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Iodine in PDB 4ihc: Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703

Protein crystallography data

The structure of Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703, PDB code: 4ihc was solved by Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, N.F.Al Obaidi, M.Stead, J.Love, J.A.Gerlt, S.C.Almo, Enzyme Functioninitiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 224.331, 224.347, 87.076, 90.00, 97.96, 90.00
R / Rfree (%) 17.3 / 22.8

Other elements in 4ihc:

The structure of Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms
Chlorine (Cl) 9 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 (pdb code 4ihc). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 19 binding sites of Iodine where determined in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703, PDB code: 4ihc:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 19 in 4ihc

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Iodine binding site 1 out of 19 in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703


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 Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:38.7
occ:0.50
 OG1 C:THR66 3.4 19.3 1.0
N A:LYS117 3.5 17.3 1.0
CA A:GLY116 3.7 13.3 1.0
CG A:LYS117 3.8 25.2 1.0
O C:THR66 4.0 12.3 1.0
C A:GLY116 4.1 21.8 1.0
CB C:THR66 4.1 16.3 1.0
CE1 A:TYR111 4.2 16.8 1.0
C C:THR66 4.3 14.0 1.0
CG C:ARG67 4.3 11.7 1.0
CB A:LYS117 4.4 15.2 1.0
O A:HOH760 4.4 33.9 1.0
CB A:GLU112 4.4 18.0 1.0
CA A:LYS117 4.5 16.3 1.0
CD1 A:TYR111 4.5 19.1 1.0
CA A:GLU112 4.7 13.8 1.0
N C:ARG67 4.7 12.8 1.0
CD A:LYS117 4.9 52.6 1.0
CA C:ARG67 4.9 14.2 1.0
CA C:THR66 4.9 14.9 1.0
O C:HOH668 5.0 24.8 1.0
N A:GLY116 5.0 13.8 1.0

Iodine binding site 2 out of 19 in 4ihc

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Iodine binding site 2 out of 19 in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703


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 Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I506

b:31.1
occ:0.50
 OG1 A:THR232 3.4 16.2 1.0
N A:THR229 3.6 12.7 1.0
CB A:PRO196 3.6 21.8 1.0
CG2 A:THR229 3.8 15.0 1.0
CB A:VAL228 3.9 12.0 1.0
CA A:VAL228 4.0 12.7 1.0
CB A:THR232 4.0 14.4 1.0
CG2 A:THR232 4.0 14.4 1.0
CG A:PRO196 4.1 12.6 1.0
OG1 A:THR229 4.1 15.4 1.0
CG A:GLU197 4.3 58.1 1.0
C A:VAL228 4.3 13.9 1.0
O D:HOH835 4.3 36.7 1.0
C A:PRO196 4.3 16.5 1.0
CG1 A:VAL228 4.4 14.0 1.0
CB A:THR229 4.4 14.0 1.0
N A:GLU197 4.4 14.8 1.0
O A:PRO196 4.5 16.8 1.0
CA A:THR229 4.6 16.8 1.0
CA A:PRO196 4.6 15.5 1.0
CD A:GLU197 4.8 0.3 1.0
CA A:GLU197 4.8 21.9 1.0

Iodine binding site 3 out of 19 in 4ihc

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Iodine binding site 3 out of 19 in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703


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 Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I506

b:15.1
occ:1.00
 N A:ILE86 3.6 11.7 1.0
N B:ILE86 3.6 9.3 1.0
CB B:ILE86 3.8 7.2 1.0
N B:PRO85 3.8 12.1 1.0
C B:GLY84 3.8 12.3 1.0
CD B:PRO85 3.8 10.3 1.0
CA B:GLY84 3.8 16.3 1.0
C A:GLY84 3.8 10.1 1.0
CA A:GLY84 3.8 8.5 1.0
CB A:ILE86 3.9 13.8 1.0
N A:MET87 3.9 11.4 1.0
N B:MET87 3.9 15.9 1.0
N A:PRO85 3.9 10.2 1.0
CD A:PRO85 4.0 9.6 1.0
CG1 B:ILE86 4.2 13.2 1.0
CA B:ILE86 4.2 10.1 1.0
CA A:ILE86 4.2 10.2 1.0
CG B:MET87 4.2 13.6 1.0
CG1 A:ILE86 4.3 10.2 1.0
O A:GLY84 4.4 9.6 1.0
CG A:MET87 4.4 15.4 1.0
O B:GLY84 4.4 12.4 1.0
CG B:PRO85 4.5 10.9 1.0
CG A:PRO85 4.5 6.7 1.0
CD1 B:ILE86 4.5 8.9 1.0
CD1 A:ILE86 4.5 10.3 1.0
C B:PRO85 4.6 11.2 1.0
C A:PRO85 4.6 12.7 1.0
C A:ILE86 4.6 15.6 1.0
C B:ILE86 4.6 15.3 1.0
CB A:MET87 4.7 11.0 1.0
CA B:PRO85 4.7 11.6 1.0
CB B:MET87 4.7 13.2 1.0
N A:GLY84 4.8 14.4 1.0
CA A:PRO85 4.8 9.4 1.0
N B:GLY84 4.8 18.0 1.0
CA A:MET87 4.9 13.9 1.0
CA B:MET87 4.9 12.2 1.0
CG2 B:ILE86 5.0 10.8 1.0

Iodine binding site 4 out of 19 in 4ihc

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Iodine binding site 4 out of 19 in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703


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 Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I507

b:32.0
occ:0.50
 OG1 B:THR66 3.4 21.1 1.0
N D:LYS117 3.6 13.0 1.0
CA D:GLY116 3.7 14.2 1.0
CG D:LYS117 3.8 31.4 1.0
CB B:THR66 4.1 8.7 1.0
O B:THR66 4.1 12.0 1.0
C D:GLY116 4.1 20.1 1.0
CE1 D:TYR111 4.2 18.3 1.0
C B:THR66 4.4 8.4 1.0
CB D:GLU112 4.4 6.2 1.0
O D:HOH663 4.5 29.7 1.0
CG B:ARG67 4.5 10.5 1.0
CB D:LYS117 4.5 17.9 1.0
CD1 D:TYR111 4.6 13.1 1.0
CA D:GLU112 4.6 7.5 1.0
CA D:LYS117 4.6 14.9 1.0
NZ B:LYS102 4.8 30.5 1.0
N B:ARG67 4.8 8.3 1.0
CE D:LYS117 4.9 34.2 1.0
CD D:LYS117 4.9 26.9 1.0
CA B:THR66 4.9 8.5 1.0
N D:GLY116 5.0 17.4 1.0
O B:HOH814 5.0 22.7 1.0
CA B:ARG67 5.0 9.0 1.0

Iodine binding site 5 out of 19 in 4ihc

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Iodine binding site 5 out of 19 in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703


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 Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I508

b:34.0
occ:0.50
 N B:THR229 3.5 10.0 1.0
OG1 B:THR232 3.6 22.1 1.0
CB B:PRO196 3.6 18.1 1.0
CB B:VAL228 3.9 16.5 1.0
CA B:VAL228 3.9 11.3 1.0
CG2 B:THR229 3.9 14.7 1.0
CG2 B:THR232 4.0 14.8 1.0
CB B:THR232 4.0 19.5 1.0
OG1 B:THR229 4.0 17.4 1.0
C B:VAL228 4.2 19.6 1.0
CG1 B:VAL228 4.2 15.4 1.0
O B:HOH831 4.3 28.5 1.0
C B:PRO196 4.3 25.0 1.0
CB B:THR229 4.4 18.6 1.0
O B:PRO196 4.4 15.6 1.0
CA B:THR229 4.5 14.6 1.0
CG B:GLU197 4.6 63.1 1.0
CG B:PRO196 4.6 15.3 1.0
CA B:PRO196 4.6 15.6 1.0
N B:GLU197 4.6 20.9 1.0
O B:ARG227 5.0 17.9 1.0

Iodine binding site 6 out of 19 in 4ihc

Go back to Iodine Binding Sites List in 4ihc
Iodine binding site 6 out of 19 in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703


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 Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I505

b:15.2
occ:1.00
 N C:ILE86 3.6 16.0 1.0
N G:ILE86 3.6 11.4 1.0
CG C:MET87 3.7 31.4 1.0
CG G:MET87 3.7 22.2 1.0
CA G:GLY84 3.8 10.8 1.0
CA C:GLY84 3.8 13.5 1.0
CB G:ILE86 3.8 11.7 1.0
C G:GLY84 3.8 9.7 1.0
CD G:PRO85 3.8 8.4 1.0
C C:GLY84 3.8 11.5 1.0
N G:PRO85 3.8 8.3 1.0
N G:MET87 3.9 12.5 1.0
CB C:ILE86 3.9 15.5 1.0
N C:PRO85 3.9 13.7 1.0
N C:MET87 3.9 11.3 1.0
CD C:PRO85 4.0 9.7 1.0
CA G:ILE86 4.2 8.9 1.0
CA C:ILE86 4.2 17.6 1.0
CG1 C:ILE86 4.3 17.4 1.0
CG1 G:ILE86 4.3 10.5 1.0
O C:GLY84 4.4 12.4 1.0
O G:GLY84 4.4 12.1 1.0
CG C:PRO85 4.4 8.9 1.0
CD1 C:ILE86 4.5 11.1 1.0
CB G:MET87 4.5 10.7 1.0
C G:ILE86 4.6 8.4 1.0
CD1 G:ILE86 4.6 7.2 1.0
C G:PRO85 4.6 7.2 1.0
CG G:PRO85 4.6 5.1 1.0
C C:PRO85 4.6 13.6 1.0
C C:ILE86 4.6 11.7 1.0
CB C:MET87 4.7 16.7 1.0
N G:GLY84 4.7 11.5 1.0
N C:GLY84 4.7 19.5 1.0
CA G:PRO85 4.8 9.9 1.0
CA C:PRO85 4.8 10.3 1.0
CA G:MET87 4.8 14.9 1.0
SD C:MET87 4.9 26.0 1.0
CG2 G:ILE86 4.9 11.6 1.0
CA C:MET87 4.9 12.8 1.0

Iodine binding site 7 out of 19 in 4ihc

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Iodine binding site 7 out of 19 in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703


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 Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I506

b:33.5
occ:0.50
 O A:HOH752 2.7 45.9 1.0
N C:LYS117 3.5 11.5 1.0
CA C:GLY116 3.6 12.4 1.0
OG1 A:THR66 3.6 21.4 1.0
C C:GLY116 4.0 11.3 1.0
CE1 C:TYR111 4.1 14.9 1.0
CB C:GLU112 4.1 12.8 1.0
O A:THR66 4.1 14.6 1.0
CB A:THR66 4.1 16.9 1.0
CG C:LYS117 4.2 40.5 1.0
CG A:ARG67 4.4 9.0 1.0
C A:THR66 4.4 12.4 1.0
CD1 C:TYR111 4.5 19.6 1.0
CA C:GLU112 4.5 11.0 1.0
CB C:LYS117 4.6 21.8 1.0
CA C:LYS117 4.6 13.7 1.0
N C:GLY116 4.8 12.1 1.0
N A:ARG67 4.9 11.9 1.0
CA A:ARG67 5.0 12.9 1.0

Iodine binding site 8 out of 19 in 4ihc

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Iodine binding site 8 out of 19 in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703


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 Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I508

b:33.9
occ:0.50
 N C:THR229 3.6 9.4 1.0
O E:HOH706 3.6 38.3 1.0
OG1 C:THR232 3.7 18.5 1.0
CB C:PRO196 3.7 16.0 1.0
CG2 C:THR229 3.9 8.5 1.0
CB C:VAL228 4.0 13.4 1.0
CG2 C:THR232 4.0 14.4 1.0
CA C:VAL228 4.0 11.3 1.0
OG1 C:THR229 4.1 15.0 1.0
CG C:PRO196 4.1 15.2 1.0
CB C:THR232 4.1 14.4 1.0
CG1 C:VAL228 4.2 19.3 1.0
C C:VAL228 4.3 16.5 1.0
C C:PRO196 4.3 16.9 1.0
N C:GLU197 4.3 13.8 1.0
CB C:THR229 4.4 12.7 1.0
CA C:THR229 4.6 14.3 1.0
O C:PRO196 4.6 14.4 1.0
CA C:PRO196 4.7 19.9 1.0
CA C:GLU197 4.7 18.0 1.0
CB C:GLU197 5.0 16.3 1.0

Iodine binding site 9 out of 19 in 4ihc

Go back to Iodine Binding Sites List in 4ihc
Iodine binding site 9 out of 19 in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703


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 Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I505

b:14.4
occ:1.00
 N D:ILE86 3.6 11.7 1.0
N H:ILE86 3.6 11.6 1.0
CA H:GLY84 3.6 11.0 1.0
CB H:ILE86 3.8 9.9 1.0
C H:GLY84 3.8 13.3 1.0
CA D:GLY84 3.8 12.5 1.0
C D:GLY84 3.8 7.3 1.0
CB D:ILE86 3.8 7.5 1.0
CD H:PRO85 3.9 10.6 1.0
N D:MET87 3.9 13.0 1.0
N D:PRO85 3.9 10.8 1.0
CD D:PRO85 3.9 9.0 1.0
N H:PRO85 3.9 11.5 1.0
N H:MET87 4.0 9.4 1.0
CG H:MET87 4.0 14.1 1.0
CA D:ILE86 4.2 12.2 1.0
CA H:ILE86 4.2 12.1 1.0
CG1 H:ILE86 4.3 10.8 1.0
CG D:MET87 4.3 13.5 1.0
O D:GLY84 4.4 13.9 1.0
CG1 D:ILE86 4.4 9.7 1.0
O H:GLY84 4.4 8.8 1.0
CD1 D:ILE86 4.4 13.6 1.0
CG D:PRO85 4.4 7.1 1.0
CD1 H:ILE86 4.5 9.5 1.0
CG H:PRO85 4.5 11.3 1.0
C D:PRO85 4.5 11.2 1.0
C D:ILE86 4.6 14.3 1.0
C H:PRO85 4.6 8.5 1.0
CB H:MET87 4.6 12.3 1.0
C H:ILE86 4.6 11.1 1.0
CB D:MET87 4.6 13.5 1.0
N H:GLY84 4.7 15.9 1.0
CA D:PRO85 4.8 8.0 1.0
CA H:PRO85 4.8 9.2 1.0
N D:GLY84 4.8 10.9 1.0
CA D:MET87 4.9 12.9 1.0
CA H:MET87 4.9 10.8 1.0
SD D:MET87 4.9 22.8 1.0
CG2 D:ILE86 5.0 9.1 1.0

Iodine binding site 10 out of 19 in 4ihc

Go back to Iodine Binding Sites List in 4ihc
Iodine binding site 10 out of 19 in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703


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 Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I507

b:33.5
occ:0.50
 OG1 D:THR66 3.5 16.0 1.0
N B:LYS117 3.6 17.2 1.0
CA B:GLY116 3.8 17.7 1.0
CE1 B:TYR111 4.1 12.7 1.0
O D:THR66 4.1 11.4 1.0
CG B:LYS117 4.1 23.5 1.0
C B:GLY116 4.2 13.7 1.0
CG D:ARG67 4.3 13.3 1.0
CB D:THR66 4.3 20.2 1.0
CB B:GLU112 4.4 7.6 1.0
C D:THR66 4.4 17.7 1.0
CB B:LYS117 4.4 24.6 1.0
CD1 B:TYR111 4.5 13.8 1.0
CA B:LYS117 4.6 20.9 1.0
CA B:GLU112 4.7 8.1 1.0
CD B:LYS117 4.7 49.7 1.0
N D:ARG67 4.8 13.8 1.0
CA D:ARG67 4.8 13.2 1.0

Reference:

Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, N.F.Al Obaidi, M.Stead, J.Love, J.A.Gerlt, S.C.Almo. Crystal Structure of Mannonate Dehydratase DD703_0947 From Dickeya Dadantii ECH703 To Be Published.
Page generated: Sun Aug 11 18:04:24 2024

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