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Iron in PDB 4eb3: Crystal Structure of Isph in Complex with Iso-Hmbpp

Enzymatic activity of Crystal Structure of Isph in Complex with Iso-Hmbpp

All present enzymatic activity of Crystal Structure of Isph in Complex with Iso-Hmbpp:
1.17.1.2;

Protein crystallography data

The structure of Crystal Structure of Isph in Complex with Iso-Hmbpp, PDB code: 4eb3 was solved by W.Wang, K.Wang, I.Span, A.Bacher, M.Groll, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.580, 80.820, 113.050, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.8

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Isph in Complex with Iso-Hmbpp (pdb code 4eb3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Isph in Complex with Iso-Hmbpp, PDB code: 4eb3:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4eb3

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Iron binding site 1 out of 8 in the Crystal Structure of Isph in Complex with Iso-Hmbpp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Isph in Complex with Iso-Hmbpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:30.9
occ:1.00
 FE1 A:SF4401 0.0 30.9 1.0
O3 A:0O3402 1.8 30.5 1.0
S4 A:SF4401 2.3 20.1 1.0
S2 A:SF4401 2.3 17.9 1.0
S3 A:SF4401 2.4 18.8 1.0
C13 A:0O3402 2.7 37.5 1.0
FE2 A:SF4401 2.8 19.0 1.0
FE3 A:SF4401 2.8 18.0 1.0
FE4 A:SF4401 2.9 17.9 1.0
C27 A:0O3402 2.9 29.4 1.0
C30 A:0O3402 3.0 37.2 1.0
C28 A:0O3402 3.6 33.9 1.0
OG1 A:THR167 3.8 16.4 1.0
S1 A:SF4401 4.0 16.8 1.0
C1 A:0O3402 4.0 33.0 1.0
CG2 A:THR168 4.3 17.5 1.0
O A:HOH697 4.3 32.9 1.0
CB A:THR167 4.6 16.4 1.0
SG A:CYS197 4.6 16.3 1.0
CB A:CYS96 4.7 17.8 1.0
SG A:CYS96 4.8 18.3 1.0
O29 A:0O3402 4.9 37.9 1.0
CG2 A:VAL99 4.9 17.7 1.0
SG A:CYS12 4.9 17.0 1.0

Iron binding site 2 out of 8 in 4eb3

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Iron binding site 2 out of 8 in the Crystal Structure of Isph in Complex with Iso-Hmbpp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Isph in Complex with Iso-Hmbpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:19.0
occ:1.00
 FE2 A:SF4401 0.0 19.0 1.0
S3 A:SF4401 2.2 18.8 1.0
S4 A:SF4401 2.3 20.1 1.0
S1 A:SF4401 2.3 16.8 1.0
SG A:CYS197 2.3 16.3 1.0
FE4 A:SF4401 2.6 17.9 1.0
FE3 A:SF4401 2.7 18.0 1.0
FE1 A:SF4401 2.8 30.9 1.0
CB A:CYS197 3.2 16.5 1.0
S2 A:SF4401 3.8 17.9 1.0
CB A:ALA199 4.3 16.2 1.0
O3 A:0O3402 4.4 30.5 1.0
OG1 A:THR200 4.5 16.6 1.0
CA A:CYS197 4.6 16.5 1.0
SG A:CYS12 4.7 17.0 1.0
CD1 A:LEU98 4.7 19.2 1.0
CB A:THR167 4.7 16.4 1.0
OG1 A:THR167 4.8 16.4 1.0
SG A:CYS96 4.8 18.3 1.0
O A:HOH530 4.9 16.2 1.0
CB A:CYS12 4.9 17.0 1.0
N A:ALA199 5.0 16.3 1.0
CB A:LEU98 5.0 19.3 1.0

Iron binding site 3 out of 8 in 4eb3

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Iron binding site 3 out of 8 in the Crystal Structure of Isph in Complex with Iso-Hmbpp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Isph in Complex with Iso-Hmbpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:18.0
occ:1.00
 FE3 A:SF4401 0.0 18.0 1.0
S4 A:SF4401 2.2 20.1 1.0
SG A:CYS96 2.3 18.3 1.0
S1 A:SF4401 2.3 16.8 1.0
S2 A:SF4401 2.3 17.9 1.0
FE2 A:SF4401 2.7 19.0 1.0
FE4 A:SF4401 2.7 17.9 1.0
FE1 A:SF4401 2.8 30.9 1.0
CB A:CYS96 3.1 17.8 1.0
S3 A:SF4401 3.9 18.8 1.0
CA A:GLY14 4.0 16.8 1.0
CB A:LEU98 4.2 19.3 1.0
O3 A:0O3402 4.2 30.5 1.0
N A:GLY14 4.4 16.9 1.0
CD1 A:LEU98 4.5 19.2 1.0
CA A:CYS96 4.5 17.8 1.0
C13 A:0O3402 4.6 37.5 1.0
SG A:CYS12 4.6 17.0 1.0
CG A:LEU98 4.7 19.6 1.0
SG A:CYS197 4.9 16.3 1.0
C30 A:0O3402 5.0 37.2 1.0

Iron binding site 4 out of 8 in 4eb3

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Iron binding site 4 out of 8 in the Crystal Structure of Isph in Complex with Iso-Hmbpp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Isph in Complex with Iso-Hmbpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:17.9
occ:1.00
 FE4 A:SF4401 0.0 17.9 1.0
SG A:CYS12 2.2 17.0 1.0
S3 A:SF4401 2.3 18.8 1.0
S2 A:SF4401 2.3 17.9 1.0
S1 A:SF4401 2.3 16.8 1.0
FE2 A:SF4401 2.6 19.0 1.0
FE3 A:SF4401 2.7 18.0 1.0
FE1 A:SF4401 2.9 30.9 1.0
CB A:CYS12 3.3 17.0 1.0
S4 A:SF4401 3.8 20.1 1.0
C28 A:0O3402 4.0 33.9 1.0
N A:GLY14 4.2 16.9 1.0
N A:VAL15 4.4 16.9 1.0
CA A:GLY14 4.4 16.8 1.0
C27 A:0O3402 4.4 29.4 1.0
CB A:ALA268 4.4 17.6 1.0
CG2 A:VAL15 4.5 17.4 1.0
C30 A:0O3402 4.5 37.2 1.0
O3 A:0O3402 4.6 30.5 1.0
CA A:CYS12 4.6 17.0 1.0
CB A:ALA199 4.6 16.2 1.0
SG A:CYS197 4.7 16.3 1.0
SG A:CYS96 4.7 18.3 1.0
C1 A:0O3402 4.8 33.0 1.0
C A:GLY14 4.8 16.8 1.0
C A:CYS12 4.9 16.9 1.0
C13 A:0O3402 4.9 37.5 1.0

Iron binding site 5 out of 8 in 4eb3

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Iron binding site 5 out of 8 in the Crystal Structure of Isph in Complex with Iso-Hmbpp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Isph in Complex with Iso-Hmbpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:31.6
occ:1.00
 FE1 B:SF4401 0.0 31.6 1.0
O3 B:0O3402 1.9 34.6 1.0
S4 B:SF4401 2.2 19.1 1.0
S2 B:SF4401 2.3 19.4 1.0
S3 B:SF4401 2.4 21.8 1.0
C13 B:0O3402 2.7 41.6 1.0
FE2 B:SF4401 2.7 20.1 1.0
FE3 B:SF4401 2.7 19.2 1.0
FE4 B:SF4401 2.8 18.6 1.0
C27 B:0O3402 2.9 32.1 1.0
C30 B:0O3402 3.1 41.5 1.0
C28 B:0O3402 3.7 36.1 1.0
OG1 B:THR167 3.8 17.2 1.0
S1 B:SF4401 4.0 18.1 1.0
C1 B:0O3402 4.1 43.1 1.0
CG2 B:THR168 4.3 18.1 1.0
O B:HOH685 4.5 37.4 1.0
SG B:CYS197 4.7 17.9 1.0
CB B:THR167 4.7 17.4 1.0
CB B:CYS96 4.7 17.9 1.0
SG B:CYS96 4.7 19.4 1.0
CG2 B:VAL99 4.9 18.0 1.0
SG B:CYS12 4.9 15.6 1.0

Iron binding site 6 out of 8 in 4eb3

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Iron binding site 6 out of 8 in the Crystal Structure of Isph in Complex with Iso-Hmbpp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Isph in Complex with Iso-Hmbpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:20.1
occ:1.00
 FE2 B:SF4401 0.0 20.1 1.0
S4 B:SF4401 2.3 19.1 1.0
S3 B:SF4401 2.3 21.8 1.0
S1 B:SF4401 2.3 18.1 1.0
SG B:CYS197 2.3 17.9 1.0
FE4 B:SF4401 2.7 18.6 1.0
FE1 B:SF4401 2.7 31.6 1.0
FE3 B:SF4401 2.7 19.2 1.0
CB B:CYS197 3.2 17.8 1.0
S2 B:SF4401 3.8 19.4 1.0
CB B:ALA199 4.2 17.1 1.0
O3 B:0O3402 4.4 34.6 1.0
OG1 B:THR200 4.6 16.7 1.0
CA B:CYS197 4.6 17.8 1.0
CD1 B:LEU98 4.7 19.5 1.0
SG B:CYS12 4.7 15.6 1.0
OG1 B:THR167 4.7 17.2 1.0
CB B:THR167 4.8 17.4 1.0
O B:HOH536 4.9 18.3 1.0
SG B:CYS96 4.9 19.4 1.0
N B:ALA199 5.0 17.1 1.0
CB B:CYS12 5.0 16.2 1.0

Iron binding site 7 out of 8 in 4eb3

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Iron binding site 7 out of 8 in the Crystal Structure of Isph in Complex with Iso-Hmbpp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Isph in Complex with Iso-Hmbpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:19.2
occ:1.00
 FE3 B:SF4401 0.0 19.2 1.0
S4 B:SF4401 2.3 19.1 1.0
S2 B:SF4401 2.3 19.4 1.0
S1 B:SF4401 2.3 18.1 1.0
SG B:CYS96 2.3 19.4 1.0
FE4 B:SF4401 2.7 18.6 1.0
FE2 B:SF4401 2.7 20.1 1.0
FE1 B:SF4401 2.7 31.6 1.0
CB B:CYS96 3.1 17.9 1.0
S3 B:SF4401 3.9 21.8 1.0
CA B:GLY14 4.0 16.9 1.0
O3 B:0O3402 4.2 34.6 1.0
CB B:LEU98 4.4 18.9 1.0
N B:GLY14 4.4 17.1 1.0
CD1 B:LEU98 4.4 19.5 1.0
CA B:CYS96 4.6 17.9 1.0
C13 B:0O3402 4.6 41.6 1.0
SG B:CYS12 4.6 15.6 1.0
CG B:LEU98 4.7 19.7 1.0
SG B:CYS197 4.9 17.9 1.0
C B:GLY14 5.0 16.9 1.0
N B:LEU98 5.0 18.4 1.0

Iron binding site 8 out of 8 in 4eb3

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Iron binding site 8 out of 8 in the Crystal Structure of Isph in Complex with Iso-Hmbpp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Isph in Complex with Iso-Hmbpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:18.6
occ:1.00
 FE4 B:SF4401 0.0 18.6 1.0
SG B:CYS12 2.2 15.6 1.0
S3 B:SF4401 2.2 21.8 1.0
S2 B:SF4401 2.3 19.4 1.0
S1 B:SF4401 2.3 18.1 1.0
FE2 B:SF4401 2.7 20.1 1.0
FE3 B:SF4401 2.7 19.2 1.0
FE1 B:SF4401 2.8 31.6 1.0
CB B:CYS12 3.2 16.2 1.0
S4 B:SF4401 3.8 19.1 1.0
C28 B:0O3402 4.1 36.1 1.0
N B:GLY14 4.2 17.1 1.0
N B:VAL15 4.3 16.8 1.0
CA B:GLY14 4.3 16.9 1.0
CB B:ALA268 4.4 18.7 1.0
C27 B:0O3402 4.4 32.1 1.0
CG2 B:VAL15 4.4 16.4 1.0
CB B:ALA199 4.6 17.1 1.0
O3 B:0O3402 4.6 34.6 1.0
CA B:CYS12 4.7 16.6 1.0
C30 B:0O3402 4.7 41.5 1.0
SG B:CYS197 4.7 17.9 1.0
C B:GLY14 4.8 16.9 1.0
SG B:CYS96 4.8 19.4 1.0
C B:CYS12 4.9 16.8 1.0
C13 B:0O3402 5.0 41.6 1.0

Reference:

W.Wang, K.Wang, I.Span, J.Jauch, A.Bacher, M.Groll, E.Oldfield. Are Free Radicals Involved in Isph Catalysis? An Epr and Crystallographic Investigation. J.Am.Chem.Soc. V. 134 11225 2012.
ISSN: ISSN 0002-7863
PubMed: 22687151
DOI: 10.1021/JA303445Z
Page generated: Mon Aug 5 01:30:42 2024

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