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Sodium in PDB 2fwf: High Resolution Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Reduced Form)

Enzymatic activity of High Resolution Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Reduced Form)

All present enzymatic activity of High Resolution Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Reduced Form):
1.8.1.8;

Protein crystallography data

The structure of High Resolution Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Reduced Form), PDB code: 2fwf was solved by C.U.Stirnimann, A.Rozhkova, U.Grauschopf, R.A.Boeckmann, R.Glockshuber, G.Capitani, M.G.Gruetter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 30.355, 46.082, 74.143, 90.00, 90.00, 90.00
R / Rfree (%) n/a / 19.6

Other elements in 2fwf:

The structure of High Resolution Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Reduced Form) also contains other interesting chemical elements:

Iodine (I) 11 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the High Resolution Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Reduced Form) (pdb code 2fwf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the High Resolution Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Reduced Form), PDB code: 2fwf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2fwf

Go back to Sodium Binding Sites List in 2fwf
Sodium binding site 1 out of 2 in the High Resolution Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Reduced Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High Resolution Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Reduced Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1101

b:24.8
occ:0.65
 I A:IOD1002 1.8 18.5 0.1
O A:HOH79 2.7 25.3 1.0
O A:HOH87 2.8 32.5 1.0
N A:GLN545 3.2 20.3 1.0
I A:IOD1002 3.4 13.7 0.7
CB A:HIS523 3.7 16.5 1.0
CA A:ARG544 3.7 14.9 1.0
CG A:HIS523 3.9 17.4 1.0
C A:ARG544 3.9 21.2 1.0
CB A:GLN545 4.0 26.7 1.0
CB A:ALA526 4.1 14.5 1.0
CD2 A:HIS523 4.1 13.2 1.0
CA A:GLN545 4.2 19.5 1.0
CB A:ARG544 4.2 12.5 1.0
O A:HOH68 4.3 4.9 0.1
CG A:ARG544 4.5 13.8 1.0
ND1 A:HIS523 4.7 19.9 1.0
O A:ASP543 4.8 24.4 1.0
N A:ARG544 4.9 17.0 1.0
NE2 A:HIS523 5.0 15.6 1.0

Sodium binding site 2 out of 2 in 2fwf

Go back to Sodium Binding Sites List in 2fwf
Sodium binding site 2 out of 2 in the High Resolution Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Reduced Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High Resolution Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Reduced Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1102

b:25.9
occ:1.00
 OE1 A:GLN442 2.7 15.3 0.5
O A:HOH37 2.8 20.1 1.0
CA A:GLN442 3.8 13.9 1.0
N A:GLN442 3.8 10.4 1.0
CD A:GLN442 3.8 17.8 0.5
C A:ASN441 4.0 11.6 1.0
CB A:GLN442 4.1 16.4 1.0
O A:ASN441 4.1 12.8 1.0
O A:HOH92 4.2 28.2 1.0
CG2 A:VAL445 4.2 19.0 1.0
CB A:ASN441 4.3 13.9 1.0
CG A:GLN442 4.5 17.9 1.0
CA A:ASN441 4.8 13.9 1.0
O A:ASP438 4.8 11.0 1.0
CB A:VAL445 4.9 15.6 1.0
NE2 A:GLN442 4.9 25.0 0.5
O A:HOH42 4.9 28.6 1.0

Reference:

C.U.Stirnimann, A.Rozhkova, U.Grauschopf, R.A.Boeckmann, R.Glockshuber, G.Capitani, M.G.Gruetter. High-Resolution Structures of Escherichia Coli Cdsbd in Different Redox States: A Combined Crystallographic, Biochemical and Computational Study J.Mol.Biol. V. 358 829 2006.
ISSN: ISSN 0022-2836
PubMed: 16545842
DOI: 10.1016/J.JMB.2006.02.030
Page generated: Mon Oct 7 02:31:00 2024

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