.0 HB3 A:ARG162 3.7 18.4 1.0 H A:GLU11 3.8 26.5 1.0 CA A:GLU11 3.8 20.0 1.0 CG A:PRO10 4.0 18.6 1.0 CB A:GLU11 4.1 22.2 1.0 C A:PRO10 4.1 22.1 1.0 CB A:PRO10 4.1 13.6 1.0 HD2 A:ARG162 4.2 27.4 1.0 HB2 A:GLU11 4.3 26.7 1.0 CD A:ARG162 4.3 22.8 1.0 HG3 A:PRO10 4.4 22.3 1.0 O A:PRO10 4.5 21.7 1.0 O A:HOH606 4.5 34.1 1.0 CB A:ARG162 4.6 15.4 1.0 CA A:PRO10 4.7 17.9 1.0 HB2 A:ARG162 4.8 18.4 1.0 HB3 A:PRO10 4.9 16.3 1.0 CG A:ARG162 5.0 22.2 1.0

Iodine binding site 4 out of 13 in the Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin


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 A Methyltransferase Involved in the Biosynthesis of Gentamicin within 5.0Å range: probe atom residue distance (Å) B Occ A:I404 b:40.4 occ:0.36 H A:GLU177 2.6 22.4 1.0 HH22 A:ARG162 2.6 30.0 1.0 HA A:ARG176 3.0 25.3 1.0 NH2 A:ARG162 3.3 25.0 1.0 N A:GLU177 3.4 18.7 1.0 HH21 A:ARG162 3.4 30.0 1.0 HD2 A:ARG176 3.5 52.4 1.0 HB3 A:GLU177 3.6 16.5 1.0 CA A:ARG176 3.9 21.1 1.0 HB3 A:ARG176 4.0 29.3 1.0 HG11 A:VAL158 4.1 22.5 1.0 C A:ARG176 4.2 17.9 1.0 CB A:GLU177 4.2 13.7 1.0 HB2 A:GLU177 4.3 16.5 1.0 O A:HOH511 4.3 42.3 1.0 CA A:GLU177 4.4 13.7 1.0 HH11 A:ARG176 4.4 65.0 1.0 CD A:ARG176 4.4 43.7 1.0 CB A:ARG176 4.4 24.4 1.0 HH12 A:ARG162 4.4 28.9 1.0 CZ A:ARG162 4.5 23.1 1.0 O A:PHE175 4.5 15.3 1.0 HG2 A:ARG176 4.6 27.3 1.0 O A:GLU177 4.6 17.5 1.0 CG A:ARG176 4.7 22.8 1.0 NH1 A:ARG162 4.9 24.1 1.0 NH1 A:ARG176 4.9 54.1 1.0 HD3 A:ARG176 5.0 52.4 1.0

Iodine binding site 5 out of 13 in the Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin


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 A Methyltransferase Involved in the Biosynthesis of Gentamicin within 5.0Å range: probe atom residue distance (Å) B Occ A:I405 b:32.1 occ:0.26 HE A:ARG162 2.4 25.8 1.0 H A:PHE175 2.5 22.1 1.0 HG2 A:ARG162 3.0 26.7 1.0 O A:HOH633 3.0 28.5 1.0 HA A:THR174 3.1 15.6 1.0 NE A:ARG162 3.2 21.5 1.0 HG23 A:THR174 3.2 37.7 1.0 N A:PHE175 3.2 18.4 1.0 HD3 A:ARG162 3.4 27.4 1.0 CD A:ARG162 3.6 22.8 1.0 HB2 A:PHE175 3.6 16.0 1.0 O A:PHE175 3.7 15.3 1.0 HD2 A:PHE175 3.7 15.0 1.0 CG A:ARG162 3.7 22.2 1.0 CA A:THR174 3.9 13.0 1.0 HH21 A:ARG162 3.9 30.0 1.0 CG2 A:THR174 4.0 31.4 1.0 HG22 A:THR174 4.0 37.7 1.0 C A:THR174 4.0 20.3 1.0 HG3 A:ARG162 4.1 26.7 1.0 CA A:PHE175 4.1 14.5 1.0 CZ A:ARG162 4.2 23.1 1.0 CB A:PHE175 4.3 13.4 1.0 C A:PHE175 4.4 18.4 1.0 NH2 A:ARG162 4.4 25.0 1.0 CB A:THR174 4.5 11.1 1.0 CD2 A:PHE175 4.5 12.5 1.0 HD2 A:ARG162 4.6 27.4 1.0 HG21 A:THR174 4.8 37.7 1.0 O A:VAL173 4.8 20.5 1.0 CG A:PHE175 4.9 13.8 1.0 HA A:ARG162 4.9 18.1 1.0 CB A:ARG162 5.0 15.4 1.0 HB3 A:ARG162 5.0 18.4 1.0 OG1 A:THR174 5.0 36.7 1.0

Iodine binding site 6 out of 13 in the Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin


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 A Methyltransferase Involved in the Biosynthesis of Gentamicin within 5.0Å range: probe atom residue distance (Å) B Occ A:I406 b:92.1 occ:0.43 H A:VAL291 2.4 26.5 1.0 HG23 A:VAL291 2.8 35.3 1.0 HB A:VAL291 3.0 31.6 1.0 HA A:PRO290 3.0 24.2 1.0 N A:VAL291 3.3 22.1 1.0 O A:HOH628 3.3 20.8 1.0 CG2 A:VAL291 3.5 29.4 1.0 CB A:VAL291 3.6 26.3 1.0 HG21 A:VAL291 3.6 35.3 1.0 CA A:PRO290 3.9 20.2 1.0 CA A:VAL291 4.1 30.1 1.0 C A:PRO290 4.1 29.3 1.0 HB3 A:PRO290 4.2 23.1 1.0 HG22 A:VAL291 4.3 35.3 1.0 CB A:PRO290 4.6 19.2 1.0 HA A:VAL291 4.7 36.1 1.0 O A:GLY289 4.9 25.2 1.0 N A:PRO290 5.0 25.5 1.0 CG1 A:VAL291 5.0 29.5 1.0

Iodine binding site 7 out of 13 in the Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin


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 A Methyltransferase Involved in the Biosynthesis of Gentamicin within 5.0Å range: probe atom residue distance (Å) B Occ A:I407 b:31.5 occ:0.33 O A:HOH607 3.2 38.9 1.0 O A:HOH638 3.3 36.1 1.0 HH22 A:ARG81 3.4 27.6 1.0 HG3 A:PRO94 3.4 22.8 1.0 HG22 A:VAL3 3.5 34.6 1.0 HG2 A:PRO94 3.6 22.8 1.0 HG21 A:VAL3 3.7 34.6 1.0 HH21 A:ARG81 3.8 27.6 1.0 NH2 A:ARG81 3.8 23.0 1.0 CG A:PRO94 4.0 19.0 1.0 CG2 A:VAL3 4.1 28.9 1.0 HG11 A:VAL96 4.3 30.9 1.0 HG13 A:VAL3 4.4 30.8 1.0 HG11 A:VAL3 4.6 30.8 1.0 O A:HOH635 4.7 43.4 1.0 HG23 A:VAL3 4.7 34.6 1.0 HB2 A:PRO94 4.7 23.8 1.0 CB A:PRO94 4.8 19.8 1.0 CG1 A:VAL3 4.9 25.6 1.0 CZ A:ARG81 4.9 22.1 1.0

Iodine binding site 8 out of 13 in the Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin


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 A Methyltransferase Involved in the Biosynthesis of Gentamicin within 5.0Å range: probe atom residue distance (Å) B Occ A:I408 b:40.3 occ:0.34 HD3 A:PRO79 3.3 27.4 1.0 HB3 A:PRO79 3.5 26.8 1.0 HB2 A:SER77 3.5 29.8 1.0 HA A:PRO79 3.5 18.2 1.0 N A:PRO79 3.6 17.0 1.0 HB3 A:SER77 3.6 29.8 1.0 C A:SER78 3.7 18.0 1.0 HG21 A:VAL70 3.7 35.1 1.0 HB A:VAL70 3.8 36.6 1.0 CD A:PRO79 3.9 22.8 1.0 CA A:PRO79 3.9 15.2 1.0 O A:SER78 4.0 15.7 1.0 CB A:SER77 4.0 24.8 1.0 CB A:PRO79 4.1 22.3 1.0 C A:SER77 4.1 27.4 1.0 HG23 A:VAL70 4.1 35.1 1.0 O A:SER77 4.1 26.1 1.0 N A:SER78 4.2 17.7 1.0 CG2 A:VAL70 4.3 29.3 1.0 HA A:SER78 4.3 20.6 1.0 CA A:SER78 4.3 17.2 1.0 O A:HOH607 4.4 38.9 1.0 CB A:VAL70 4.5 30.5 1.0 H A:SER78 4.5 21.3 1.0 CG A:PRO79 4.5 20.0 1.0 HG3 A:PRO79 4.6 24.0 1.0 CA A:SER77 4.7 18.4 1.0 HD2 A:PRO79 4.7 27.4 1.0 HG11 A:VAL70 4.8 37.1 1.0 HB2 A:PRO79 4.9 26.8 1.0

Iodine binding site 9 out of 13 in the Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin


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 A Methyltransferase Involved in the Biosynthesis of Gentamicin within 5.0Å range: probe atom residue distance (Å) B Occ A:I409 b:67.1 occ:0.39 HB A:ILE214 3.2 21.5 1.0 HB1 A:ALA210 3.2 19.7 1.0 O A:HOH573 3.3 21.7 1.0 HD1 A:PHE204 3.4 24.7 1.0 HD12 A:ILE214 3.8 30.0 1.0 HG13 A:ILE214 3.8 28.1 1.0 O A:ALA210 3.9 16.6 1.0 CB A:ILE214 4.0 17.9 1.0 HE1 A:PHE204 4.0 27.3 1.0 HB2 A:PRO213 4.0 21.4 1.0 CD1 A:PHE204 4.1 20.6 1.0 HA A:ILE214 4.1 14.8 1.0 CB A:ALA210 4.2 16.4 1.0 H A:ILE214 4.2 18.0 1.0 CG1 A:ILE214 4.3 23.4 1.0 HN61 A:SAH414 4.3 21.3 1.0 N A:ILE214 4.4 15.0 1.0 CE1 A:PHE204 4.4 22.7 1.0 CA A:ILE214 4.4 12.3 1.0 HB3 A:ALA210 4.5 19.7 1.0 CD1 A:ILE214 4.5 25.0 1.0 HB2 A:ALA210 4.7 19.7 1.0 HB2 A:PHE204 4.7 28.3 1.0 C A:ALA210 4.7 18.4 1.0 CA A:ALA210 5.0 24.1 1.0

Iodine binding site 10 out of 13 in the Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin


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 A Methyltransferase Involved in the Biosynthesis of Gentamicin within 5.0Å range: probe atom residue distance (Å) B Occ A:I410 b:47.5 occ:0.33 H A:GLY87 2.4 22.8 1.0 HG2 A:GLN84 3.1 34.9 1.0 H A:HIS86 3.3 21.8 1.0 N A:GLY87 3.3 19.0 1.0 HA A:LEU85 3.4 17.3 1.0 N A:HIS86 3.5 18.2 1.0 HA2 A:GLY87 3.5 21.6 1.0 C A:LEU85 3.7 15.8 1.0 CA A:LEU85 3.8 14.4 1.0 N A:LEU85 3.9 17.1 1.0 CG A:GLN84 3.9 29.1 1.0 CA A:GLY87 3.9 18.0 1.0 HG3 A:GLN84 3.9 34.9 1.0 H A:LEU85 4.0 20.6 1.0 O A:HOH621 4.0 23.2 1.0 H A:VAL88 4.2 21.0 1.0 C A:HIS86 4.3 20.8 1.0 CA A:HIS86 4.3 18.2 1.0 C A:GLN84 4.4 16.0 1.0 OE1 A:GLN84 4.4 32.5 1.0 O A:LEU85 4.4 14.6 1.0 HA A:HIS86 4.4 21.8 1.0 CD A:GLN84 4.6 24.4 1.0 N A:VAL88 4.6 17.5 1.0 C A:GLY87 4.6 22.4 1.0 O A:GLN84 4.7 19.8 1.0 HA3 A:GLY87 4.7 21.6 1.0 O A:HOH609 4.9 46.6 1.0 CB A:GLN84 5.0 19.5 1.0

P.D.S.Bury, F.Huang, S.Li, Y.Sun, P.F.Leadlay, M.V.B.Dias. Structural Basis of the Selectivity of Genn, An Aminoglycoside N-Methyltransferase Involved in Gentamicin Biosynthesis. Acs Chem. Biol. V. 12 2779 2017.
ISSN: ESSN 1554-8937
PubMed: 28876898
DOI: 10.1021/ACSCHEMBIO.7B00466