Atomistry » Iron » PDB 3k9z-3kyw » 3kef
Atomistry »
  Iron »
    PDB 3k9z-3kyw »
      3kef »

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

Go back to Iron Binding Sites List in 3kef
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

Go back to Iron Binding Sites List in 3kef
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

Go back to Iron Binding Sites List in 3kef
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

Last articles

Cl in 3ZO9
Cl in 3ZNX
Cl in 3ZNV
Cl in 3ZN5
Cl in 3ZNO
Cl in 3ZN6
Cl in 3ZMJ
Cl in 3ZMD
Cl in 3ZN4
Cl in 3ZMH
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy