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Iodine in PDB 2fwe: Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form)

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

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

Protein crystallography data

The structure of Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form), PDB code: 2fwe 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) 20.00 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 30.265, 45.961, 73.768, 90.00, 90.00, 90.00
R / Rfree (%) n/a / 23.5

Other elements in 2fwe:

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

Nickel (Ni) 1 atom
Sodium (Na) 1 atom

Iodine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form) (pdb code 2fwe). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 11 binding sites of Iodine where determined in the Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form), PDB code: 2fwe:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in 2fwe

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Iodine binding site 1 out of 11 in the Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form)


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1001

b:23.3
occ:0.48
 I A:IOD1001 0.0 23.3 0.5
O A:HOH109 3.3 21.7 1.0
I A:IOD1001 3.3 22.0 0.3
N A:LEU429 3.4 14.9 1.0
CB A:PHE472 3.9 9.7 1.0
CA A:HIS428 3.9 37.4 1.0
CB A:HIS428 3.9 30.3 1.0
CG A:GLU468 4.0 13.6 1.0
CD2 A:PHE472 4.1 12.3 1.0
C A:HIS428 4.1 36.6 1.0
CE2 A:PHE431 4.1 10.8 1.0
CB A:LEU429 4.3 13.1 1.0
CA A:LEU429 4.3 10.6 1.0
CG A:PHE472 4.4 8.0 1.0
CB A:GLU468 4.5 13.7 1.0
CG A:LEU429 4.5 11.3 1.0
O A:LEU429 4.5 15.5 1.0
OE2 A:GLU468 4.6 17.2 0.5
CD2 A:PHE431 4.6 12.3 1.0
CA A:GLU468 4.7 9.8 1.0
CD A:GLU468 4.7 7.9 0.5
O A:HOH117 4.8 45.8 1.0
CG A:HIS428 4.8 30.3 0.0
O A:HOH43 4.8 29.3 1.0
CD1 A:LEU429 4.9 14.7 1.0
CD2 A:HIS428 4.9 30.3 0.0
C A:LEU429 4.9 12.2 1.0

Iodine binding site 2 out of 11 in 2fwe

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Iodine binding site 2 out of 11 in the Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized 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 Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1001

b:22.0
occ:0.35
 I A:IOD1001 0.0 22.0 0.3
OE2 A:GLU468 2.3 17.2 0.5
CG A:GLU468 2.7 13.6 1.0
CD A:GLU468 2.9 7.9 0.5
I A:IOD1001 3.3 23.3 0.5
O A:HOH102 3.4 12.4 1.0
NE2 A:GLN488 3.6 11.5 1.0
O A:HOH117 4.0 45.8 1.0
CD2 A:PHE472 4.1 12.3 1.0
CB A:GLU468 4.1 13.7 1.0
OE1 A:GLU468 4.1 11.8 0.5
CE2 A:PHE431 4.1 10.8 1.0
CE2 A:PHE472 4.4 10.9 1.0
O A:HOH121 4.5 34.0 0.5
CD1 A:TYR457 4.6 12.3 1.0
CD A:GLN488 4.6 13.3 1.0
O A:HOH121 4.6 33.3 0.5
CD2 A:PHE431 4.7 12.3 1.0
OD2 A:ASP455 4.7 10.4 1.0
CE1 A:TYR457 4.8 14.2 1.0
OE1 A:GLN488 4.8 16.5 1.0
CA A:GLU468 4.8 9.8 1.0
CZ A:PHE431 5.0 9.5 1.0

Iodine binding site 3 out of 11 in 2fwe

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Iodine binding site 3 out of 11 in the Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1002

b:13.6
occ:0.70
 I A:IOD1002 0.0 13.6 0.7
O A:HOH19 1.5 16.4 0.1
I A:IOD1002 1.5 19.4 0.1
O A:HOH19 3.0 24.6 0.8
NA A:NA1101 3.3 21.1 0.7
O A:HOH6 3.6 14.1 1.0
CD2 A:HIS523 3.9 13.2 1.0
C A:PHE516 4.0 9.2 1.0
O A:PHE516 4.0 10.8 1.0
N A:ASP517 4.0 10.4 1.0
CA A:ASP517 4.0 12.0 1.0
CB A:PHE515 4.0 8.9 1.0
CB A:ASP517 4.1 10.8 1.0
CB A:ARG544 4.1 10.3 1.0
CG A:ARG544 4.2 12.9 1.0
CD A:ARG544 4.2 15.1 1.0
N A:GLN545 4.3 24.9 1.0
C A:PHE515 4.3 8.6 1.0
N A:PHE516 4.3 7.8 1.0
CB A:GLN545 4.5 26.6 1.0
O A:PHE515 4.5 10.4 1.0
CA A:PHE516 4.6 5.8 1.0
CG A:HIS523 4.7 13.7 1.0
O A:GLN545 4.7 25.4 1.0
NE2 A:HIS523 4.8 14.5 1.0
CA A:PHE515 4.8 8.9 1.0
CA A:ARG544 4.8 19.9 1.0
CB A:HIS523 4.9 11.6 1.0
CA A:GLN545 4.9 25.5 1.0
C A:ARG544 5.0 22.5 1.0

Iodine binding site 4 out of 11 in 2fwe

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Iodine binding site 4 out of 11 in the Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1002

b:19.4
occ:0.15
 I A:IOD1002 0.0 19.4 0.1
I A:IOD1002 1.5 13.6 0.7
NA A:NA1101 1.9 21.1 0.7
O A:HOH19 2.9 16.4 0.1
CD2 A:HIS523 3.5 13.2 1.0
CB A:HIS523 3.8 11.6 1.0
CG A:HIS523 3.8 13.7 1.0
N A:GLN545 3.8 24.9 1.0
O A:HOH19 4.0 24.6 0.8
CB A:PHE515 4.1 8.9 1.0
CB A:ARG544 4.1 10.3 1.0
CG A:ARG544 4.1 12.9 1.0
CB A:GLN545 4.3 26.6 1.0
CA A:ARG544 4.3 19.9 1.0
CB A:ALA526 4.4 13.2 1.0
NE2 A:HIS523 4.5 14.5 1.0
O A:HOH126 4.5 21.5 1.0
O A:PHE515 4.5 10.4 1.0
C A:ARG544 4.6 22.5 1.0
CD A:ARG544 4.6 15.1 1.0
O A:HOH77 4.6 24.3 1.0
C A:PHE515 4.7 8.6 1.0
CA A:GLN545 4.7 25.5 1.0
O A:HOH6 4.8 14.1 1.0
ND1 A:HIS523 5.0 15.3 1.0
CA A:HIS523 5.0 11.3 1.0
N A:HIS523 5.0 13.0 1.0
N A:ASP517 5.0 10.4 1.0

Iodine binding site 5 out of 11 in 2fwe

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Iodine binding site 5 out of 11 in the Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1003

b:21.8
occ:0.33
 I A:IOD1003 0.0 21.8 0.3
O A:HOH37 2.9 22.5 1.0
NE2 A:GLN545 3.3 52.1 1.0
I A:IOD1003 3.4 19.6 0.2
N A:GLY518 3.7 11.4 1.0
O A:HOH181 3.9 6.0 0.3
O A:HOH31 4.0 29.2 1.0
CG A:GLN519 4.1 13.3 1.0
NE2 A:GLN519 4.2 23.8 1.0
CA A:GLY518 4.2 12.0 1.0
N A:GLN519 4.3 10.6 1.0
CB A:ASP517 4.4 10.8 1.0
O A:PRO546 4.4 20.8 1.0
C A:GLY518 4.5 12.0 1.0
CD A:GLN545 4.5 39.3 1.0
CG A:ASP517 4.5 13.7 1.0
CD A:GLN519 4.7 26.0 1.0
C A:ASP517 4.8 10.4 1.0
OD1 A:ASP517 4.8 10.3 1.0
OD2 A:ASP517 4.9 16.4 1.0

Iodine binding site 6 out of 11 in 2fwe

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Iodine binding site 6 out of 11 in the Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1003

b:19.6
occ:0.20
 I A:IOD1003 0.0 19.6 0.2
O A:HOH181 2.9 6.0 0.3
O A:HIS547 3.3 73.0 1.0
O A:HOH37 3.3 22.5 1.0
I A:IOD1003 3.4 21.8 0.3
NE2 A:HIS549 3.7 16.0 0.5
C A:HIS547 3.8 49.7 1.0
CA A:GLY518 3.8 12.0 1.0
O A:HOH152 3.9 50.9 1.0
CA A:HIS547 3.9 41.4 1.0
O A:GLY449 3.9 15.4 1.0
CD2 A:HIS549 4.0 19.8 0.5
N A:GLY518 4.1 11.4 1.0
CB A:HIS547 4.2 41.7 1.0
C A:GLY449 4.5 19.2 1.0
CD A:PRO451 4.6 10.3 1.0
C A:GLY518 4.8 12.0 1.0
N A:HIS548 4.8 39.8 1.0
CE1 A:HIS549 4.8 17.7 0.5
N A:PRO451 4.9 9.5 1.0
CA A:LYS450 4.9 12.7 1.0
C A:LYS450 5.0 9.2 1.0

Iodine binding site 7 out of 11 in 2fwe

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Iodine binding site 7 out of 11 in the Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form)


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1005

b:26.4
occ:0.25
 N A:ASP438 3.2 9.8 1.0
CG A:ASP438 3.3 17.4 1.0
O A:HOH160 3.3 46.6 1.0
OD1 A:ASP438 3.5 18.3 1.0
OD2 A:ASP438 3.5 31.9 1.0
O A:HOH157 3.7 35.6 1.0
N A:VAL437 3.8 7.6 1.0
CB A:THR436 3.8 9.1 1.0
CB A:VAL437 3.8 9.6 1.0
CB A:ASP438 3.8 11.2 1.0
CA A:ASP438 4.1 11.5 1.0
CA A:VAL437 4.1 10.8 1.0
OG1 A:THR436 4.1 12.7 1.0
C A:VAL437 4.1 9.4 1.0
O A:HOH12 4.2 12.0 1.0
C A:THR436 4.5 8.8 1.0
CG2 A:VAL437 4.5 12.5 1.0
O A:HOH171 4.6 43.0 1.0
CG2 A:THR436 4.6 10.6 1.0
CA A:THR436 4.7 11.3 1.0
CG1 A:VAL437 4.7 10.1 1.0
O A:HOH69 4.8 19.7 1.0

Iodine binding site 8 out of 11 in 2fwe

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Iodine binding site 8 out of 11 in the Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1006

b:23.5
occ:0.20
 O A:HOH167 3.0 44.9 1.0
O A:HOH153 3.7 48.2 1.0
CG A:GLU466 3.7 7.7 1.0
CD A:LYS469 3.7 18.6 1.0
N A:GLU466 3.8 6.5 1.0
C A:LYS465 3.8 8.0 1.0
O A:LYS465 3.9 10.8 1.0
CA A:GLU466 3.9 5.8 1.0
CB A:LYS465 4.0 12.8 1.0
CB A:LYS469 4.2 10.7 1.0
CB A:GLU466 4.4 9.9 1.0
O A:HOH65 4.4 23.2 0.5
CA A:LYS465 4.6 8.1 1.0
CG A:LYS469 4.6 11.8 1.0
O A:VAL462 4.7 11.4 1.0
O A:HOH91 4.8 29.1 1.0
O A:HOH65 4.8 16.8 0.5
CE A:LYS469 4.8 26.6 1.0
CD A:GLU466 4.9 12.2 1.0

Iodine binding site 9 out of 11 in 2fwe

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Iodine binding site 9 out of 11 in the Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1006

b:22.1
occ:0.15
 NZ A:LYS448 2.6 25.1 1.0
O A:HOH100 3.0 38.2 1.0
CE A:LYS448 3.9 32.7 1.0
O A:HOH143 4.1 26.6 0.5
O A:HOH125 4.3 22.5 1.0
O A:GLN519 4.8 18.0 1.0
CD A:LYS448 4.8 23.4 1.0

Iodine binding site 10 out of 11 in 2fwe

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Iodine binding site 10 out of 11 in the Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of the C-Terminal Domain of the Electron Transfer Catalyst Dsbd (Oxidized Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1013

b:29.2
occ:0.21
 O A:HOH79 3.2 27.0 1.0
O A:HOH115 3.3 19.0 1.0
CZ3 A:TRP460 3.7 20.6 1.0
CA A:CYS461 3.7 7.3 1.0
CB A:CYS461 3.8 7.8 1.0
SG A:CYS461 3.8 12.0 1.0
O A:LEU510 3.8 19.2 1.0
CE3 A:TRP460 4.1 15.4 1.0
O A:HOH8 4.2 13.0 1.0
CB A:LEU510 4.4 15.0 1.0
C A:LEU510 4.5 9.3 1.0
N A:VAL462 4.6 9.9 1.0
C A:CYS461 4.6 8.8 1.0
N A:CYS461 4.7 8.1 1.0
O A:TRP460 4.7 13.7 1.0
CA A:LEU510 4.9 10.7 1.0
CH2 A:TRP460 4.9 26.1 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 Dec 13 19:23:51 2020

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