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Iodine 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:

Sodium (Na) 2 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Iodine 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 Iodine atom.
In total 11 binding sites of Iodine 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 Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in 2fwf

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Iodine binding site 1 out of 11 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 Iodine with other atoms in the I 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:I1001

b:20.4
occ:0.35
 I A:IOD1001 0.0 20.4 0.3
OE2 A:GLU468 2.3 46.9 1.0
CG A:GLU468 2.8 19.6 1.0
CD A:GLU468 2.9 35.6 1.0
I A:IOD1001 3.2 19.9 0.5
O A:HOH15 3.5 20.0 1.0
O A:HOH119 3.5 44.2 1.0
NE2 A:GLN488 3.6 10.5 1.0
OE1 A:GLU468 4.2 31.7 1.0
CD2 A:PHE472 4.2 11.3 1.0
CE2 A:PHE431 4.2 13.0 1.0
CB A:GLU468 4.2 15.1 1.0
CD1 A:TYR457 4.4 11.9 1.0
CE2 A:PHE472 4.5 12.0 1.0
CE1 A:TYR457 4.5 15.4 1.0
O A:HOH91 4.6 53.7 1.0
CD A:GLN488 4.7 12.6 1.0
OD2 A:ASP455 4.8 9.9 0.8
CD2 A:PHE431 4.8 12.3 1.0
OE1 A:GLN488 4.8 18.3 1.0
NE2 A:HIS428 4.8 37.1 0.0
CD2 A:HIS428 4.8 37.1 0.0
CA A:GLU468 4.8 10.2 1.0

Iodine binding site 2 out of 11 in 2fwf

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Iodine binding site 2 out of 11 in the High Resolution Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Reduced Form)


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Stereo pair view

A full contact list of Iodine with other atoms in the I 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:I1001

b:19.9
occ:0.48
 I A:IOD1001 0.0 19.9 0.5
O A:HOH33 3.0 21.1 1.0
I A:IOD1001 3.2 20.4 0.3
N A:LEU429 3.5 16.6 1.0
CD2 A:HIS428 3.6 37.1 0.0
CA A:HIS428 3.8 29.9 1.0
CG A:HIS428 3.9 37.1 0.0
CB A:PHE472 3.9 10.0 1.0
CG A:GLU468 4.0 19.6 1.0
CD2 A:PHE472 4.0 11.3 1.0
CE2 A:PHE431 4.2 13.0 1.0
NE2 A:HIS428 4.2 37.1 0.0
C A:HIS428 4.2 26.0 1.0
CB A:HIS428 4.2 37.1 1.0
O A:HOH119 4.3 44.2 1.0
CB A:LEU429 4.4 13.8 1.0
CG A:PHE472 4.4 8.8 1.0
ND1 A:HIS428 4.5 37.1 0.0
CA A:LEU429 4.5 12.8 1.0
CG A:LEU429 4.5 11.9 1.0
OE2 A:GLU468 4.5 46.9 1.0
CB A:GLU468 4.6 15.1 1.0
CE1 A:HIS428 4.6 37.1 0.0
CD A:GLU468 4.7 35.6 1.0
O A:LEU429 4.7 16.3 1.0
CA A:GLU468 4.7 10.2 1.0
CD2 A:PHE431 4.8 12.3 1.0
CD1 A:LEU429 4.8 11.8 1.0
O A:HOH90 5.0 32.3 1.0

Iodine binding site 3 out of 11 in 2fwf

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Iodine binding site 3 out of 11 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 Iodine with other atoms in the I binding site number 3 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:I1002

b:13.7
occ:0.65
 I A:IOD1002 0.0 13.7 0.7
O A:HOH68 1.6 4.9 0.1
I A:IOD1002 1.6 18.5 0.1
O A:HOH68 3.2 18.0 0.7
NA A:NA1101 3.4 24.8 0.7
O A:HOH6 3.6 12.2 1.0
CD2 A:HIS523 3.9 13.2 1.0
C A:PHE516 3.9 10.8 1.0
N A:ASP517 3.9 11.1 1.0
O A:PHE516 4.0 11.0 1.0
CB A:PHE515 4.0 10.3 1.0
CA A:ASP517 4.1 12.8 1.0
CB A:ASP517 4.2 12.7 1.0
CD A:ARG544 4.2 14.3 1.0
CB A:ARG544 4.2 12.5 1.0
CG A:ARG544 4.2 13.8 1.0
C A:PHE515 4.4 10.6 1.0
N A:GLN545 4.4 20.3 1.0
N A:PHE516 4.4 10.4 1.0
O A:PHE515 4.5 11.8 1.0
CA A:PHE516 4.6 8.7 1.0
CB A:GLN545 4.6 26.7 1.0
CG A:HIS523 4.6 17.4 1.0
NE2 A:HIS523 4.7 15.6 1.0
CB A:HIS523 4.8 16.5 1.0
CA A:PHE515 4.8 8.5 1.0
CA A:ARG544 4.8 14.9 1.0
O A:GLN545 4.9 25.6 1.0

Iodine binding site 4 out of 11 in 2fwf

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Iodine binding site 4 out of 11 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 Iodine with other atoms in the I binding site number 4 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:I1002

b:18.5
occ:0.15
 I A:IOD1002 0.0 18.5 0.1
I A:IOD1002 1.6 13.7 0.7
NA A:NA1101 1.8 24.8 0.7
O A:HOH68 2.8 4.9 0.1
CD2 A:HIS523 3.7 13.2 1.0
N A:GLN545 3.8 20.3 1.0
CB A:HIS523 3.8 16.5 1.0
CG A:HIS523 3.9 17.4 1.0
CB A:ARG544 4.0 12.5 1.0
CG A:ARG544 4.0 13.8 1.0
O A:HOH79 4.1 25.3 1.0
CA A:ARG544 4.1 14.9 1.0
CB A:PHE515 4.2 10.3 1.0
CB A:ALA526 4.2 14.5 1.0
O A:HOH68 4.3 18.0 0.7
CB A:GLN545 4.3 26.7 1.0
O A:HOH87 4.4 32.5 1.0
C A:ARG544 4.5 21.2 1.0
CD A:ARG544 4.5 14.3 1.0
NE2 A:HIS523 4.7 15.6 1.0
CA A:GLN545 4.7 19.5 1.0
O A:PHE515 4.8 11.8 1.0
O A:HOH6 4.8 12.2 1.0
C A:PHE515 4.9 10.6 1.0

Iodine binding site 5 out of 11 in 2fwf

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Iodine binding site 5 out of 11 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 Iodine with other atoms in the I binding site number 5 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:I1003

b:17.2
occ:0.33
 I A:IOD1003 0.0 17.2 0.3
I A:IOD1003 3.1 22.3 0.2
NE2 A:GLN545 3.7 36.4 1.0
N A:GLY518 3.7 14.1 1.0
CA A:GLY518 3.9 13.6 1.0
O A:HOH124 4.0 25.5 1.0
NE2 A:GLN519 4.1 26.1 1.0
O A:PRO546 4.2 26.3 1.0
N A:GLN519 4.3 14.7 1.0
CG A:GLN519 4.3 18.9 1.0
C A:GLY518 4.3 15.6 1.0
CB A:ASP517 4.4 12.7 1.0
CG A:ASP517 4.6 13.8 1.0
CD A:GLN519 4.8 19.9 1.0
C A:ASP517 4.8 11.4 1.0
CD A:GLN545 4.8 30.5 1.0
CA A:HIS547 4.9 30.8 1.0
OD1 A:ASP517 4.9 12.9 1.0
OD2 A:ASP517 4.9 15.5 1.0
O A:HOH48 4.9 36.8 1.0

Iodine binding site 6 out of 11 in 2fwf

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Iodine binding site 6 out of 11 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 Iodine with other atoms in the I binding site number 6 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:I1003

b:22.3
occ:0.20
 I A:IOD1003 0.0 22.3 0.2
O A:HOH124 3.0 25.5 1.0
I A:IOD1003 3.1 17.2 0.3
O A:HIS547 3.3 74.8 1.0
O A:HOH141 3.4 32.5 1.0
CA A:HIS547 3.6 30.8 1.0
C A:HIS547 3.6 39.0 1.0
CA A:GLY518 3.6 13.6 1.0
CB A:HIS547 3.8 31.1 1.0
CE1 A:HIS549 3.8 45.0 0.5
ND1 A:HIS549 4.0 44.4 0.5
O A:GLY449 4.0 17.5 1.0
N A:GLY518 4.0 14.1 1.0
CD2 A:HIS549 4.3 44.2 0.5
NE2 A:HIS549 4.3 44.3 0.5
N A:HIS548 4.6 24.3 1.0
C A:GLY449 4.6 18.5 1.0
C A:GLY518 4.7 15.6 1.0
CD A:PRO451 4.8 11.9 1.0
O A:PRO546 4.8 26.3 1.0
N A:HIS547 4.9 26.2 1.0
NE2 A:HIS549 4.9 41.5 0.5
CA A:LYS450 5.0 11.4 1.0
N A:PRO451 5.0 9.1 1.0

Iodine binding site 7 out of 11 in 2fwf

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Iodine binding site 7 out of 11 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 Iodine with other atoms in the I binding site number 7 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:I1005

b:29.2
occ:0.25
 O A:HOH103 3.0 40.5 1.0
N A:ASP438 3.3 11.2 1.0
CG A:ASP438 3.5 24.3 1.0
OD1 A:ASP438 3.6 19.8 1.0
CB A:THR436 3.7 12.8 1.0
CB A:ASP438 3.7 15.9 1.0
N A:VAL437 3.8 11.2 1.0
OD2 A:ASP438 3.8 42.7 1.0
O A:HOH99 3.9 34.3 1.0
CB A:VAL437 3.9 9.8 1.0
OG1 A:THR436 4.0 14.2 1.0
O A:HOH13 4.1 14.5 1.0
CA A:ASP438 4.1 12.5 1.0
O A:HOH153 4.2 57.9 1.0
C A:VAL437 4.2 11.1 1.0
CA A:VAL437 4.2 9.8 1.0
C A:THR436 4.5 10.1 1.0
CG2 A:THR436 4.6 14.6 1.0
CA A:THR436 4.7 10.3 1.0
CG2 A:VAL437 4.7 13.0 1.0
O A:HOH41 4.8 21.9 1.0
CG1 A:VAL437 4.8 12.8 1.0

Iodine binding site 8 out of 11 in 2fwf

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Iodine binding site 8 out of 11 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 Iodine with other atoms in the I binding site number 8 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:I1006

b:27.9
occ:0.25
 O A:HOH150 2.9 31.5 1.0
O A:HOH94 4.0 25.8 1.0
O A:HOH165 4.1 43.1 1.0

Iodine binding site 9 out of 11 in 2fwf

Go back to Iodine Binding Sites List in 2fwf
Iodine binding site 9 out of 11 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 Iodine with other atoms in the I binding site number 9 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:I1010

b:24.6
occ:0.20
 I A:IOD1010 0.0 24.6 0.2
I A:IOD1010 2.3 22.5 0.1
O A:HOH142 2.9 38.2 1.0

Iodine binding site 10 out of 11 in 2fwf

Go back to Iodine Binding Sites List in 2fwf
Iodine binding site 10 out of 11 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 Iodine with other atoms in the I binding site number 10 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:I1010

b:22.5
occ:0.10
 I A:IOD1010 0.0 22.5 0.1
I A:IOD1010 2.3 24.6 0.2
O A:HOH142 2.6 38.2 1.0
C A:HIS550 4.3 54.9 1.0
O A:HIS550 4.6 65.4 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: Sun Aug 11 13:48:48 2024

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