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Iron in PDB 3hpy: Crystal Structure Analysis of the 2,3-Dioxygenase Lapb From Pseudomonas in the Complex with 4-Methylcatechol

Enzymatic activity of Crystal Structure Analysis of the 2,3-Dioxygenase Lapb From Pseudomonas in the Complex with 4-Methylcatechol

All present enzymatic activity of Crystal Structure Analysis of the 2,3-Dioxygenase Lapb From Pseudomonas in the Complex with 4-Methylcatechol:
1.13.11.2;

Protein crystallography data

The structure of Crystal Structure Analysis of the 2,3-Dioxygenase Lapb From Pseudomonas in the Complex with 4-Methylcatechol, PDB code: 3hpy was solved by J.-H.Cho, S.Rhee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.100, 97.600, 133.700, 90.00, 90.00, 90.00
R / Rfree (%) 24.4 / 27.8

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure Analysis of the 2,3-Dioxygenase Lapb From Pseudomonas in the Complex with 4-Methylcatechol (pdb code 3hpy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure Analysis of the 2,3-Dioxygenase Lapb From Pseudomonas in the Complex with 4-Methylcatechol, PDB code: 3hpy:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3hpy

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Iron binding site 1 out of 4 in the Crystal Structure Analysis of the 2,3-Dioxygenase Lapb From Pseudomonas in the Complex with 4-Methylcatechol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure Analysis of the 2,3-Dioxygenase Lapb From Pseudomonas in the Complex with 4-Methylcatechol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe310

b:33.5
occ:1.00
 O3 A:MCT311 2.0 51.7 1.0
NE2 A:HIS154 2.3 19.3 1.0
OE1 A:GLU267 2.3 23.8 1.0
NE2 A:HIS216 2.4 14.8 1.0
O4 A:MCT311 2.9 51.9 1.0
CD A:GLU267 3.0 23.6 1.0
C3 A:MCT311 3.1 52.5 1.0
CE1 A:HIS216 3.1 16.2 1.0
CE1 A:HIS154 3.2 19.8 1.0
CD2 A:HIS154 3.3 18.9 1.0
OE2 A:GLU267 3.3 23.9 1.0
C4 A:MCT311 3.4 51.7 1.0
CD2 A:HIS216 3.5 18.4 1.0
CB A:SER218 3.8 20.4 1.0
OG A:SER218 3.9 21.8 1.0
NE2 A:HIS201 4.1 27.2 1.0
OH A:TYR257 4.1 26.0 1.0
CG A:GLU267 4.3 22.3 1.0
C2 A:MCT311 4.3 52.3 1.0
ND1 A:HIS154 4.3 18.3 1.0
ND1 A:HIS216 4.3 15.8 1.0
CB A:GLU267 4.4 20.6 1.0
CG A:HIS154 4.4 18.3 1.0
CG A:HIS216 4.6 17.1 1.0
CE1 A:TYR257 4.6 26.1 1.0
NE2 A:HIS248 4.8 40.5 1.0
C5 A:MCT311 4.8 51.3 1.0
CZ A:TYR257 4.9 25.6 1.0

Iron binding site 2 out of 4 in 3hpy

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Iron binding site 2 out of 4 in the Crystal Structure Analysis of the 2,3-Dioxygenase Lapb From Pseudomonas in the Complex with 4-Methylcatechol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure Analysis of the 2,3-Dioxygenase Lapb From Pseudomonas in the Complex with 4-Methylcatechol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe310

b:29.8
occ:1.00
 O3 B:MCT311 1.9 46.1 1.0
OE1 B:GLU267 2.1 20.8 1.0
NE2 B:HIS154 2.2 20.6 1.0
NE2 B:HIS216 2.4 18.1 1.0
O4 B:MCT311 2.8 42.3 1.0
C3 B:MCT311 2.9 45.0 1.0
CD B:GLU267 2.9 20.1 1.0
CE1 B:HIS216 3.2 19.0 1.0
CD2 B:HIS154 3.2 22.2 1.0
OE2 B:GLU267 3.2 20.4 1.0
CE1 B:HIS154 3.2 20.9 1.0
C4 B:MCT311 3.3 44.3 1.0
CD2 B:HIS216 3.5 19.1 1.0
CB B:SER218 4.0 21.6 1.0
NE2 B:HIS201 4.1 32.3 1.0
OG B:SER218 4.1 21.0 1.0
C2 B:MCT311 4.2 46.7 1.0
CG B:GLU267 4.2 18.4 1.0
ND1 B:HIS154 4.3 22.6 1.0
CG B:HIS154 4.3 21.6 1.0
ND1 B:HIS216 4.4 19.1 1.0
OH B:TYR257 4.5 26.8 1.0
CB B:GLU267 4.5 18.9 1.0
CG B:HIS216 4.5 19.2 1.0
C5 B:MCT311 4.7 43.9 1.0
CE1 B:TYR257 4.7 26.6 1.0
CE1 B:HIS201 4.8 32.8 1.0
NE2 B:HIS248 5.0 38.5 1.0
CB B:LEU156 5.0 25.0 1.0

Iron binding site 3 out of 4 in 3hpy

Go back to Iron Binding Sites List in 3hpy
Iron binding site 3 out of 4 in the Crystal Structure Analysis of the 2,3-Dioxygenase Lapb From Pseudomonas in the Complex with 4-Methylcatechol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure Analysis of the 2,3-Dioxygenase Lapb From Pseudomonas in the Complex with 4-Methylcatechol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe310

b:31.1
occ:1.00
 O3 C:MCT311 1.9 51.7 1.0
O4 C:MCT311 2.1 50.2 1.0
OE1 C:GLU267 2.2 27.3 1.0
NE2 C:HIS216 2.3 22.0 1.0
NE2 C:HIS154 2.4 30.8 1.0
C3 C:MCT311 2.6 50.3 1.0
C4 C:MCT311 2.7 50.3 1.0
CD C:GLU267 2.9 27.4 1.0
OE2 C:GLU267 3.1 26.4 1.0
CE1 C:HIS216 3.2 20.9 1.0
CE1 C:HIS154 3.3 29.7 1.0
CD2 C:HIS154 3.4 30.1 1.0
CD2 C:HIS216 3.4 21.4 1.0
CB C:SER218 3.9 26.1 1.0
C2 C:MCT311 4.0 50.0 1.0
OG C:SER218 4.1 23.8 1.0
OH C:TYR257 4.1 30.7 1.0
C5 C:MCT311 4.1 50.0 1.0
NE2 C:HIS201 4.3 38.1 1.0
CG C:GLU267 4.3 24.6 1.0
ND1 C:HIS216 4.4 21.9 1.0
ND1 C:HIS154 4.4 30.0 1.0
CG C:HIS154 4.5 28.1 1.0
CG C:HIS216 4.5 20.6 1.0
CB C:GLU267 4.6 24.4 1.0
CE1 C:TYR257 4.6 29.9 1.0
CE1 C:HIS248 4.8 38.0 1.0
CZ C:TYR257 4.9 31.4 1.0
CE1 C:HIS201 5.0 38.8 1.0

Iron binding site 4 out of 4 in 3hpy

Go back to Iron Binding Sites List in 3hpy
Iron binding site 4 out of 4 in the Crystal Structure Analysis of the 2,3-Dioxygenase Lapb From Pseudomonas in the Complex with 4-Methylcatechol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure Analysis of the 2,3-Dioxygenase Lapb From Pseudomonas in the Complex with 4-Methylcatechol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe310

b:59.6
occ:1.00
 NE2 D:HIS154 2.0 22.3 1.0
NE2 D:HIS216 2.2 19.2 1.0
OE1 D:GLU267 2.4 33.1 1.0
CD2 D:HIS154 2.6 26.1 1.0
CE1 D:HIS216 3.0 20.5 1.0
CE1 D:HIS154 3.2 23.9 1.0
CD2 D:HIS216 3.2 22.5 1.0
CB D:SER218 3.2 22.4 1.0
CD D:GLU267 3.4 30.3 1.0
OG D:SER218 3.8 21.0 1.0
CG D:HIS154 3.8 26.6 1.0
OE2 D:GLU267 4.0 31.4 1.0
ND1 D:HIS154 4.0 27.1 1.0
ND1 D:HIS216 4.2 20.4 1.0
CG D:HIS216 4.3 22.3 1.0
CB D:GLU267 4.4 26.2 1.0
NE2 D:HIS201 4.4 36.3 1.0
CA D:SER218 4.5 21.9 1.0
CG D:GLU267 4.5 28.5 1.0
N D:SER218 4.6 22.4 1.0
CB D:LEU156 4.8 27.7 1.0
N D:LEU156 4.9 25.3 1.0
OH D:TYR257 5.0 31.3 1.0
C D:CYS155 5.0 26.9 1.0

Reference:

J.-H.Cho, D.-K.Jung, K.Lee, S.Rhee. Crystal Structure and Functional Analysis of the Extradiol Dioxygenase Lapb From A Long-Chain Alkylphenol Degradation Pathway in Pseudomonas J.Biol.Chem. V. 284 34321 2009.
ISSN: ISSN 0021-9258
PubMed: 19828456
DOI: 10.1074/JBC.M109.031054
Page generated: Sun Aug 4 11:42:54 2024

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