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Iodine in PDB 8dop: Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)

Enzymatic activity of Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)

All present enzymatic activity of Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form):
4.1.1.23;

Protein crystallography data

The structure of Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form), PDB code: 8dop was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.41 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.021, 71.159, 93.183, 108.39, 102.23, 89.99
R / Rfree (%) 18.8 / 24.6

Other elements in 8dop:

The structure of Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) also contains other interesting chemical elements:

Sodium (Na) 6 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) (pdb code 8dop). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form), PDB code: 8dop:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in 8dop

Go back to Iodine Binding Sites List in 8dop
Iodine binding site 1 out of 12 in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)


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 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I301

b:62.4
occ:0.92
 O B:HOH419 3.2 48.8 1.0
CD A:LYS36 4.2 40.5 1.0
CB B:LEU61 4.2 27.7 1.0
CB A:LEU61 4.3 23.1 1.0
CG A:LYS36 4.3 28.9 1.0
CD1 B:LEU61 4.3 25.0 1.0
CE1 B:PHE63 4.4 25.0 1.0
CD2 A:LEU61 4.5 22.3 1.0
O A:LEU61 4.6 30.1 1.0
O B:LEU61 4.6 34.9 1.0
CG B:LEU61 4.6 28.8 1.0
CD1 A:LEU61 4.6 28.1 1.0
CD2 B:LEU61 4.7 30.9 1.0
CG A:LEU61 4.7 23.1 1.0
CD1 B:PHE63 4.7 27.3 1.0
CE1 A:PHE63 4.8 26.1 1.0

Iodine binding site 2 out of 12 in 8dop

Go back to Iodine Binding Sites List in 8dop
Iodine binding site 2 out of 12 in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)


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 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:86.8
occ:0.63
 OD1 A:ASP60 3.6 29.3 1.0
OD2 A:ASP60 3.8 30.9 1.0
CG A:ASP60 3.8 24.6 1.0
NZ A:LYS62 3.8 24.2 1.0
CG2 A:VAL156 4.1 27.6 1.0
CG1 A:VAL156 4.1 36.6 1.0
CE A:LYS62 4.2 26.8 1.0
CE2 A:PHE58 4.2 27.3 1.0
ND2 A:ASN86 4.2 25.4 1.0
CZ A:PHE58 4.4 25.5 1.0
CB A:PRO178 4.5 35.9 1.0
NA A:NA303 4.6 38.8 1.0
CD A:LYS33 4.6 24.7 1.0
CB A:VAL156 4.7 29.5 1.0
CG A:PRO178 4.8 34.6 1.0
CB A:ASP60 4.8 22.8 1.0
CE A:LYS33 4.9 21.9 1.0

Iodine binding site 3 out of 12 in 8dop

Go back to Iodine Binding Sites List in 8dop
Iodine binding site 3 out of 12 in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)


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 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I301

b:69.1
occ:0.63
 OD2 B:ASP60 3.7 34.4 1.0
O B:HOH430 3.7 51.3 1.0
OD1 B:ASP60 3.9 39.2 1.0
CG B:ASP60 3.9 37.6 1.0
CG2 B:VAL156 3.9 37.1 1.0
NZ B:LYS62 3.9 31.4 1.0
ND2 B:ASN86 4.0 38.0 1.0
CZ B:PHE58 4.1 35.7 1.0
CE2 B:PHE58 4.1 28.4 1.0
CG1 B:VAL156 4.2 39.6 1.0
CE B:LYS62 4.2 31.5 1.0
CB B:PRO178 4.4 49.4 1.0
CD B:LYS33 4.6 32.8 1.0
NA B:NA302 4.6 47.7 1.0
CB B:VAL156 4.7 42.9 1.0
CE B:LYS33 4.7 32.2 1.0
CG2 B:VAL116 4.8 34.3 1.0
CB B:ASP60 4.8 29.2 1.0

Iodine binding site 4 out of 12 in 8dop

Go back to Iodine Binding Sites List in 8dop
Iodine binding site 4 out of 12 in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)


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 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I301

b:69.2
occ:1.00
 O C:HOH426 3.7 43.3 1.0
CG C:LYS36 4.2 32.3 1.0
CD1 D:LEU61 4.3 24.2 1.0
CE1 D:PHE63 4.3 24.7 1.0
CB D:LEU61 4.3 26.3 1.0
CD C:LYS36 4.4 47.3 1.0
CB C:LEU61 4.4 29.9 1.0
CD1 C:LEU61 4.5 31.0 1.0
CD2 C:LEU61 4.5 30.9 1.0
CD2 D:LEU61 4.5 27.4 1.0
CG D:LEU61 4.6 21.4 1.0
CG C:LEU61 4.7 23.6 1.0
CD1 D:PHE63 4.7 27.8 1.0
O D:LEU61 4.8 29.5 1.0
O C:LEU61 4.8 29.1 1.0
CD2 D:PHE39 4.8 34.3 1.0
CD2 C:PHE39 4.9 29.9 1.0
CE1 C:PHE63 4.9 25.2 1.0
CE2 D:PHE39 5.0 36.3 1.0
OG1 C:THR40 5.0 42.8 1.0

Iodine binding site 5 out of 12 in 8dop

Go back to Iodine Binding Sites List in 8dop
Iodine binding site 5 out of 12 in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)


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 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I302

b:118.2
occ:0.75
 OD2 C:ASP60 3.6 31.2 1.0
OD1 C:ASP60 3.8 33.9 1.0
CG C:ASP60 3.8 35.4 1.0
NZ C:LYS62 4.0 28.2 1.0
CB C:PRO178 4.1 53.5 1.0
CE C:LYS62 4.2 28.8 1.0
CE2 C:PHE58 4.3 36.7 1.0
CZ C:PHE58 4.4 24.8 1.0
CD C:LYS33 4.4 25.2 1.0
CG1 C:VAL156 4.4 44.7 1.0
CE C:LYS33 4.5 26.6 1.0
CG2 C:VAL156 4.5 36.8 1.0
NA C:NA303 4.5 39.6 1.0
ND2 C:ASN86 4.6 34.6 1.0
CA C:PRO178 4.6 46.5 1.0
CG2 C:VAL208 4.8 38.3 1.0
CB C:ASP60 4.8 29.9 1.0

Iodine binding site 6 out of 12 in 8dop

Go back to Iodine Binding Sites List in 8dop
Iodine binding site 6 out of 12 in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)


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 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I301

b:81.7
occ:0.62
 OD1 D:ASP60 3.4 30.0 1.0
CG D:ASP60 3.7 30.5 1.0
OD2 D:ASP60 3.8 33.0 1.0
NZ D:LYS62 4.0 28.2 1.0
CG2 D:VAL156 4.1 32.4 1.0
CE2 D:PHE58 4.1 23.6 1.0
CB D:PRO178 4.1 38.7 1.0
CG1 D:VAL156 4.2 31.1 1.0
CZ D:PHE58 4.2 23.6 1.0
ND2 D:ASN86 4.3 26.9 1.0
CD D:LYS33 4.4 27.3 1.0
CE D:LYS62 4.6 24.8 1.0
CA D:PRO178 4.7 44.1 1.0
CE D:LYS33 4.7 28.8 1.0
CB D:VAL156 4.8 25.4 1.0
CB D:ASP60 4.8 22.3 1.0
NA D:NA302 4.8 43.0 1.0

Iodine binding site 7 out of 12 in 8dop

Go back to Iodine Binding Sites List in 8dop
Iodine binding site 7 out of 12 in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)


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 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I301

b:71.6
occ:0.94
 CD1 E:LEU61 4.1 40.2 1.0
CE1 E:PHE63 4.1 36.0 1.0
CB F:LEU61 4.3 29.1 1.0
CB E:LEU61 4.3 33.9 1.0
CD2 F:LEU61 4.4 28.1 1.0
O F:LEU61 4.5 28.3 1.0
CD1 E:PHE63 4.5 27.7 1.0
CG F:LYS36 4.5 37.9 1.0
CG E:LEU61 4.6 33.5 1.0
CD1 F:LEU61 4.6 27.6 1.0
CG F:LEU61 4.7 31.5 1.0
O E:LEU61 4.8 25.2 1.0
CG E:LYS36 4.8 41.8 1.0
CD2 E:LEU61 4.9 28.3 1.0
CE F:LYS36 4.9 33.9 1.0
CA F:LEU61 5.0 23.5 1.0

Iodine binding site 8 out of 12 in 8dop

Go back to Iodine Binding Sites List in 8dop
Iodine binding site 8 out of 12 in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)


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 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I302

b:48.8
occ:0.61
 O E:HOH424 2.9 33.0 1.0
CB E:PRO178 3.6 46.2 1.0
CG E:PRO178 3.8 40.6 1.0
CG1 E:VAL156 4.1 34.1 1.0
CG2 E:VAL208 4.1 33.0 1.0
CE E:LYS33 4.3 35.6 1.0
CD E:LYS33 4.4 33.8 1.0
CD E:PRO178 4.4 37.9 1.0
CG1 E:VAL208 4.5 38.4 1.0
CE2 E:PHE58 4.5 36.8 1.0
CB E:VAL208 4.5 33.8 1.0
OD2 E:ASP60 4.6 34.6 1.0
CA E:PRO178 4.7 38.0 1.0
N E:PRO178 4.7 41.3 1.0
CG1 E:VAL176 4.9 42.7 1.0
NA E:NA303 4.9 47.5 1.0
CG E:ASP60 5.0 29.9 1.0

Iodine binding site 9 out of 12 in 8dop

Go back to Iodine Binding Sites List in 8dop
Iodine binding site 9 out of 12 in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)


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 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:I301

b:35.6
occ:0.84
 O F:HOH449 3.2 32.6 1.0
O F:HOH434 3.8 40.5 1.0
CG F:PRO178 3.9 27.5 1.0
CB F:PRO178 4.0 33.3 1.0
CG2 F:VAL208 4.1 30.5 1.0
CG1 F:VAL156 4.1 26.6 1.0
CD F:PRO178 4.2 30.5 1.0
CE F:LYS33 4.3 28.9 1.0
CG1 F:VAL208 4.3 29.8 1.0
CB F:VAL208 4.4 28.5 1.0
CD F:LYS33 4.5 24.1 1.0
CE2 F:PHE58 4.6 27.9 1.0
OD2 F:ASP60 4.7 31.5 1.0
N F:PRO178 4.7 26.6 1.0
CG2 F:VAL156 4.8 22.3 1.0
CG1 F:VAL176 4.9 32.5 1.0
NZ F:LYS33 4.9 33.9 1.0
CA F:PRO178 4.9 30.6 1.0

Iodine binding site 10 out of 12 in 8dop

Go back to Iodine Binding Sites List in 8dop
Iodine binding site 10 out of 12 in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)


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 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:I301

b:32.5
occ:0.86
 O G:HOH445 3.4 38.1 1.0
O G:HOH413 3.5 37.1 1.0
CE G:LYS33 3.7 30.6 1.0
CB G:PRO178 4.0 27.1 1.0
CG G:PRO178 4.0 30.9 1.0
CG1 G:VAL156 4.1 25.4 1.0
CD G:LYS33 4.2 26.2 1.0
CD G:PRO178 4.2 30.8 1.0
CG1 G:VAL208 4.3 30.3 1.0
CG2 G:VAL208 4.3 35.0 1.0
CB G:VAL208 4.4 31.0 1.0
OD2 G:ASP60 4.5 30.8 1.0
CE2 G:PHE58 4.6 28.4 1.0
NZ G:LYS33 4.6 31.5 1.0
N G:PRO178 4.8 32.3 1.0
CA G:PRO178 5.0 32.8 1.0

Reference:

S.Lovell, L.Liu, S.Seibold, K.P.Battaile. Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) To Be Published.
Page generated: Mon Aug 12 02:40:35 2024

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