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Iodine in PDB 5myq: Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative

Protein crystallography data

The structure of Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative, PDB code: 5myq was solved by P.Strzelczyk, G.Bujacz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.60 / 1.89
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.933, 82.081, 74.601, 90.00, 106.29, 90.00
R / Rfree (%) 18.6 / 23.2

Other elements in 5myq:

The structure of Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative (pdb code 5myq). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 21 binding sites of Iodine where determined in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative, PDB code: 5myq:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 21 in 5myq

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Iodine binding site 1 out of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:32.9
occ:0.70
 N A:SER102 3.6 23.6 1.0
O A:HOH411 3.9 26.9 1.0
C16 A:HBF301 3.9 29.1 1.0
C15 A:HBF301 4.1 27.0 1.0
N A:SER75 4.1 21.1 1.0
OG A:SER73 4.1 26.2 1.0
CB A:SER75 4.2 18.9 1.0
CB A:SER101 4.2 24.9 1.0
CA A:SER101 4.2 21.9 1.0
CB A:SER102 4.2 25.5 0.5
N A:GLU74 4.4 22.6 1.0
CB A:GLU74 4.4 26.3 1.0
C A:SER101 4.4 21.6 1.0
O A:SER102 4.5 27.9 1.0
CA A:SER102 4.5 24.2 1.0
OG A:SER101 4.5 26.3 1.0
C A:GLU74 4.6 22.1 1.0
CA A:SER75 4.6 19.1 1.0
CA A:GLU74 4.7 23.8 1.0
OG A:SER75 4.9 19.6 1.0
C A:SER102 5.0 26.7 1.0

Iodine binding site 2 out of 21 in 5myq

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Iodine binding site 2 out of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:59.4
occ:0.70
 OE1 A:GLU91 3.3 57.2 1.0
CD A:ARG122 3.5 47.0 1.0
NE A:ARG122 3.6 49.3 1.0
N A:GLU91 3.6 48.0 1.0
O A:GLY89 3.7 61.3 1.0
CA A:LYS90 3.9 55.8 1.0
CG A:ARG122 4.1 43.4 1.0
CD A:GLU91 4.2 52.9 1.0
CG A:GLU91 4.2 50.3 1.0
C A:LYS90 4.3 50.9 1.0
CB A:GLU91 4.3 45.3 1.0
O A:HOH424 4.4 39.0 1.0
CB A:ARG122 4.5 41.8 1.0
CA A:GLU91 4.6 44.1 1.0
CB A:LYS90 4.7 58.2 1.0
C A:GLY89 4.7 61.4 1.0
CG A:LYS90 4.8 56.9 1.0
N A:LYS90 4.8 59.8 1.0
CZ A:ARG122 4.8 46.6 1.0

Iodine binding site 3 out of 21 in 5myq

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Iodine binding site 3 out of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative


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 Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:40.8
occ:0.50
 N A:LYS9 3.7 31.1 1.0
NH1 A:ARG122 3.9 51.9 1.0
CD A:ARG122 4.0 47.0 1.0
O A:LYS9 4.1 31.4 1.0
CA A:GLY8 4.2 32.0 1.0
C A:GLY8 4.5 30.1 1.0
CA A:LYS9 4.5 31.7 1.0
CB A:LYS9 4.5 35.9 1.0
CZ A:ARG122 4.5 46.6 1.0
NE A:ARG122 4.6 49.3 1.0
CG A:ARG122 4.7 43.4 1.0
C A:LYS9 4.8 30.5 1.0
CB A:ARG122 4.9 41.8 1.0

Iodine binding site 4 out of 21 in 5myq

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Iodine binding site 4 out of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative


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 Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I306

b:47.4
occ:0.50
 N A:PRO48 3.6 24.5 1.0
OE2 A:GLU46 3.6 38.4 1.0
C A:SER47 3.7 23.6 1.0
CD A:PRO48 3.8 26.6 1.0
CG2 A:THR32 3.9 24.3 1.0
O A:HOH449 3.9 40.5 1.0
CA A:PRO48 4.0 23.8 1.0
CG A:GLU46 4.0 31.0 1.0
O A:SER47 4.1 22.7 1.0
O A:HOH483 4.1 44.7 1.0
CA A:SER47 4.2 23.6 1.0
O A:GLU46 4.2 25.5 1.0
N A:SER47 4.2 24.4 1.0
CB A:THR32 4.2 23.1 1.0
CB A:PRO48 4.3 26.4 1.0
CD A:GLU46 4.3 37.0 1.0
C A:GLU46 4.3 25.1 1.0
CG A:PRO48 4.5 26.6 1.0
CA A:THR32 4.8 20.6 1.0
CB A:GLU46 4.9 30.4 1.0
O A:GLY31 4.9 19.2 1.0

Iodine binding site 5 out of 21 in 5myq

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Iodine binding site 5 out of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative


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 Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I203

b:37.7
occ:1.00
 NH1 B:ARG2 3.6 38.9 1.0
N B:GLU91 3.6 31.5 1.0
CG B:ARG122 4.0 32.6 1.0
CA B:LYS90 4.1 32.6 1.0
O B:HOH308 4.3 33.5 1.0
CB B:GLU91 4.4 32.4 1.0
NE B:ARG122 4.4 38.1 1.0
C B:LYS90 4.4 30.8 1.0
NZ B:LYS90 4.4 40.7 1.0
CA B:GLU91 4.6 30.2 1.0
OE1 B:GLU91 4.6 48.5 1.0
CG B:GLU91 4.6 36.2 1.0
CD B:GLU91 4.6 40.5 1.0
CD B:LYS90 4.6 38.2 1.0
CB B:LYS90 4.7 32.5 1.0
O B:GLY89 4.7 34.7 1.0
CD B:ARG122 4.8 34.9 1.0
CB B:ARG122 4.8 33.0 1.0
CZ B:ARG2 4.9 36.0 1.0
CE B:LYS90 4.9 38.1 1.0

Iodine binding site 6 out of 21 in 5myq

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Iodine binding site 6 out of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative


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 Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I204

b:27.6
occ:0.50
 N B:SER102 3.6 25.9 1.0
O B:HOH362 3.9 38.8 1.0
C16 B:HBF201 4.0 35.8 1.0
N B:SER75 4.1 26.0 1.0
CA B:SER101 4.1 24.4 1.0
CB B:SER101 4.1 25.7 1.0
CB B:SER102 4.1 29.7 1.0
CB B:GLU74 4.2 32.2 1.0
CB B:SER75 4.2 24.5 1.0
OG B:SER73 4.3 27.9 1.0
C B:GLU74 4.3 27.5 1.0
OG B:SER101 4.3 26.1 1.0
C B:SER101 4.4 24.9 1.0
C15 B:HBF201 4.4 37.9 1.0
CA B:SER102 4.4 27.9 1.0
N B:GLU74 4.4 29.5 1.0
O B:SER102 4.4 30.5 1.0
CA B:SER75 4.5 23.9 1.0
CA B:GLU74 4.5 29.8 1.0
OE1 B:GLU74 4.8 42.8 1.0
O B:GLU74 4.9 26.9 1.0
C B:SER102 4.9 30.4 1.0

Iodine binding site 7 out of 21 in 5myq

Go back to Iodine Binding Sites List in 5myq
Iodine binding site 7 out of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I205

b:42.9
occ:0.50
 O B:HOH302 3.5 31.2 1.0
NH2 D:ARG114 3.6 36.4 1.0
O B:LYS111 3.8 22.6 1.0
CG B:LYS111 4.2 31.4 1.0
CB B:SER101 4.2 25.7 1.0
CE B:LYS111 4.3 37.1 1.0
CD B:LYS111 4.4 35.1 1.0
C B:LYS111 4.4 23.4 1.0
CA B:ALA112 4.5 20.9 1.0
CG1 B:VAL103 4.5 30.1 1.0
OG B:SER101 4.6 26.1 1.0
CZ D:ARG114 4.6 35.0 1.0
NH1 B:ARG114 4.7 34.0 1.0
NE D:ARG114 4.8 33.2 1.0
N B:ALA112 4.8 22.0 1.0
CB B:LYS111 4.9 29.3 1.0
NZ B:LYS111 5.0 41.5 1.0

Iodine binding site 8 out of 21 in 5myq

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Iodine binding site 8 out of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative


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 Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I206

b:43.8
occ:1.00
 O B:HOH366 3.4 63.9 1.0
OG1 B:THR32 3.5 27.9 1.0
OG1 B:THR19 3.7 37.9 1.0
OG1 B:THR34 3.7 33.9 1.0
CA B:MET18 3.9 30.1 1.0
N B:THR19 3.9 32.0 1.0
O B:ASN17 4.0 28.4 1.0
O B:THR32 4.0 26.1 1.0
C B:MET18 4.0 31.3 1.0
C B:ASN17 4.1 29.4 1.0
CB B:ASN17 4.2 32.0 1.0
N B:MET18 4.2 27.7 1.0
OE2 B:GLU46 4.2 42.0 1.0
C B:THR32 4.2 25.6 1.0
N B:THR34 4.3 26.7 1.0
CB B:THR34 4.3 31.6 1.0
CB B:THR19 4.4 35.7 1.0
CB B:THR32 4.5 27.6 1.0
CE B:LYS9 4.5 43.4 1.0
N B:TYR33 4.5 25.5 1.0
CA B:TYR33 4.7 24.0 1.0
C B:TYR33 4.7 26.1 1.0
CA B:THR19 4.8 33.5 1.0
O B:MET18 4.8 30.8 1.0
CD B:GLU46 4.9 39.7 1.0
CA B:ASN17 4.9 29.1 1.0
O B:HOH346 4.9 39.3 1.0
CA B:THR34 5.0 29.3 1.0
CG B:GLU46 5.0 35.4 1.0
CA B:THR32 5.0 26.5 1.0

Iodine binding site 9 out of 21 in 5myq

Go back to Iodine Binding Sites List in 5myq
Iodine binding site 9 out of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative


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 Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I207

b:49.2
occ:0.70
 N B:PRO48 3.8 29.6 1.0
C B:SER47 3.9 28.9 1.0
CG2 B:THR32 3.9 29.0 1.0
CD B:PRO48 4.0 32.3 1.0
O B:GLU46 4.0 32.2 1.0
CE B:LYS71 4.2 45.2 1.0
CA B:SER47 4.2 29.1 1.0
CA B:PRO48 4.2 29.1 1.0
CB B:PRO48 4.2 31.3 1.0
O B:SER47 4.3 27.7 1.0
C B:GLU46 4.4 31.0 1.0
N B:SER47 4.4 30.4 1.0
CG B:GLU46 4.4 35.4 1.0
CG B:PRO48 4.6 32.0 1.0
O B:HOH354 4.6 37.4 1.0
CB B:THR32 4.7 27.6 1.0
O A:HOH468 4.7 38.6 1.0
CD B:GLU46 4.7 39.7 1.0
O B:HOH330 4.8 30.8 1.0
CB B:GLU46 4.9 35.3 1.0
OE2 B:GLU46 5.0 42.0 1.0

Iodine binding site 10 out of 21 in 5myq

Go back to Iodine Binding Sites List in 5myq
Iodine binding site 10 out of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative


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 Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I208

b:58.9
occ:0.50
 NH2 B:ARG2 3.4 37.1 1.0
N B:ARG2 3.5 44.0 1.0
CG B:ARG2 3.9 44.1 1.0
CD B:ARG2 4.0 43.5 1.0
CG2 B:ILE85 4.1 32.8 1.0
CZ B:ARG2 4.4 36.0 1.0
CB B:ARG2 4.5 43.5 1.0
CG1 B:ILE85 4.5 30.6 1.0
CA B:ARG2 4.6 43.6 1.0
NE B:ARG2 4.7 42.3 1.0
CB B:ILE85 4.9 30.2 1.0
O B:ARG2 5.0 39.9 1.0
CD1 B:ILE85 5.0 31.3 1.0

Reference:

P.Strzelczyk, D.Plazuk, G.Bujacz. Structural Investigation of the Interactions of Ferrocene Homobiotin Derivative with Avidin. To Be Published.
Page generated: Sun Aug 11 21:32:30 2024

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