Iodine in PDB 5aur: Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region

Protein crystallography data

The structure of Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region, PDB code: 5aur was solved by C.Ren, S.Nagao, M.Yamanaka, H.Kamikubo, H.Komori, Y.Shomura, Y.Higuchi, S.Hirota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.26
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 32.850, 42.898, 53.591, 86.73, 86.51, 89.83
R / Rfree (%) 18.1 / 22.9

Other elements in 5aur:

The structure of Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Iodine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iodine atom in the Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region (pdb code 5aur). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 11 binding sites of Iodine where determined in the Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region, PDB code: 5aur:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in 5aur

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Iodine binding site 1 out of 11 in the Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I102

b:42.3
occ:0.60
 O A:HOH273 2.7 31.6 1.0
O A:HOH217 3.4 30.5 1.0
OD2 A:ASP69 3.7 29.0 0.5
CG A:ASP69 3.7 21.2 0.5
OD1 A:ASP69 3.8 23.8 0.5
O A:ALA46 3.9 15.3 1.0
CG A:ASP69 4.0 18.9 0.5
OD1 A:ASP69 4.0 25.6 0.5
C A:ALA46 4.0 13.1 1.0
N A:GLY47 4.1 15.0 1.0
CB A:ALA46 4.1 13.8 1.0
CB A:ASP69 4.2 17.6 0.5
CA A:GLY47 4.3 13.4 1.0
CA A:ASP69 4.3 16.6 0.5
CA A:ASP69 4.3 16.3 0.5
CD A:LYS50 4.3 20.6 1.0
CB A:ASP69 4.4 18.8 0.5
OD2 A:ASP69 4.4 24.3 0.5
CB A:ALA72 4.5 11.5 1.0
CB A:LYS50 4.6 16.9 1.0
O A:ASP69 4.7 16.8 0.5
CA A:ALA46 4.7 13.6 1.0
O A:ASP69 4.7 14.1 0.5
CE A:LYS73 4.8 34.4 1.0
C A:ASP69 5.0 14.9 0.5

Iodine binding site 2 out of 11 in 5aur

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Iodine binding site 2 out of 11 in the Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I103

b:24.0
occ:0.60
 O A:HOH257 2.7 36.2 1.0
O A:HOH268 2.9 32.2 1.0
OE1 A:GLN7 3.6 28.4 1.0
CD1 A:LEU4 3.9 19.8 1.0
CB A:GLN7 4.0 19.8 1.0
CE A:LYS8 4.1 18.3 1.0
CD A:LYS8 4.5 16.9 1.0
CD A:GLN7 4.6 25.2 1.0
CG A:LYS8 4.6 17.1 1.0
OE2 C:GLU71 4.8 18.5 1.0
NZ A:LYS8 4.8 16.8 1.0
CG A:GLN7 4.9 21.9 1.0
O A:HOH253 5.0 46.4 1.0
C A:GLN7 5.0 20.4 1.0

Iodine binding site 3 out of 11 in 5aur

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Iodine binding site 3 out of 11 in the Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I104

b:45.8
occ:0.40
 NZ A:LYS51 2.9 30.9 1.0
O A:HOH211 3.6 40.5 1.0
NZ A:LYS50 3.7 34.6 1.0
CE A:LYS51 3.8 24.8 1.0
O A:HOH252 4.2 38.1 1.0
CD A:LYS51 4.9 27.8 1.0

Iodine binding site 4 out of 11 in 5aur

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Iodine binding site 4 out of 11 in the Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I105

b:50.9
occ:0.60
 O A:HOH277 2.4 44.9 1.0
O A:HOH254 2.7 33.3 1.0
O A:HOH265 3.4 63.4 1.0
O A:HOH211 3.5 40.5 1.0
CA A:THR68 4.3 14.2 1.0
CG2 A:THR68 4.4 13.9 1.0
CE A:LYS50 4.4 30.2 1.0
CB A:THR68 4.5 13.9 1.0
O A:VAL67 4.7 15.1 1.0
O A:HOH210 4.8 22.3 1.0
NZ A:LYS50 4.9 34.6 1.0

Iodine binding site 5 out of 11 in 5aur

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Iodine binding site 5 out of 11 in the Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I106

b:29.2
occ:0.50
 O A:HOH235 3.5 29.1 1.0
O A:HOH269 4.7 46.9 1.0

Iodine binding site 6 out of 11 in 5aur

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Iodine binding site 6 out of 11 in the Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I107

b:25.6
occ:0.40
 O A:HOH248 3.2 44.7 1.0
O A:HOH229 3.4 16.4 1.0
O C:HOH215 3.5 22.0 1.0
CE A:LYS23 4.0 17.2 1.0
CD A:LYS23 4.1 16.6 1.0
O A:HOH251 4.3 31.9 1.0
O C:HOH238 4.4 14.7 1.0
C A:LYS22 4.6 14.0 1.0
CB A:LYS22 4.6 26.2 1.0
N A:LYS23 4.7 14.9 1.0
O A:LYS22 4.7 15.1 1.0
O C:ALA12 4.8 14.3 1.0
CA A:LYS23 4.8 15.3 1.0
CG A:LYS23 4.9 16.4 1.0

Iodine binding site 7 out of 11 in 5aur

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Iodine binding site 7 out of 11 in the Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I108

b:36.2
occ:0.50
 NE2 A:GLN65 3.5 14.3 1.0
CMC A:HEC101 3.9 13.9 1.0
OE1 A:GLN65 4.1 18.0 1.0
CG A:PRO63 4.1 22.8 1.0
CBC A:HEC101 4.2 15.2 1.0
CD A:GLN65 4.2 15.4 1.0
CB A:PRO63 4.4 21.8 1.0
O A:HOH238 4.5 19.7 1.0
O C:HOH240 4.7 30.5 1.0
CD A:PRO63 4.7 18.4 1.0
O A:HOH203 4.7 29.4 1.0
C2C A:HEC101 4.8 13.0 1.0
O A:PRO64 4.9 18.8 1.0

Iodine binding site 8 out of 11 in 5aur

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Iodine binding site 8 out of 11 in the Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I102

b:28.5
occ:0.50
 O E:HOH218 3.3 41.4 1.0
O E:HOH217 3.5 30.9 1.0
NE2 C:GLN65 3.8 17.1 1.0
CBC C:HEC101 3.8 19.3 1.0
CG C:PRO63 3.9 19.8 1.0
NZ E:LYS22 3.9 37.2 1.0
CB C:PRO63 4.1 18.2 1.0
CMC C:HEC101 4.3 15.4 1.0
CE E:LYS22 4.4 34.4 1.0
CD C:PRO63 4.4 15.7 1.0
OE1 C:GLN65 4.6 17.5 1.0
CD C:GLN65 4.7 16.8 1.0
C2C C:HEC101 5.0 14.6 1.0

Iodine binding site 9 out of 11 in 5aur

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Iodine binding site 9 out of 11 in the Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I103

b:23.5
occ:0.80
 O C:HOH262 3.0 29.0 1.0
O C:HOH271 3.0 31.7 1.0
OE1 C:GLN7 3.6 23.8 1.0
CD1 C:LEU4 4.0 18.8 1.0
CE C:LYS8 4.1 14.1 1.0
CB C:GLN7 4.1 17.3 1.0
CD C:LYS8 4.5 15.5 1.0
CD C:GLN7 4.5 19.4 1.0
OE2 A:GLU71 4.6 16.3 1.0
NZ C:LYS8 4.7 12.9 1.0
O C:HOH254 4.7 33.7 1.0
CG C:LYS8 4.8 17.1 1.0
O C:HOH246 4.8 38.0 1.0
O A:HOH207 4.8 19.9 1.0
CG C:GLN7 4.9 16.6 1.0

Iodine binding site 10 out of 11 in 5aur

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Iodine binding site 10 out of 11 in the Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Hydrogenobacter Thermophilus Cytochrome C552 Dimer Formed By Domain Swapping at N-Terminal Region within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I104

b:35.8
occ:0.70
 O C:HOH279 3.1 36.5 1.0
CB C:LYS39 3.8 28.9 1.0
CB C:ASP40 4.3 18.5 1.0
N C:ASP40 4.3 20.6 1.0
C C:LYS39 4.3 22.1 1.0
O C:LYS39 4.5 22.2 1.0
CA C:ASP40 4.6 16.3 1.0
CD C:LYS39 4.7 41.5 1.0
CA C:LYS39 4.7 25.6 1.0
CG C:LYS39 4.9 36.3 1.0

Reference:

C.Ren, S.Nagao, M.Yamanaka, H.Komori, Y.Shomura, Y.Higuchi, S.Hirota. Oligomerization Enhancement and Two Domain Swapping Mode Detection For Thermostable Cytochrome C552VIA the Elongation of the Major Hinge Loop. Mol Biosyst V. 11 3218 2015.
ISSN: ESSN 1742-2051
PubMed: 26451671
DOI: 10.1039/C5MB00545K
Page generated: Sun Dec 13 19:38:25 2020

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