Atomistry » Sodium » PDB 3cq8-3dfh » 3ddr
Atomistry »
  Sodium »
    PDB 3cq8-3dfh »
      3ddr »

Sodium 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:

Iron (Fe) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3ddr

Go back to Sodium Binding Sites List in 3ddr
Sodium 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 Sodium with other atoms in the Na 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
A:Na866

b:0.5
occ:1.00
NE2 A:HIS189 3.1 95.5 1.0
NE2 A:HIS603 3.3 0.6 1.0
CD2 A:HIS189 3.4 82.1 1.0
CE1 A:HIS189 4.1 0.4 1.0
CE1 A:HIS603 4.2 0.3 1.0
CD2 A:HIS603 4.2 0.6 1.0
CG A:HIS189 4.6 0.6 1.0
CMA C:HEM200 4.6 0.5 0.9
ND1 A:HIS189 4.9 0.3 1.0

Sodium binding site 2 out of 2 in 3ddr

Go back to Sodium Binding Sites List in 3ddr
Sodium 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 Sodium with other atoms in the Na 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
B:Na866

b:0.4
occ:1.00
NE2 B:HIS189 3.5 92.5 1.0
CD2 B:HIS189 3.6 89.3 1.0
NE2 B:HIS603 3.7 0.5 1.0
CE1 B:HIS189 4.4 0.7 1.0
CD2 B:HIS603 4.5 0.8 1.0
CE1 B:HIS603 4.5 0.5 1.0
CG B:HIS189 4.6 0.6 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: Tue Dec 15 06:08:41 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy