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Iodine in PDB 2eix: The Structure of Physarum Polycephalum Cytochrome B5 Reductase

Enzymatic activity of The Structure of Physarum Polycephalum Cytochrome B5 Reductase

All present enzymatic activity of The Structure of Physarum Polycephalum Cytochrome B5 Reductase:
1.6.2.2;

Protein crystallography data

The structure of The Structure of Physarum Polycephalum Cytochrome B5 Reductase, PDB code: 2eix was solved by S.W.Kim, M.Suga, K.Ogasahara, T.Ikegami, Y.Minami, T.Yubisui, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.35 / 1.56
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.084, 136.369, 45.718, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 22.6

Other elements in 2eix:

The structure of The Structure of Physarum Polycephalum Cytochrome B5 Reductase also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the The Structure of Physarum Polycephalum Cytochrome B5 Reductase (pdb code 2eix). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the The Structure of Physarum Polycephalum Cytochrome B5 Reductase, PDB code: 2eix:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 2eix

Go back to Iodine Binding Sites List in 2eix
Iodine binding site 1 out of 4 in the The Structure of Physarum Polycephalum Cytochrome B5 Reductase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of The Structure of Physarum Polycephalum Cytochrome B5 Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1501

b:16.5
occ:1.00
O A:HOH1603 3.6 12.5 1.0
ND2 A:ASN70 3.7 12.3 1.0
CB A:ASN70 3.8 9.0 1.0
CE A:MET53 4.1 10.8 1.0
CB A:MET53 4.2 9.0 1.0
CG A:ASN70 4.2 9.2 1.0
SD A:MET53 4.4 14.9 1.0
O A:LEU71 4.5 11.3 1.0
CG A:MET53 4.9 10.6 1.0
O A:HOH1644 4.9 27.1 1.0

Iodine binding site 2 out of 4 in 2eix

Go back to Iodine Binding Sites List in 2eix
Iodine binding site 2 out of 4 in the The Structure of Physarum Polycephalum Cytochrome B5 Reductase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of The Structure of Physarum Polycephalum Cytochrome B5 Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1502

b:24.1
occ:1.00
NZ A:LYS181 3.5 28.5 1.0
CG A:LYS181 3.8 24.9 1.0
CD A:LYS181 4.1 26.2 1.0
CB A:PRO180 4.2 16.9 1.0
CG A:PRO180 4.2 20.3 1.0
CD A:PRO180 4.3 16.6 1.0
CE A:LYS181 4.4 24.9 1.0
OD1 A:ASN179 4.6 14.8 1.0
N A:LYS181 4.7 18.9 1.0
CB A:LYS181 4.9 21.2 1.0

Iodine binding site 3 out of 4 in 2eix

Go back to Iodine Binding Sites List in 2eix
Iodine binding site 3 out of 4 in the The Structure of Physarum Polycephalum Cytochrome B5 Reductase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of The Structure of Physarum Polycephalum Cytochrome B5 Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1503

b:35.0
occ:1.00
OG A:SER87 3.2 18.9 1.0
O A:HOH1682 3.3 29.2 1.0
C A:ARG99 3.7 5.4 1.0
N A:PRO100 3.7 7.7 1.0
CD A:PRO100 3.8 5.2 1.0
CB A:SER87 3.9 12.2 1.0
CA A:ARG99 4.0 5.5 1.0
N A:ARG99 4.1 8.4 1.0
O A:ARG99 4.1 7.5 1.0
C A:TYR98 4.2 7.0 1.0
CB A:TYR98 4.3 9.4 1.0
CB A:PRO100 4.3 8.8 1.0
CA A:PRO100 4.3 7.6 1.0
CA A:SER87 4.3 9.9 1.0
O A:TYR98 4.5 7.1 1.0
CG A:PRO100 4.6 7.3 1.0
O B:HOH1792 4.8 38.1 1.0
CA A:TYR98 4.9 8.5 1.0

Iodine binding site 4 out of 4 in 2eix

Go back to Iodine Binding Sites List in 2eix
Iodine binding site 4 out of 4 in the The Structure of Physarum Polycephalum Cytochrome B5 Reductase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of The Structure of Physarum Polycephalum Cytochrome B5 Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1504

b:40.5
occ:1.00
O B:HOH1694 2.8 30.8 1.0
OG B:SER87 3.1 23.2 1.0
C B:ARG99 3.7 7.5 1.0
N B:PRO100 3.7 8.3 1.0
CD B:PRO100 3.8 6.6 1.0
CB B:SER87 3.9 15.5 1.0
O B:ARG99 4.0 7.6 1.0
CA B:ARG99 4.1 7.9 1.0
N B:ARG99 4.1 10.1 1.0
CA B:PRO100 4.3 9.1 1.0
CA B:SER87 4.3 14.2 1.0
CB B:TYR98 4.3 8.6 1.0
CB B:PRO100 4.4 8.7 1.0
C B:TYR98 4.4 11.0 1.0
O B:TYR98 4.6 10.4 1.0
CG B:PRO100 4.7 8.2 1.0
O B:HOH1753 4.7 37.0 1.0
CA B:TYR98 5.0 10.6 1.0

Reference:

S.Kim, M.Suga, K.Ogasahara, T.Ikegami, Y.Minami, T.Yubisui, T.Tsukihara. Structure of Physarum Polycephalum Cytochrome B5 Reductase at 1.56 A Resolution. Acta Crystallogr.,Sect.F V. 63 274 2007.
ISSN: ESSN 1744-3091
PubMed: 17401193
DOI: 10.1107/S1744309107010731
Page generated: Sun Aug 11 13:45:57 2024

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