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Iodine in PDB 2d8w: Structure of Hyper-Vil-Trypsin

Enzymatic activity of Structure of Hyper-Vil-Trypsin

All present enzymatic activity of Structure of Hyper-Vil-Trypsin:
3.4.21.4;

Protein crystallography data

The structure of Structure of Hyper-Vil-Trypsin, PDB code: 2d8w was solved by H.Miyatake, T.Hasegawa, A.Yamano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.31 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.323, 58.197, 66.620, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 25.6

Other elements in 2d8w:

The structure of Structure of Hyper-Vil-Trypsin also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of Hyper-Vil-Trypsin (pdb code 2d8w). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Structure of Hyper-Vil-Trypsin, PDB code: 2d8w:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 2d8w

Go back to Iodine Binding Sites List in 2d8w
Iodine binding site 1 out of 7 in the Structure of Hyper-Vil-Trypsin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Hyper-Vil-Trypsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I48

b:30.6
occ:0.42
 IE A:IYR48 0.0 30.6 0.4
CE A:IYR48 2.1 26.1 1.0
CF A:IYR48 3.0 25.1 1.0
CD A:IYR48 3.1 24.4 1.0
OF A:IYR48 3.2 25.4 1.0
CA A:LYS49 4.0 22.7 1.0
CG A:IYR48 4.3 23.0 1.0
CC A:IYR48 4.4 21.7 1.0
N A:SER50 4.4 25.6 1.0
C A:LYS49 4.5 23.8 1.0
N A:LYS49 4.6 20.3 1.0
O A:IYR48 4.7 16.1 1.0
CH A:IYR48 4.9 21.0 1.0
C A:IYR48 4.9 18.5 1.0
CB A:LYS49 4.9 25.3 1.0

Iodine binding site 2 out of 7 in 2d8w

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Iodine binding site 2 out of 7 in the Structure of Hyper-Vil-Trypsin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Hyper-Vil-Trypsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I137

b:51.0
occ:0.59
 IE A:IYR137 0.0 51.0 0.6
CE A:IYR137 2.1 48.5 1.0
CD A:IYR137 3.0 46.4 1.0
CF A:IYR137 3.0 49.3 1.0
OF A:IYR137 3.2 49.6 1.0
O A:GLN180 3.4 19.5 1.0
C A:GLN180 4.0 20.4 1.0
N A:ASN129 4.2 19.1 1.0
CB A:GLN180 4.3 25.7 1.0
CB A:ASN129 4.3 20.7 1.0
CG A:IYR137 4.3 48.2 1.0
CC A:IYR137 4.3 43.7 1.0
CA A:GLY181 4.4 19.4 1.0
N A:GLY181 4.4 19.9 1.0
CA A:ASN129 4.6 20.3 1.0
CA A:GLN180 4.8 22.0 1.0
CH A:IYR137 4.8 46.4 1.0
C A:GLY128 4.9 19.0 1.0
CG2 A:THR135 5.0 32.3 1.0

Iodine binding site 3 out of 7 in 2d8w

Go back to Iodine Binding Sites List in 2d8w
Iodine binding site 3 out of 7 in the Structure of Hyper-Vil-Trypsin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Hyper-Vil-Trypsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I171

b:33.4
occ:1.00
 I1 A:TYI171 0.0 33.4 1.0
CE1 A:TYI171 2.1 35.7 1.0
CD1 A:TYI171 3.0 34.2 1.0
CZ A:TYI171 3.1 36.2 1.0
O A:LYS145 3.2 21.1 1.0
OH A:TYI171 3.2 36.9 1.0
CD A:LYS176 3.8 30.6 1.0
CA A:ALA146 3.9 22.1 1.0
CB A:ALA146 3.9 21.6 1.0
CD A:PRO147 4.1 19.4 1.0
C A:LYS145 4.2 22.0 1.0
CB A:LYS176 4.2 24.5 1.0
CG A:TYI171 4.3 34.3 1.0
CE2 A:TYI171 4.4 37.8 1.0
CD1 A:LEU144 4.4 20.9 1.0
N A:ALA146 4.5 21.5 1.0
CG A:LYS176 4.6 27.4 1.0
NZ A:LYS176 4.8 33.6 1.0
CD2 A:TYI171 4.8 36.5 1.0
CE A:LYS176 4.9 31.8 1.0
CG A:LEU144 5.0 21.1 1.0

Iodine binding site 4 out of 7 in 2d8w

Go back to Iodine Binding Sites List in 2d8w
Iodine binding site 4 out of 7 in the Structure of Hyper-Vil-Trypsin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Hyper-Vil-Trypsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I171

b:41.8
occ:0.67
 I2 A:TYI171 0.0 41.8 0.7
CE2 A:TYI171 2.1 37.8 1.0
CD2 A:TYI171 3.0 36.5 1.0
CZ A:TYI171 3.1 36.2 1.0
OH A:TYI171 3.2 36.9 1.0
I A:IOD403 3.6 76.7 0.6
CG A:TYI171 4.4 34.3 1.0
CE1 A:TYI171 4.4 35.7 1.0
CG A:PRO147 4.5 20.0 1.0
CD1 A:TYI171 4.9 34.2 1.0

Iodine binding site 5 out of 7 in 2d8w

Go back to Iodine Binding Sites List in 2d8w
Iodine binding site 5 out of 7 in the Structure of Hyper-Vil-Trypsin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Hyper-Vil-Trypsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:55.3
occ:0.46
 OG A:SER81 3.1 19.7 1.0
O A:PRO80 3.7 16.4 1.0
CB A:SER81 4.0 19.0 1.0
CA A:SER81 4.0 18.4 1.0
C A:PRO80 4.1 17.2 1.0
N A:SER81 4.3 16.8 1.0
CB A:PRO80 4.9 15.9 1.0

Iodine binding site 6 out of 7 in 2d8w

Go back to Iodine Binding Sites List in 2d8w
Iodine binding site 6 out of 7 in the Structure of Hyper-Vil-Trypsin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Hyper-Vil-Trypsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:42.8
occ:0.56
 NE2 A:GLN121 3.0 36.1 1.0
CG A:GLN121 3.7 32.4 1.0
CD A:GLN121 3.8 34.8 1.0
C A:CYS122 3.9 21.1 1.0
N A:LEU123 4.0 18.4 1.0
CD A:LYS145 4.1 22.8 1.0
CG A:LYS145 4.1 21.8 1.0
O A:CYS122 4.1 21.7 1.0
CA A:CYS122 4.2 22.7 1.0
CE A:LYS145 4.2 21.7 1.0
O A:GLN121 4.3 25.6 1.0
N A:CYS122 4.3 24.2 1.0
CB A:LEU123 4.3 18.4 1.0
C A:GLN121 4.4 25.9 1.0
CA A:LEU123 4.5 16.8 1.0
CB A:GLN121 4.7 28.2 1.0
CB A:LYS145 4.7 22.7 1.0
NZ A:LYS145 4.8 19.5 1.0
O A:VAL188 4.9 18.9 1.0
OE1 A:GLN121 5.0 37.2 1.0

Iodine binding site 7 out of 7 in 2d8w

Go back to Iodine Binding Sites List in 2d8w
Iodine binding site 7 out of 7 in the Structure of Hyper-Vil-Trypsin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of Hyper-Vil-Trypsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:76.7
occ:0.62
 CE2 A:TYI171 3.3 37.8 1.0
CD2 A:TYI171 3.6 36.5 1.0
I2 A:TYI171 3.6 41.8 0.7
CZ A:TYI171 3.6 36.2 1.0
OH A:TYI171 4.1 36.9 1.0
CE1 A:TYI171 4.3 35.7 1.0
CG A:TYI171 4.3 34.3 1.0
OE1 A:GLU173 4.3 46.1 1.0
CD1 A:TYI171 4.6 34.2 1.0

Reference:

H.Miyatake, T.Hasegawa, A.Yamano. New Methods to Prepare Iodinated Derivatives By Vaporizing Iodine Labelling (Vil) and Hydrogen Peroxide Vil (Hyper-Vil) Acta Crystallogr.,Sect.D V. 62 280 2006.
ISSN: ISSN 0907-4449
PubMed: 16510975
DOI: 10.1107/S0907444905041909
Page generated: Fri Aug 8 13:03:15 2025

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