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Iron in PDB 3ddr: Structure of the Serratia Marcescens Hemophore Receptor Hasr-ILE671GLY Mutant in Complex with Its Hemophore Hasa and Heme

Protein crystallography data

The structure of Structure of the Serratia Marcescens Hemophore Receptor Hasr-ILE671GLY Mutant in Complex with Its Hemophore Hasa and Heme, PDB code: 3ddr was solved by S.Krieg, K.Diederichs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.25 / 2.80
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 157.410, 162.720, 597.010, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 26.2

Other elements in 3ddr:

The structure of Structure of the Serratia Marcescens Hemophore Receptor Hasr-ILE671GLY Mutant in Complex with Its Hemophore Hasa and Heme also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of the Serratia Marcescens Hemophore Receptor Hasr-ILE671GLY Mutant in Complex with Its Hemophore Hasa and Heme (pdb code 3ddr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structure of the Serratia Marcescens Hemophore Receptor Hasr-ILE671GLY Mutant in Complex with Its Hemophore Hasa and Heme, PDB code: 3ddr:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3ddr

Go back to Iron Binding Sites List in 3ddr
Iron binding site 1 out of 2 in the Structure of the Serratia Marcescens Hemophore Receptor Hasr-ILE671GLY Mutant in Complex with Its Hemophore Hasa and Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Serratia Marcescens Hemophore Receptor Hasr-ILE671GLY Mutant in Complex with Its Hemophore Hasa and Heme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe200

b:0.5
occ:0.89
FE C:HEM200 0.0 0.5 0.9
NC C:HEM200 2.0 0.8 0.9
ND C:HEM200 2.1 86.2 0.9
NB C:HEM200 2.1 0.3 0.9
NA C:HEM200 2.1 0.3 0.9
OH C:TYR75 2.2 0.9 1.0
C4C C:HEM200 3.0 0.5 0.9
C1C C:HEM200 3.0 0.1 0.9
C1D C:HEM200 3.1 88.9 0.9
C4A C:HEM200 3.1 0.4 0.9
C4B C:HEM200 3.1 0.9 0.9
C1B C:HEM200 3.1 97.0 0.9
C1A C:HEM200 3.1 0.3 0.9
C4D C:HEM200 3.1 0.6 0.9
CZ C:TYR75 3.1 0.7 1.0
CHD C:HEM200 3.4 0.2 0.9
CHC C:HEM200 3.4 77.7 0.9
CHB C:HEM200 3.5 0.3 0.9
CHA C:HEM200 3.5 0.7 0.9
ND1 C:HIS83 3.8 0.3 1.0
CE2 C:TYR75 3.9 0.5 1.0
CE1 C:TYR75 3.9 0.3 1.0
OG A:SER605 4.0 0.7 1.0
C3C C:HEM200 4.2 0.5 0.9
C2C C:HEM200 4.2 0.7 0.9
C2D C:HEM200 4.3 94.6 0.9
C3A C:HEM200 4.3 0.6 0.9
C2B C:HEM200 4.3 0.8 0.9
C3B C:HEM200 4.3 0.5 0.9
C2A C:HEM200 4.3 0.6 0.9
C3D C:HEM200 4.4 0.7 0.9
CB C:HIS83 4.4 93.1 1.0
CG C:HIS83 4.5 0.1 1.0
CE1 C:HIS83 4.8 0.3 1.0

Iron binding site 2 out of 2 in 3ddr

Go back to Iron Binding Sites List in 3ddr
Iron binding site 2 out of 2 in the Structure of the Serratia Marcescens Hemophore Receptor Hasr-ILE671GLY Mutant in Complex with Its Hemophore Hasa and Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Serratia Marcescens Hemophore Receptor Hasr-ILE671GLY Mutant in Complex with Its Hemophore Hasa and Heme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe200

b:1.0
occ:0.91
FE D:HEM200 0.0 1.0 0.9
ND D:HEM200 2.0 93.3 0.9
NA D:HEM200 2.1 0.9 0.9
NC D:HEM200 2.1 93.4 0.9
NB D:HEM200 2.1 0.1 0.9
OH D:TYR75 2.2 0.9 1.0
C4D D:HEM200 3.0 0.6 0.9
C1D D:HEM200 3.0 93.2 0.9
C4C D:HEM200 3.1 97.3 0.9
C1A D:HEM200 3.1 0.7 0.9
C4A D:HEM200 3.1 0.5 0.9
C1B D:HEM200 3.1 0.4 0.9
C1C D:HEM200 3.1 0.7 0.9
CZ D:TYR75 3.1 0.4 1.0
C4B D:HEM200 3.1 0.7 0.9
CHA D:HEM200 3.4 95.2 0.9
CHD D:HEM200 3.4 93.2 0.9
CHB D:HEM200 3.5 0.1 0.9
CHC D:HEM200 3.5 93.5 0.9
CE1 D:TYR75 3.9 0.0 1.0
CE2 D:TYR75 3.9 0.8 1.0
ND1 D:HIS83 3.9 0.5 1.0
OG B:SER605 4.1 0.9 1.0
C3D D:HEM200 4.2 93.1 0.9
C2D D:HEM200 4.2 98.7 0.9
C3C D:HEM200 4.3 0.1 0.9
C2A D:HEM200 4.3 0.4 0.9
C3A D:HEM200 4.3 0.0 0.9
C2C D:HEM200 4.3 0.2 0.9
C2B D:HEM200 4.4 0.9 0.9
C3B D:HEM200 4.4 0.4 0.9
CB D:HIS83 4.4 0.7 1.0
CG D:HIS83 4.5 0.3 1.0
CE1 D:HIS83 4.9 0.9 1.0

Reference:

S.Krieg, F.Huche, K.Diederichs, N.Izadi-Pruneyre, A.Lecroisey, C.Wandersman, P.Delepelaire, W.Welte. Heme Uptake Across the Outer Membrane As Revealed By Crystal Structures of the Receptor-Hemophore Complex. Proc.Natl.Acad.Sci.Usa V. 106 1045 2009.
ISSN: ISSN 0027-8424
PubMed: 19144921
DOI: 10.1073/PNAS.0809406106
Page generated: Sun Dec 13 15:03:40 2020

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