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Iron in PDB 3kef: Crystal Structure of Isph:Dmapp-Complex

Enzymatic activity of Crystal Structure of Isph:Dmapp-Complex

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

Protein crystallography data

The structure of Crystal Structure of Isph:Dmapp-Complex, PDB code: 3kef 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) 10.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.120, 80.380, 110.840, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 23.7

Iron Binding Sites:

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

Iron binding site 1 out of 6 in 3kef

Go back to Iron Binding Sites List in 3kef
Iron binding site 1 out of 6 in the Crystal Structure of Isph:Dmapp-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:Dmapp-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe997

b:11.4
occ:1.00
FE1 A:F3S997 0.0 11.4 1.0
S3 A:F3S997 2.1 14.1 1.0
S1 A:F3S997 2.2 14.9 1.0
S2 A:F3S997 2.2 15.3 1.0
SG A:CYS197 2.3 11.3 1.0
FE3 A:F3S997 2.7 10.3 1.0
FE4 A:F3S997 2.7 12.1 1.0
CB A:CYS197 3.2 11.4 1.0
S4 A:F3S997 3.9 14.2 1.0
C4 A:DMA998 4.0 24.2 1.0
CB A:ALA199 4.3 10.8 1.0
OG1 A:THR200 4.5 11.4 1.0
OG1 A:THR167 4.5 13.0 1.0
CD1 A:LEU98 4.6 13.2 1.0
C3 A:DMA998 4.6 25.7 1.0
CA A:CYS197 4.7 10.2 1.0
C2 A:DMA998 4.7 23.9 1.0
CB A:THR167 4.7 13.5 1.0
SG A:CYS12 4.7 11.1 1.0
O A:HOH341 4.8 13.1 1.0
SG A:CYS96 4.9 11.0 1.0

Iron binding site 2 out of 6 in 3kef

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Iron binding site 2 out of 6 in the Crystal Structure of Isph:Dmapp-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:Dmapp-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe997

b:10.3
occ:1.00
FE3 A:F3S997 0.0 10.3 1.0
S4 A:F3S997 2.2 14.2 1.0
S3 A:F3S997 2.2 14.1 1.0
S1 A:F3S997 2.2 14.9 1.0
SG A:CYS12 2.3 11.1 1.0
FE1 A:F3S997 2.7 11.4 1.0
FE4 A:F3S997 2.8 12.1 1.0
CB A:CYS12 3.3 11.2 1.0
C2 A:DMA998 3.7 23.9 1.0
S2 A:F3S997 4.0 15.3 1.0
C3 A:DMA998 4.1 25.7 1.0
C1 A:DMA998 4.1 21.5 1.0
N A:GLY14 4.2 11.0 1.0
CB A:ALA268 4.3 12.1 1.0
N A:VAL15 4.3 11.2 1.0
CA A:GLY14 4.4 11.3 1.0
C4 A:DMA998 4.4 24.2 1.0
CG2 A:VAL15 4.5 10.2 1.0
CB A:ALA199 4.6 10.8 1.0
CA A:CYS12 4.7 11.0 1.0
SG A:CYS197 4.7 11.3 1.0
C A:GLY14 4.8 10.9 1.0
SG A:CYS96 4.8 11.0 1.0
C5 A:DMA998 4.9 25.0 1.0
C A:CYS12 4.9 11.7 1.0
N A:ALA13 5.0 10.8 1.0

Iron binding site 3 out of 6 in 3kef

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Iron binding site 3 out of 6 in the Crystal Structure of Isph:Dmapp-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:Dmapp-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe997

b:12.1
occ:1.00
FE4 A:F3S997 0.0 12.1 1.0
S3 A:F3S997 2.1 14.1 1.0
S4 A:F3S997 2.2 14.2 1.0
S2 A:F3S997 2.2 15.3 1.0
SG A:CYS96 2.3 11.0 1.0
FE1 A:F3S997 2.7 11.4 1.0
FE3 A:F3S997 2.8 10.3 1.0
CB A:CYS96 3.1 10.5 1.0
S1 A:F3S997 4.1 14.9 1.0
CA A:GLY14 4.1 11.3 1.0
C4 A:DMA998 4.1 24.2 1.0
CB A:LEU98 4.3 11.2 1.0
C3 A:DMA998 4.3 25.7 1.0
CD1 A:LEU98 4.4 13.2 1.0
N A:GLY14 4.4 11.0 1.0
CA A:CYS96 4.6 10.3 1.0
CG A:LEU98 4.6 13.2 1.0
C5 A:DMA998 4.7 25.0 1.0
SG A:CYS12 4.7 11.1 1.0
C2 A:DMA998 4.8 23.9 1.0
SG A:CYS197 4.9 11.3 1.0
N A:LEU98 5.0 12.4 1.0

Iron binding site 4 out of 6 in 3kef

Go back to Iron Binding Sites List in 3kef
Iron binding site 4 out of 6 in the Crystal Structure of Isph:Dmapp-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:Dmapp-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe997

b:11.4
occ:1.00
FE1 B:F3S997 0.0 11.4 1.0
S3 B:F3S997 2.1 13.7 1.0
S1 B:F3S997 2.2 16.0 1.0
S2 B:F3S997 2.2 14.1 1.0
SG B:CYS197 2.3 11.3 1.0
FE3 B:F3S997 2.7 10.7 1.0
FE4 B:F3S997 2.8 11.1 1.0
CB B:CYS197 3.2 12.3 1.0
S4 B:F3S997 3.9 14.5 1.0
CB B:ALA199 4.2 11.4 1.0
C4 B:DMA998 4.3 22.7 1.0
OG1 B:THR200 4.5 11.8 1.0
OG1 B:THR167 4.5 12.6 1.0
CA B:CYS197 4.7 10.8 1.0
CB B:THR167 4.7 12.5 1.0
CD1 B:LEU98 4.7 12.2 1.0
C3 B:DMA998 4.7 23.4 1.0
C2 B:DMA998 4.7 22.3 1.0
SG B:CYS12 4.8 11.0 1.0
O B:HOH333 4.8 14.2 1.0
SG B:CYS96 4.9 10.2 1.0

Iron binding site 5 out of 6 in 3kef

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Iron binding site 5 out of 6 in the Crystal Structure of Isph:Dmapp-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:Dmapp-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe997

b:10.7
occ:1.00
FE3 B:F3S997 0.0 10.7 1.0
S4 B:F3S997 2.2 14.5 1.0
S3 B:F3S997 2.2 13.7 1.0
S1 B:F3S997 2.2 16.0 1.0
SG B:CYS12 2.3 11.0 1.0
FE1 B:F3S997 2.7 11.4 1.0
FE4 B:F3S997 2.8 11.1 1.0
CB B:CYS12 3.3 11.5 1.0
C2 B:DMA998 3.8 22.3 1.0
S2 B:F3S997 4.0 14.1 1.0
C1 B:DMA998 4.2 20.8 1.0
N B:GLY14 4.2 11.2 1.0
C3 B:DMA998 4.2 23.4 1.0
CB B:ALA268 4.3 9.2 1.0
CA B:GLY14 4.3 10.8 1.0
N B:VAL15 4.3 10.5 1.0
CG2 B:VAL15 4.5 9.8 1.0
CB B:ALA199 4.6 11.4 1.0
CA B:CYS12 4.6 11.5 1.0
C4 B:DMA998 4.7 22.7 1.0
SG B:CYS197 4.7 11.3 1.0
SG B:CYS96 4.8 10.2 1.0
C B:GLY14 4.8 9.9 1.0
C B:CYS12 4.9 12.0 1.0
C5 B:DMA998 4.9 23.2 1.0

Iron binding site 6 out of 6 in 3kef

Go back to Iron Binding Sites List in 3kef
Iron binding site 6 out of 6 in the Crystal Structure of Isph:Dmapp-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:Dmapp-Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe997

b:11.1
occ:1.00
FE4 B:F3S997 0.0 11.1 1.0
S3 B:F3S997 2.1 13.7 1.0
S4 B:F3S997 2.2 14.5 1.0
S2 B:F3S997 2.2 14.1 1.0
SG B:CYS96 2.3 10.2 1.0
FE1 B:F3S997 2.8 11.4 1.0
FE3 B:F3S997 2.8 10.7 1.0
CB B:CYS96 3.1 9.1 1.0
CA B:GLY14 4.1 10.8 1.0
S1 B:F3S997 4.1 16.0 1.0
CB B:LEU98 4.3 11.9 1.0
C4 B:DMA998 4.4 22.7 1.0
N B:GLY14 4.4 11.2 1.0
C3 B:DMA998 4.5 23.4 1.0
CD1 B:LEU98 4.5 12.2 1.0
CA B:CYS96 4.6 10.0 1.0
CG B:LEU98 4.6 12.5 1.0
SG B:CYS12 4.7 11.0 1.0
C5 B:DMA998 4.7 23.2 1.0
SG B:CYS197 4.9 11.3 1.0
C2 B:DMA998 4.9 22.3 1.0
N B:LEU98 5.0 10.5 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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