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Iron in PDB 3t0f: Isph:Hmbpp (Substrate) Structure of the E126D Mutant

Enzymatic activity of Isph:Hmbpp (Substrate) Structure of the E126D Mutant

All present enzymatic activity of Isph:Hmbpp (Substrate) Structure of the E126D Mutant:
1.17.1.2;

Protein crystallography data

The structure of Isph:Hmbpp (Substrate) Structure of the E126D Mutant, PDB code: 3t0f was solved by I.Span, T.Graewert, A.Bacher, W.Eisenreich, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.850, 80.180, 114.510, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24.2

Iron Binding Sites:

The binding sites of Iron atom in the Isph:Hmbpp (Substrate) Structure of the E126D Mutant (pdb code 3t0f). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Isph:Hmbpp (Substrate) Structure of the E126D Mutant, PDB code: 3t0f:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3t0f

Go back to Iron Binding Sites List in 3t0f
Iron binding site 1 out of 6 in the Isph:Hmbpp (Substrate) Structure of the E126D Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Isph:Hmbpp (Substrate) Structure of the E126D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe317

b:2.0
occ:1.00
 FE1 A:F3S317 0.0 2.0 1.0
S2 A:F3S317 2.3 2.0 1.0
S3 A:F3S317 2.3 2.0 1.0
S1 A:F3S317 2.3 2.4 1.0
SG A:CYS12 2.3 2.2 1.0
FE3 A:F3S317 2.6 2.1 1.0
FE4 A:F3S317 2.7 2.0 1.0
CB A:CYS12 3.2 2.0 1.0
S4 A:F3S317 3.9 2.7 1.0
N A:GLY14 4.3 2.0 1.0
N A:VAL15 4.3 2.0 1.0
C28 A:H6P998 4.3 14.5 1.0
C27 A:H6P998 4.3 14.1 1.0
CA A:GLY14 4.4 2.0 1.0
CG2 A:VAL15 4.5 2.2 1.0
CB A:ALA268 4.5 2.0 1.0
CA A:CYS12 4.6 2.0 1.0
SG A:CYS197 4.6 2.0 1.0
CB A:ALA199 4.6 2.0 1.0
C30 A:H6P998 4.8 17.5 1.0
C A:GLY14 4.8 2.0 1.0
SG A:CYS96 4.8 2.0 1.0
C A:CYS12 4.9 2.0 1.0
O A:HOH329 5.0 7.6 1.0
N A:ALA13 5.0 2.0 1.0

Iron binding site 2 out of 6 in 3t0f

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Iron binding site 2 out of 6 in the Isph:Hmbpp (Substrate) Structure of the E126D Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Isph:Hmbpp (Substrate) Structure of the E126D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe317

b:2.1
occ:1.00
 FE3 A:F3S317 0.0 2.1 1.0
S1 A:F3S317 2.3 2.4 1.0
S4 A:F3S317 2.3 2.7 1.0
S3 A:F3S317 2.4 2.0 1.0
SG A:CYS197 2.4 2.0 1.0
FE1 A:F3S317 2.6 2.0 1.0
FE4 A:F3S317 2.7 2.0 1.0
CB A:CYS197 3.2 2.0 1.0
S2 A:F3S317 3.8 2.0 1.0
CB A:ALA199 4.5 2.0 1.0
OG1 A:THR200 4.5 2.6 1.0
OG1 A:THR167 4.6 2.0 1.0
O A:HOH329 4.6 7.6 1.0
CD2 A:LEU98 4.7 5.2 1.0
CA A:CYS197 4.7 2.0 1.0
CB A:THR167 4.7 2.0 1.0
SG A:CYS12 4.7 2.2 1.0
SG A:CYS96 4.9 2.0 1.0
C31 A:H6P998 4.9 20.0 1.0
CB A:CYS12 5.0 2.0 1.0
O A:THR167 5.0 2.0 1.0
C27 A:H6P998 5.0 14.1 1.0

Iron binding site 3 out of 6 in 3t0f

Go back to Iron Binding Sites List in 3t0f
Iron binding site 3 out of 6 in the Isph:Hmbpp (Substrate) Structure of the E126D Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Isph:Hmbpp (Substrate) Structure of the E126D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe317

b:2.0
occ:1.00
 FE4 A:F3S317 0.0 2.0 1.0
S4 A:F3S317 2.3 2.7 1.0
S2 A:F3S317 2.3 2.0 1.0
SG A:CYS96 2.3 2.0 1.0
S3 A:F3S317 2.3 2.0 1.0
FE1 A:F3S317 2.7 2.0 1.0
FE3 A:F3S317 2.7 2.1 1.0
CB A:CYS96 3.0 2.0 1.0
S1 A:F3S317 4.1 2.4 1.0
CA A:GLY14 4.1 2.0 1.0
CB A:LEU98 4.2 2.0 1.0
CD2 A:LEU98 4.4 5.2 1.0
N A:GLY14 4.5 2.0 1.0
CA A:CYS96 4.5 2.0 1.0
SG A:CYS12 4.7 2.2 1.0
C31 A:H6P998 4.8 20.0 1.0
C30 A:H6P998 4.8 17.5 1.0
SG A:CYS197 4.9 2.0 1.0
CG A:LEU98 4.9 5.4 1.0
N A:LEU98 5.0 2.0 1.0
C A:GLY14 5.0 2.0 1.0

Iron binding site 4 out of 6 in 3t0f

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Iron binding site 4 out of 6 in the Isph:Hmbpp (Substrate) Structure of the E126D Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Isph:Hmbpp (Substrate) Structure of the E126D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe317

b:2.0
occ:1.00
 FE1 B:F3S317 0.0 2.0 1.0
S2 B:F3S317 2.2 3.2 1.0
SG B:CYS12 2.2 2.4 1.0
S3 B:F3S317 2.3 2.8 1.0
S1 B:F3S317 2.3 3.2 1.0
FE3 B:F3S317 2.6 2.0 1.0
FE4 B:F3S317 2.7 2.5 1.0
CB B:CYS12 3.2 2.0 1.0
S4 B:F3S317 3.9 2.0 1.0
N B:GLY14 4.2 2.0 1.0
N B:VAL15 4.2 2.0 1.0
CG2 B:VAL15 4.3 2.9 1.0
CA B:GLY14 4.4 2.0 1.0
C27 B:H6P998 4.4 11.2 1.0
C28 B:H6P998 4.4 13.6 1.0
CB B:ALA268 4.5 2.0 1.0
CB B:ALA199 4.5 3.6 1.0
CA B:CYS12 4.6 2.3 1.0
C30 B:H6P998 4.7 11.1 1.0
SG B:CYS197 4.7 2.0 1.0
SG B:CYS96 4.8 2.7 1.0
C B:GLY14 4.8 2.0 1.0
C B:CYS12 4.8 2.0 1.0
O B:HOH346 5.0 7.9 1.0

Iron binding site 5 out of 6 in 3t0f

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Iron binding site 5 out of 6 in the Isph:Hmbpp (Substrate) Structure of the E126D Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Isph:Hmbpp (Substrate) Structure of the E126D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe317

b:2.0
occ:1.00
 FE3 B:F3S317 0.0 2.0 1.0
S1 B:F3S317 2.3 3.2 1.0
S4 B:F3S317 2.3 2.0 1.0
S3 B:F3S317 2.3 2.8 1.0
SG B:CYS197 2.4 2.0 1.0
FE1 B:F3S317 2.6 2.0 1.0
FE4 B:F3S317 2.7 2.5 1.0
CB B:CYS197 3.2 2.0 1.0
S2 B:F3S317 3.8 3.2 1.0
CB B:ALA199 4.3 3.6 1.0
OG1 B:THR200 4.5 2.0 1.0
O B:HOH346 4.6 7.9 1.0
CA B:CYS197 4.7 2.0 1.0
SG B:CYS12 4.7 2.4 1.0
CB B:THR167 4.7 2.1 1.0
OG1 B:THR167 4.8 2.0 1.0
O B:THR167 4.9 2.6 1.0
C31 B:H6P998 4.9 10.5 1.0
SG B:CYS96 4.9 2.7 1.0
CD2 B:LEU98 4.9 3.5 1.0
C27 B:H6P998 5.0 11.2 1.0
N B:ALA199 5.0 2.3 1.0
N B:THR200 5.0 2.1 1.0

Iron binding site 6 out of 6 in 3t0f

Go back to Iron Binding Sites List in 3t0f
Iron binding site 6 out of 6 in the Isph:Hmbpp (Substrate) Structure of the E126D Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Isph:Hmbpp (Substrate) Structure of the E126D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe317

b:2.5
occ:1.00
 FE4 B:F3S317 0.0 2.5 1.0
S4 B:F3S317 2.2 2.0 1.0
S2 B:F3S317 2.3 3.2 1.0
S3 B:F3S317 2.3 2.8 1.0
SG B:CYS96 2.3 2.7 1.0
FE1 B:F3S317 2.7 2.0 1.0
FE3 B:F3S317 2.7 2.0 1.0
CB B:CYS96 3.1 2.0 1.0
S1 B:F3S317 4.0 3.2 1.0
CA B:GLY14 4.1 2.0 1.0
CB B:LEU98 4.4 3.4 1.0
N B:GLY14 4.5 2.0 1.0
CA B:CYS96 4.5 2.0 1.0
CD2 B:LEU98 4.6 3.5 1.0
SG B:CYS12 4.7 2.4 1.0
C31 B:H6P998 4.7 10.5 1.0
C30 B:H6P998 4.7 11.1 1.0
C21 B:H6P998 4.8 14.4 1.0
SG B:CYS197 4.9 2.0 1.0
CG2 B:VAL99 5.0 4.2 1.0
C B:GLY14 5.0 2.0 1.0

Reference:

I.Span, T.Grawert, A.Bacher, W.Eisenreich, M.Groll. Crystal Structures of Mutant Isph Proteins Reveal A Rotation of the Substrate'S Hydroxymethyl Group During Catalysis. J.Mol.Biol. V. 416 1 2012.
ISSN: ISSN 0022-2836
PubMed: 22137895
DOI: 10.1016/J.JMB.2011.11.033
Page generated: Sun Aug 4 20:12:30 2024

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