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Iodine in PDB 4ik0: Crystal Structure of Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli

Enzymatic activity of Crystal Structure of Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli

All present enzymatic activity of Crystal Structure of Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli:
5.1.1.7;

Protein crystallography data

The structure of Crystal Structure of Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli, PDB code: 4ik0 was solved by L.Hor, R.C.J.Dobson, C.A.Hutton, M.A.Perugini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.68 / 2.05
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 89.180, 89.180, 179.450, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.7

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 Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli (pdb code 4ik0). 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 Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli, PDB code: 4ik0:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 13 in 4ik0

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Iodine binding site 1 out of 13 in the Crystal Structure of Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli


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 Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I301

b:21.8
occ:1.00
 O A:HOH442 3.5 24.9 1.0
O A:HOH434 3.6 32.4 1.0
N A:CYS79 3.7 14.9 1.0
N A:ARG78 3.8 15.9 1.0
CB A:ARG78 3.8 16.6 1.0
CA A:GLY76 3.9 16.6 1.0
C A:GLY76 3.9 15.9 1.0
SG A:CYS79 4.0 18.1 1.0
N A:GLY76 4.1 18.6 1.0
CZ A:ARG78 4.1 19.6 1.0
N A:ALA77 4.1 16.2 1.0
CA A:GLY8 4.2 16.2 1.0
CA A:ARG78 4.2 16.2 1.0
CG A:ARG78 4.2 17.2 1.0
NH2 A:ARG78 4.3 18.7 1.0
NH1 A:ARG78 4.3 19.8 1.0
CE2 A:PHE13 4.3 16.5 1.0
O A:GLY76 4.3 15.4 1.0
NE A:ARG78 4.4 18.2 1.0
C A:ARG78 4.4 15.2 1.0
CB A:CYS79 4.6 14.1 1.0
N A:GLY8 4.7 15.3 1.0
CA A:CYS79 4.7 14.8 1.0
C A:ALA77 4.8 16.0 1.0
CZ A:PHE13 4.9 16.2 1.0
CD A:ARG78 4.9 18.6 1.0

Iodine binding site 2 out of 13 in 4ik0

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Iodine binding site 2 out of 13 in the Crystal Structure of Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli


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 Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:28.9
occ:1.00
 O A:HOH452 3.4 21.9 1.0
O A:HOH473 3.4 30.6 1.0
N A:ASN133 3.7 32.1 1.0
CB A:ALA132 4.1 29.9 1.0
OD1 A:ASN133 4.1 33.3 1.0
CD2 A:TYR139 4.1 22.6 1.0
CB A:ASN133 4.2 34.4 1.0
CG A:GLU136 4.2 34.8 1.0
CE2 A:TYR139 4.5 23.8 1.0
O A:LYS134 4.5 31.2 1.0
CA A:ASN133 4.5 34.2 1.0
CG A:ASN133 4.5 33.5 1.0
OE1 A:GLU136 4.6 38.1 1.0
N A:LYS134 4.6 35.3 1.0
CA A:ALA132 4.6 30.4 1.0
C A:ALA132 4.7 32.6 1.0
NH2 A:ARG184 4.8 25.4 1.0
CD A:GLU136 4.9 37.3 1.0

Iodine binding site 3 out of 13 in 4ik0

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Iodine binding site 3 out of 13 in the Crystal Structure of Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli


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 Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:28.0
occ:1.00
 NH2 A:ARG78 3.5 18.7 1.0
NH1 A:ARG78 3.6 19.8 1.0
ND2 A:ASN11 3.7 21.8 1.0
N A:GLY218 3.9 20.8 1.0
CZ A:ARG78 4.0 19.6 1.0
CA A:GLY218 4.1 19.9 1.0
O A:GLY8 4.1 17.9 1.0
CB A:ALA216 4.1 23.5 1.0
CD1 A:LEU9 4.1 23.4 1.0
CB A:LEU9 4.3 20.1 1.0
CD1 A:LEU247 4.4 16.8 1.0
CG A:LEU9 4.4 21.9 1.0
O A:ALA216 4.5 24.3 1.0
C A:ALA216 4.6 24.2 1.0
C A:GLY8 4.6 17.5 1.0
CD2 A:LEU247 4.6 18.4 1.0
C A:CYS217 4.7 21.1 1.0
N A:CYS217 4.8 21.4 1.0
CG A:ASN11 4.9 22.1 1.0
CA A:ALA216 5.0 23.4 1.0

Iodine binding site 4 out of 13 in 4ik0

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Iodine binding site 4 out of 13 in the Crystal Structure of Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli


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 Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:59.1
occ:1.00
 N A:ALA171 3.4 29.8 1.0
CD1 A:LEU175 3.6 36.3 1.0
CA A:ALA170 4.0 27.7 1.0
CB A:ALA171 4.1 31.1 1.0
CG1 A:VAL164 4.1 20.3 1.0
C A:ALA170 4.2 28.6 1.0
CA A:ALA171 4.3 31.3 1.0
CB A:ALA170 4.4 27.6 1.0
NE2 A:GLN146 4.5 51.1 1.0
CD1 A:PHE193 4.6 19.3 1.0
O A:HOH512 4.6 48.4 1.0
CE1 A:PHE193 4.6 20.6 1.0
CG A:LEU175 4.8 39.3 1.0
O A:HOH558 4.9 24.6 1.0
C A:ALA171 5.0 30.2 1.0

Iodine binding site 5 out of 13 in 4ik0

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Iodine binding site 5 out of 13 in the Crystal Structure of Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli


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 Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:75.6
occ:1.00
 NE2 A:HIS201 3.5 29.1 1.0
CE1 A:HIS201 3.7 30.2 1.0
CG A:ARG203 3.8 24.8 1.0
CD A:ARG203 3.8 28.4 1.0
CG A:GLU241 3.9 23.4 1.0
NE A:ARG203 3.9 32.6 1.0
CB A:GLU241 4.1 21.0 1.0
NH2 A:ARG239 4.3 36.8 1.0
CD A:GLU241 4.7 25.4 1.0
CD2 A:HIS201 4.8 27.2 1.0
O A:HOH467 4.8 35.2 1.0
CZ A:ARG239 5.0 35.4 1.0

Iodine binding site 6 out of 13 in 4ik0

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Iodine binding site 6 out of 13 in the Crystal Structure of Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli


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 Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I306

b:83.8
occ:1.00
 CE1 A:HIS37 3.8 24.4 1.0
NE B:ARG36 3.9 20.1 1.0
I B:IOD307 3.9 91.8 1.0
CB A:ARG36 4.1 17.8 1.0
CD B:ARG36 4.2 20.4 1.0
ND1 A:HIS37 4.4 25.2 1.0
CD A:ARG36 4.4 19.0 1.0
O B:HOH503 4.5 45.2 1.0
CG B:ARG36 4.5 20.7 1.0
CZ B:ARG36 4.5 19.6 1.0
O B:HOH433 4.8 37.3 1.0
NE2 A:HIS37 4.8 26.0 1.0
CG A:ARG36 4.8 17.8 1.0
NH2 B:ARG36 5.0 17.5 1.0

Iodine binding site 7 out of 13 in 4ik0

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Iodine binding site 7 out of 13 in the Crystal Structure of Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli


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 Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I301

b:19.9
occ:1.00
 O B:HOH415 3.5 28.6 1.0
O B:HOH452 3.6 20.4 1.0
N B:CYS79 3.8 14.1 1.0
CB B:ARG78 3.8 16.1 1.0
N B:ARG78 3.8 14.9 1.0
CA B:GLY76 3.8 15.4 1.0
C B:GLY76 3.9 15.0 1.0
SG B:CYS79 4.0 16.4 1.0
N B:GLY76 4.0 16.1 1.0
CZ B:ARG78 4.1 23.5 1.0
N B:ALA77 4.2 14.9 1.0
CE2 B:PHE13 4.2 15.4 1.0
CA B:GLY8 4.2 16.4 1.0
CA B:ARG78 4.2 15.1 1.0
NH1 B:ARG78 4.3 24.4 1.0
O B:GLY76 4.3 13.9 1.0
NE B:ARG78 4.4 24.3 1.0
CG B:ARG78 4.4 17.7 1.0
NH2 B:ARG78 4.5 21.4 1.0
CB B:CYS79 4.5 13.5 1.0
C B:ARG78 4.5 14.6 1.0
N B:GLY8 4.6 15.4 1.0
CA B:CYS79 4.7 13.7 1.0
CZ B:PHE13 4.8 14.9 1.0
C B:ALA77 4.8 14.8 1.0
CD B:ARG78 4.8 20.3 1.0

Iodine binding site 8 out of 13 in 4ik0

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Iodine binding site 8 out of 13 in the Crystal Structure of Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli


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 Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I302

b:28.4
occ:1.00
 ND2 B:ASN133 3.5 36.1 1.0
O B:HOH536 3.6 30.7 1.0
N B:ASN133 3.7 35.8 1.0
O B:HOH439 3.7 27.8 1.0
CB B:ASN133 4.0 36.6 1.0
CG B:ASN133 4.1 37.1 1.0
CD1 B:TYR139 4.2 26.0 1.0
CA B:ASN133 4.4 37.8 1.0
CB B:ALA132 4.4 32.5 1.0
CG B:GLU136 4.5 32.6 1.0
O B:LYS134 4.5 36.0 1.0
N B:LYS134 4.6 37.9 1.0
CE1 B:TYR139 4.6 25.7 1.0
C B:ALA132 4.6 35.5 1.0
CA B:ALA132 4.6 33.8 1.0
NH2 B:ARG184 4.9 31.5 1.0

Iodine binding site 9 out of 13 in 4ik0

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Iodine binding site 9 out of 13 in the Crystal Structure of Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli


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 Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I303

b:28.4
occ:1.00
 NH1 B:ARG78 2.9 24.4 1.0
O B:HOH461 3.3 42.0 1.0
ND2 B:ASN11 3.6 25.2 1.0
N B:GLY218 3.7 21.0 1.0
NH2 B:ARG78 3.8 21.4 1.0
CZ B:ARG78 3.8 23.5 1.0
CA B:GLY218 3.8 19.9 1.0
O B:GLY8 4.0 20.6 1.0
CB B:ALA216 4.2 23.6 1.0
CD1 B:LEU9 4.3 22.3 1.0
CD1 B:LEU247 4.3 12.5 1.0
C B:GLY8 4.4 17.9 1.0
CB B:LEU9 4.4 20.2 1.0
CD2 B:LEU247 4.6 13.0 1.0
C B:CYS217 4.6 20.3 1.0
CG B:LEU9 4.6 21.2 1.0
O B:ALA216 4.6 23.6 1.0
C B:ALA216 4.6 24.6 1.0
O B:HOH465 4.7 31.1 1.0
CG B:ASN11 4.8 24.7 1.0
N B:CYS217 4.8 21.0 1.0
CG B:LEU247 4.9 13.2 1.0
NE B:ARG78 5.0 24.3 1.0

Iodine binding site 10 out of 13 in 4ik0

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Iodine binding site 10 out of 13 in the Crystal Structure of Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli


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 Diaminopimelate Epimerase Y268A Mutant From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I304

b:67.7
occ:1.00
 N B:ALA171 3.4 36.9 1.0
CD2 B:LEU175 3.8 42.8 1.0
CA B:ALA170 4.0 37.2 1.0
CG1 B:VAL164 4.2 27.1 1.0
CB B:ALA171 4.2 39.8 1.0
C B:ALA170 4.2 37.7 1.0
NE2 B:GLN146 4.3 60.4 1.0
CA B:ALA171 4.3 38.6 1.0
CB B:ALA170 4.4 35.2 1.0
CE1 B:PHE193 4.7 24.7 1.0
CD1 B:PHE193 4.7 23.6 1.0
C B:ALA171 5.0 37.2 1.0

Reference:

L.Hor, R.C.J.Dobson, M.T.Downton, J.Wagner, C.A.Hutton, M.A.Perugini. Dimerization of Bacterial Diaminopimelate Epimerase Is Essential For Catalysis J.Biol.Chem. V. 288 9238 2013.
ISSN: ISSN 0021-9258
PubMed: 23426375
DOI: 10.1074/JBC.M113.450148
Page generated: Sun Aug 11 18:06:18 2024

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