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Iodine in PDB 7v8t: Crystal Structure of Class II Pyruvate Aldolase From Pseudomonas Aeruginosa.

Enzymatic activity of Crystal Structure of Class II Pyruvate Aldolase From Pseudomonas Aeruginosa.

All present enzymatic activity of Crystal Structure of Class II Pyruvate Aldolase From Pseudomonas Aeruginosa.:
4.1.2.52;

Protein crystallography data

The structure of Crystal Structure of Class II Pyruvate Aldolase From Pseudomonas Aeruginosa., PDB code: 7v8t was solved by P.W.Seo, J.S.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.54 / 2.48
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.952, 131.077, 84.202, 90, 106.8, 90
R / Rfree (%) 18.6 / 22.7

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Class II Pyruvate Aldolase From Pseudomonas Aeruginosa. (pdb code 7v8t). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Crystal Structure of Class II Pyruvate Aldolase From Pseudomonas Aeruginosa., PDB code: 7v8t:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 7v8t

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Iodine binding site 1 out of 10 in the Crystal Structure of Class II Pyruvate Aldolase From Pseudomonas Aeruginosa.


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 Class II Pyruvate Aldolase From Pseudomonas Aeruginosa. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I301

b:57.3
occ:1.00
 O A:HOH417 3.6 39.8 1.0
CB A:ALA177 3.8 33.2 1.0
CD A:PRO189 4.0 39.4 1.0
CG A:PRO189 4.0 39.5 1.0
CA A:GLY187 4.1 36.0 1.0
CA A:ALA177 4.2 32.6 1.0
C A:GLY187 4.6 40.8 1.0
CD1 D:LEU138 4.6 39.6 1.0
N A:GLY187 4.6 45.9 1.0
CG1 D:VAL121 4.6 39.7 1.0
CB A:PRO189 5.0 39.0 1.0
O A:GLY187 5.0 32.0 1.0

Iodine binding site 2 out of 10 in 7v8t

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Iodine binding site 2 out of 10 in the Crystal Structure of Class II Pyruvate Aldolase From Pseudomonas Aeruginosa.


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 Class II Pyruvate Aldolase From Pseudomonas Aeruginosa. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:106.3
occ:1.00
 O C:HOH457 3.7 44.2 1.0
CA A:GLY122 3.9 47.0 1.0
CB A:ALA124 4.2 61.1 1.0
C A:GLY122 4.3 50.4 1.0
O A:GLY122 4.5 47.7 1.0
CB C:ALA177 4.6 51.9 1.0
N A:ALA124 4.6 46.8 1.0
O A:VAL121 4.7 50.0 1.0
N A:SER123 4.8 54.3 1.0
CD2 C:LEU215 4.9 39.6 1.0
N A:GLY122 4.9 48.1 1.0
CA A:ALA124 4.9 49.5 1.0

Iodine binding site 3 out of 10 in 7v8t

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Iodine binding site 3 out of 10 in the Crystal Structure of Class II Pyruvate Aldolase From Pseudomonas Aeruginosa.


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 Class II Pyruvate Aldolase From Pseudomonas Aeruginosa. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I300

b:60.3
occ:1.00
 O B:HOH406 3.5 43.2 1.0
CD B:PRO189 3.9 35.6 1.0
CG B:PRO189 4.0 30.8 1.0
CB B:ALA177 4.1 37.3 1.0
CA B:GLY187 4.1 40.0 1.0
CA B:ALA177 4.2 37.5 1.0
CD1 F:LEU138 4.3 40.9 1.0
C B:GLY187 4.5 35.6 1.0
N B:GLY187 4.6 39.0 1.0
O B:GLY187 4.8 40.3 1.0

Iodine binding site 4 out of 10 in 7v8t

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Iodine binding site 4 out of 10 in the Crystal Structure of Class II Pyruvate Aldolase From Pseudomonas Aeruginosa.


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 Class II Pyruvate Aldolase From Pseudomonas Aeruginosa. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I301

b:115.1
occ:1.00
 O E:HOH446 3.1 40.5 1.0
CA B:GLY122 4.2 35.3 1.0
O E:HOH443 4.4 40.0 1.0
CB B:ALA124 4.4 57.9 1.0
C B:GLY122 4.6 43.7 1.0
CB E:ALA177 4.6 46.4 1.0
CD2 E:LEU215 4.8 38.8 1.0
O B:VAL121 4.9 44.5 1.0
O B:GLY122 4.9 42.3 1.0
N B:ALA124 4.9 45.2 1.0

Iodine binding site 5 out of 10 in 7v8t

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Iodine binding site 5 out of 10 in the Crystal Structure of Class II Pyruvate Aldolase From Pseudomonas Aeruginosa.


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 Class II Pyruvate Aldolase From Pseudomonas Aeruginosa. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I300

b:80.1
occ:1.00
 CB C:ALA177 3.8 51.9 1.0
CD C:PRO189 3.8 45.6 1.0
CG C:PRO189 3.9 43.7 1.0
CA C:ALA177 4.0 49.4 1.0
CA C:GLY187 4.2 44.4 1.0
CD1 A:LEU138 4.3 44.4 1.0
C C:GLY187 4.6 57.4 1.0
N C:GLY187 4.6 46.9 1.0
N C:ALA177 4.9 48.5 1.0
CB C:PRO189 4.9 45.6 1.0
CG1 A:VAL121 4.9 44.3 1.0
O C:GLY187 5.0 62.7 1.0

Iodine binding site 6 out of 10 in 7v8t

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Iodine binding site 6 out of 10 in the Crystal Structure of Class II Pyruvate Aldolase From Pseudomonas Aeruginosa.


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 Class II Pyruvate Aldolase From Pseudomonas Aeruginosa. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I301

b:83.4
occ:1.00
 O C:HOH447 3.6 41.5 1.0
CB C:ALA124 4.1 55.6 1.0
CA C:GLY122 4.2 43.8 1.0
CB D:ALA177 4.5 43.5 1.0
C C:GLY122 4.5 51.4 1.0
N C:ALA124 4.6 49.3 1.0
CD2 D:LEU215 4.8 34.8 1.0
O C:GLY122 4.8 49.3 1.0
CA C:ALA124 4.9 51.6 1.0
O C:VAL121 4.9 42.8 1.0
N C:SER123 4.9 52.7 1.0

Iodine binding site 7 out of 10 in 7v8t

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Iodine binding site 7 out of 10 in the Crystal Structure of Class II Pyruvate Aldolase From Pseudomonas Aeruginosa.


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 Class II Pyruvate Aldolase From Pseudomonas Aeruginosa. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I300

b:89.8
occ:1.00
 CB D:ALA177 4.0 43.5 1.0
CD1 C:LEU138 4.1 45.3 1.0
O C:HOH447 4.1 41.5 1.0
CD D:PRO189 4.1 44.2 1.0
CG D:PRO189 4.1 40.7 1.0
CA D:ALA177 4.2 42.7 1.0
CA D:GLY187 4.2 49.0 1.0
N D:GLY187 4.6 48.2 1.0
C D:GLY187 4.7 46.2 1.0

Iodine binding site 8 out of 10 in 7v8t

Go back to Iodine Binding Sites List in 7v8t
Iodine binding site 8 out of 10 in the Crystal Structure of Class II Pyruvate Aldolase From Pseudomonas Aeruginosa.


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 Class II Pyruvate Aldolase From Pseudomonas Aeruginosa. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I301

b:64.7
occ:1.00
 CG E:PRO189 3.6 50.3 1.0
CB E:ALA177 3.9 46.4 1.0
CD E:PRO189 4.0 51.8 1.0
CA E:GLY187 4.1 48.9 1.0
CA E:ALA177 4.1 42.2 1.0
C E:GLY187 4.5 51.3 1.0
N E:GLY187 4.5 50.3 1.0
CD1 B:LEU138 4.6 45.1 1.0
CG1 B:VAL121 4.8 41.7 1.0
O E:GLY187 4.9 49.7 1.0
O E:HOH443 5.0 40.0 1.0
N E:ASN188 5.0 52.2 1.0

Iodine binding site 9 out of 10 in 7v8t

Go back to Iodine Binding Sites List in 7v8t
Iodine binding site 9 out of 10 in the Crystal Structure of Class II Pyruvate Aldolase From Pseudomonas Aeruginosa.


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 Class II Pyruvate Aldolase From Pseudomonas Aeruginosa. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I302

b:104.8
occ:1.00
 CB E:ALA124 4.0 61.9 1.0
CA E:GLY122 4.1 47.7 1.0
C E:GLY122 4.4 52.0 1.0
N E:ALA124 4.5 51.7 1.0
O E:GLY122 4.6 43.2 1.0
CB F:ALA177 4.7 47.1 1.0
CD2 F:LEU215 4.8 34.1 1.0
CA E:ALA124 4.8 58.8 1.0
N E:SER123 4.8 61.2 1.0
O E:VAL121 4.9 53.4 1.0
N E:LEU125 4.9 54.6 1.0

Iodine binding site 10 out of 10 in 7v8t

Go back to Iodine Binding Sites List in 7v8t
Iodine binding site 10 out of 10 in the Crystal Structure of Class II Pyruvate Aldolase From Pseudomonas Aeruginosa.


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 Class II Pyruvate Aldolase From Pseudomonas Aeruginosa. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:I302

b:96.8
occ:1.00
 CB F:ALA177 3.8 47.1 1.0
CA F:ALA177 4.0 52.3 1.0
CD F:PRO189 4.2 53.5 1.0
CA F:GLY187 4.2 61.9 1.0
CD1 E:LEU138 4.2 60.0 1.0
CG F:PRO189 4.3 51.4 1.0
N F:GLY187 4.6 65.0 1.0
C F:GLY187 4.6 64.6 1.0
O F:ALA177 4.8 54.9 1.0
CG1 E:VAL121 4.8 49.4 1.0
C F:ALA177 4.9 51.5 1.0
N F:ALA177 4.9 55.3 1.0

Reference:

Y.J.Jeong, T.K.Le, P.W.Seo, S.B.Ju, J.S.Kim, S.J.Yeom. Biochemical and Molecular Characterization of Pyruvate Aldolase For the Synthesis of 2-Keto-4-Hydroxybutyrate. To Be Published.
Page generated: Mon Aug 12 02:15:42 2024

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