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Iron in PDB 3ke8: Crystal Structure of Isph:Hmbpp-Complex

Enzymatic activity of Crystal Structure of Isph:Hmbpp-Complex

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

Protein crystallography data

The structure of Crystal Structure of Isph:Hmbpp-Complex, PDB code: 3ke8 was solved by M.Groll, T.Graewert, I.Span, W.Eisenreich, A.Bacher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 9.99 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.890, 80.660, 111.160, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 26.9

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Isph:Hmbpp-Complex (pdb code 3ke8). 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:Hmbpp-Complex, PDB code: 3ke8:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3ke8

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


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:Hmbpp-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe997

b:12.5
occ:1.00
 FE1 A:SF4997 0.0 12.5 1.0
S2 A:SF4997 2.2 13.3 1.0
SG A:CYS96 2.3 10.9 1.0
S4 A:SF4997 2.3 11.0 1.0
S3 A:SF4997 2.3 10.9 1.0
FE2 A:SF4997 2.7 12.0 1.0
FE3 A:SF4997 2.7 14.2 1.0
FE4 A:SF4997 2.8 14.6 1.0
CB A:CYS96 3.2 10.9 1.0
S1 A:SF4997 3.9 10.4 1.0
CA A:GLY14 4.0 12.6 1.0
CB A:LEU98 4.2 14.4 1.0
CD2 A:LEU98 4.3 17.0 1.0
N A:GLY14 4.3 12.6 1.0
O15 A:EIP998 4.4 7.7 1.0
CA A:CYS96 4.6 11.6 1.0
SG A:CYS12 4.7 12.1 1.0
SG A:CYS197 4.9 12.2 1.0
CG A:LEU98 4.9 19.5 1.0
N A:LEU98 4.9 13.2 1.0
C A:GLY14 5.0 12.9 1.0
CE1 A:PHE302 5.0 14.3 1.0

Iron binding site 2 out of 8 in 3ke8

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


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:Hmbpp-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe997

b:12.0
occ:1.00
 FE2 A:SF4997 0.0 12.0 1.0
S4 A:SF4997 2.2 11.0 1.0
S3 A:SF4997 2.2 10.9 1.0
S1 A:SF4997 2.2 10.4 1.0
SG A:CYS12 2.3 12.1 1.0
FE1 A:SF4997 2.7 12.5 1.0
FE3 A:SF4997 2.7 14.2 1.0
FE4 A:SF4997 2.8 14.6 1.0
CB A:CYS12 3.3 10.5 1.0
S2 A:SF4997 3.8 13.3 1.0
N A:GLY14 4.2 12.6 1.0
CA A:GLY14 4.3 12.6 1.0
N A:VAL15 4.3 12.3 1.0
C10 A:EIP998 4.3 13.3 1.0
C11 A:EIP998 4.4 11.5 1.0
CB A:ALA268 4.6 11.9 1.0
CB A:ALA199 4.6 11.2 1.0
CG2 A:VAL15 4.6 12.0 1.0
CA A:CYS12 4.7 11.3 1.0
SG A:CYS96 4.7 10.9 1.0
C A:GLY14 4.7 12.9 1.0
SG A:CYS197 4.7 12.2 1.0
C12 A:EIP998 4.8 10.0 1.0
O15 A:EIP998 4.9 7.7 1.0
C A:CYS12 4.9 12.0 1.0
O A:HOH379 5.0 13.5 1.0

Iron binding site 3 out of 8 in 3ke8

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


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:Hmbpp-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe997

b:14.2
occ:1.00
 FE3 A:SF4997 0.0 14.2 1.0
SG A:CYS197 2.3 12.2 1.0
S2 A:SF4997 2.3 13.3 1.0
S4 A:SF4997 2.3 11.0 1.0
S1 A:SF4997 2.3 10.4 1.0
FE2 A:SF4997 2.7 12.0 1.0
FE1 A:SF4997 2.7 12.5 1.0
FE4 A:SF4997 2.8 14.6 1.0
CB A:CYS197 3.2 12.4 1.0
S3 A:SF4997 3.9 10.9 1.0
CB A:ALA199 4.1 11.2 1.0
CD2 A:LEU98 4.5 17.0 1.0
O15 A:EIP998 4.5 7.7 1.0
CA A:CYS197 4.6 11.9 1.0
OG1 A:THR200 4.7 13.2 1.0
O A:HOH379 4.7 13.5 1.0
SG A:CYS12 4.7 12.1 1.0
CB A:THR167 4.8 11.4 1.0
OG1 A:THR167 4.8 12.8 1.0
SG A:CYS96 4.9 10.9 1.0
N A:ALA199 4.9 12.7 1.0
CB A:LEU98 4.9 14.4 1.0

Iron binding site 4 out of 8 in 3ke8

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


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:Hmbpp-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe997

b:14.6
occ:1.00
 FE4 A:SF4997 0.0 14.6 1.0
O15 A:EIP998 2.1 7.7 1.0
S1 A:SF4997 2.3 10.4 1.0
S2 A:SF4997 2.4 13.3 1.0
S3 A:SF4997 2.4 10.9 1.0
FE3 A:SF4997 2.8 14.2 1.0
FE2 A:SF4997 2.8 12.0 1.0
FE1 A:SF4997 2.8 12.5 1.0
C12 A:EIP998 2.9 10.0 1.0
C13 A:EIP998 3.0 11.9 1.0
C11 A:EIP998 3.0 11.5 1.0
C14 A:EIP998 3.7 10.2 1.0
OG1 A:THR167 3.8 12.8 1.0
S4 A:SF4997 3.9 11.0 1.0
C10 A:EIP998 4.0 13.3 1.0
CG2 A:THR168 4.6 11.5 1.0
CB A:THR167 4.6 11.4 1.0
SG A:CYS197 4.6 12.2 1.0
CB A:CYS96 4.6 10.9 1.0
SG A:CYS96 4.7 10.9 1.0
CG2 A:VAL99 4.7 10.5 1.0
SG A:CYS12 4.9 12.1 1.0

Iron binding site 5 out of 8 in 3ke8

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


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:Hmbpp-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe997

b:13.8
occ:1.00
 FE1 B:SF4997 0.0 13.8 1.0
S2 B:SF4997 2.2 13.4 1.0
SG B:CYS96 2.3 12.9 1.0
S4 B:SF4997 2.3 12.7 1.0
S3 B:SF4997 2.3 12.9 1.0
FE2 B:SF4997 2.7 11.8 1.0
FE3 B:SF4997 2.7 13.7 1.0
FE4 B:SF4997 2.8 15.1 1.0
CB B:CYS96 3.2 8.7 1.0
S1 B:SF4997 3.9 13.4 1.0
CA B:GLY14 4.0 11.9 1.0
CD2 B:LEU98 4.0 21.5 1.0
CB B:LEU98 4.1 17.7 1.0
N B:GLY14 4.2 12.9 1.0
O15 B:EIP998 4.3 8.1 1.0
CA B:CYS96 4.6 11.5 1.0
SG B:CYS12 4.7 12.1 1.0
CG B:LEU98 4.7 22.1 1.0
SG B:CYS197 4.9 12.3 1.0
N B:LEU98 4.9 13.3 1.0

Iron binding site 6 out of 8 in 3ke8

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


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:Hmbpp-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe997

b:11.8
occ:1.00
 FE2 B:SF4997 0.0 11.8 1.0
S4 B:SF4997 2.2 12.7 1.0
S3 B:SF4997 2.2 12.9 1.0
S1 B:SF4997 2.2 13.4 1.0
SG B:CYS12 2.3 12.1 1.0
FE1 B:SF4997 2.7 13.8 1.0
FE3 B:SF4997 2.7 13.7 1.0
FE4 B:SF4997 2.8 15.1 1.0
CB B:CYS12 3.3 12.9 1.0
S2 B:SF4997 3.8 13.4 1.0
N B:GLY14 4.2 12.9 1.0
CA B:GLY14 4.3 11.9 1.0
C10 B:EIP998 4.3 14.8 1.0
N B:VAL15 4.3 12.3 1.0
C11 B:EIP998 4.4 14.3 1.0
CG2 B:VAL15 4.5 11.3 1.0
CB B:ALA268 4.6 12.1 1.0
CB B:ALA199 4.6 13.3 1.0
CA B:CYS12 4.7 13.1 1.0
SG B:CYS96 4.7 12.9 1.0
C B:GLY14 4.7 12.2 1.0
SG B:CYS197 4.7 12.3 1.0
O15 B:EIP998 4.8 8.1 1.0
C12 B:EIP998 4.8 11.7 1.0
C B:CYS12 4.9 12.4 1.0
N B:ALA13 5.0 11.7 1.0
O B:HOH346 5.0 12.6 1.0

Iron binding site 7 out of 8 in 3ke8

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


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:Hmbpp-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe997

b:13.7
occ:1.00
 FE3 B:SF4997 0.0 13.7 1.0
S2 B:SF4997 2.3 13.4 1.0
SG B:CYS197 2.3 12.3 1.0
S4 B:SF4997 2.3 12.7 1.0
S1 B:SF4997 2.3 13.4 1.0
FE2 B:SF4997 2.7 11.8 1.0
FE1 B:SF4997 2.7 13.8 1.0
FE4 B:SF4997 2.8 15.1 1.0
CB B:CYS197 3.1 12.8 1.0
S3 B:SF4997 3.9 12.9 1.0
CB B:ALA199 4.2 13.3 1.0
CD2 B:LEU98 4.3 21.5 1.0
O15 B:EIP998 4.4 8.1 1.0
CA B:CYS197 4.6 12.6 1.0
OG1 B:THR200 4.6 12.1 1.0
O B:HOH346 4.7 12.6 1.0
SG B:CYS12 4.7 12.1 1.0
CB B:THR167 4.8 11.9 1.0
OG1 B:THR167 4.8 11.9 1.0
SG B:CYS96 4.9 12.9 1.0
N B:ALA199 4.9 14.2 1.0
CB B:LEU98 4.9 17.7 1.0

Iron binding site 8 out of 8 in 3ke8

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


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:Hmbpp-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe997

b:15.1
occ:1.00
 FE4 B:SF4997 0.0 15.1 1.0
O15 B:EIP998 2.0 8.1 1.0
S1 B:SF4997 2.3 13.4 1.0
S2 B:SF4997 2.4 13.4 1.0
S3 B:SF4997 2.4 12.9 1.0
FE3 B:SF4997 2.8 13.7 1.0
FE2 B:SF4997 2.8 11.8 1.0
FE1 B:SF4997 2.8 13.8 1.0
C12 B:EIP998 2.9 11.7 1.0
C13 B:EIP998 3.0 14.1 1.0
C11 B:EIP998 3.0 14.3 1.0
C14 B:EIP998 3.7 12.4 1.0
OG1 B:THR167 3.9 11.9 1.0
S4 B:SF4997 3.9 12.7 1.0
C10 B:EIP998 3.9 14.8 1.0
CG2 B:THR168 4.6 7.6 1.0
CB B:CYS96 4.6 8.7 1.0
CB B:THR167 4.6 11.9 1.0
SG B:CYS197 4.7 12.3 1.0
SG B:CYS96 4.7 12.9 1.0
CG2 B:VAL99 4.7 12.6 1.0
SG B:CYS12 4.9 12.1 1.0

Reference:

T.Grawert, I.Span, W.Eisenreich, F.Rohdich, J.Eppinger, A.Bacher, M.Groll. Probing the Reaction Mechanism of Isph Protein By X-Ray Structure Analysis. Proc.Natl.Acad.Sci.Usa V. 107 1077 2010.
ISSN: ISSN 0027-8424
PubMed: 20080550
DOI: 10.1073/PNAS.0913045107
Page generated: Sun Aug 4 13:54:23 2024

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