Atomistry » Iodine » PDB 5r4d-5w1i » 5u4t
Atomistry »
  Iodine »
    PDB 5r4d-5w1i »
      5u4t »

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

Protein crystallography data

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

Iodine Binding Sites:

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 5u4t

Go back to Iodine Binding Sites List in 5u4t
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 5u4t

Go back to Iodine Binding Sites List in 5u4t
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 5u4t

Go back to Iodine Binding Sites List in 5u4t
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 5u4t

Go back to Iodine Binding Sites List in 5u4t
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 5u4t

Go back to Iodine Binding Sites List in 5u4t
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 5u4t

Go back to Iodine Binding Sites List in 5u4t
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 5u4t

Go back to Iodine Binding Sites List in 5u4t
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 5u4t

Go back to Iodine Binding Sites List in 5u4t
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 5u4t

Go back to Iodine Binding Sites List in 5u4t
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 5u4t

Go back to Iodine Binding Sites List in 5u4t
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

Reference:

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
Page generated: Sun Dec 13 19:41:20 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy