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Iodine in PDB 8d8w: Crystal Structure of Choe with SER38 Adopting Alternative Conformations

Protein crystallography data

The structure of Crystal Structure of Choe with SER38 Adopting Alternative Conformations, PDB code: 8d8w was solved by V.D.Pham, R.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.08 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.717, 81.569, 81.489, 90, 99.89, 90
R / Rfree (%) 16.9 / 19.7

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Choe with SER38 Adopting Alternative Conformations (pdb code 8d8w). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 14 binding sites of Iodine where determined in the Crystal Structure of Choe with SER38 Adopting Alternative Conformations, PDB code: 8d8w:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 14 in 8d8w

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Iodine binding site 1 out of 14 in the Crystal Structure of Choe with SER38 Adopting Alternative Conformations


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 Choe with SER38 Adopting Alternative Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:27.7
occ:0.60
 O A:HOH532 3.5 30.0 1.0
O A:HOH781 3.6 34.2 1.0
CB A:GLN268 3.8 35.0 1.0
CG A:GLN268 4.0 34.8 1.0
CA A:ALA200 4.0 12.5 1.0
CG A:GLU286 4.0 17.7 1.0
CB A:ALA203 4.1 13.5 1.0
CB A:ALA200 4.2 12.5 1.0
CB A:GLU286 4.2 16.4 1.0
O A:ALA200 4.7 12.8 1.0
N A:ALA200 4.8 12.7 1.0
CD A:GLU286 4.8 20.7 1.0
C A:ALA200 4.9 13.3 1.0
O A:PRO199 5.0 13.8 1.0

Iodine binding site 2 out of 14 in 8d8w

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Iodine binding site 2 out of 14 in the Crystal Structure of Choe with SER38 Adopting Alternative Conformations


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 Choe with SER38 Adopting Alternative Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:31.0
occ:0.50
 O A:HOH650 2.8 33.3 1.0
I A:IOD404 2.9 40.3 0.5
N A:GLY102 3.5 12.0 1.0
ND2 A:ASN171 3.8 15.3 1.0
CB A:LYS100 3.8 12.7 1.0
CA A:GLY102 3.9 13.0 1.0
CD A:LYS100 4.1 16.6 1.0
OG A:SER101 4.1 11.8 1.0
O A:HOH558 4.2 31.0 1.0
OD1 A:ASP148 4.3 14.0 1.0
O A:HOH691 4.3 27.6 1.0
CE A:LYS100 4.3 19.4 1.0
N A:SER101 4.4 11.2 1.0
NZ A:LYS100 4.4 21.3 1.0
CG A:ASP148 4.4 13.5 1.0
OD2 A:ASP148 4.5 15.7 1.0
CG A:LYS100 4.5 15.2 1.0
C A:SER101 4.5 12.0 1.0
O A:HOH684 4.8 30.4 1.0
C A:GLY102 4.8 13.6 1.0
CA A:SER101 4.9 11.6 1.0
C A:LYS100 4.9 10.8 1.0
CA A:LYS100 4.9 11.7 1.0

Iodine binding site 3 out of 14 in 8d8w

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Iodine binding site 3 out of 14 in the Crystal Structure of Choe with SER38 Adopting Alternative Conformations


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 Choe with SER38 Adopting Alternative Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I404

b:40.3
occ:0.50
 I A:IOD403 2.9 31.0 0.5
NZ A:LYS100 3.4 21.3 1.0
N A:ASP104 3.4 17.3 1.0
CE A:LYS100 3.5 19.4 1.0
O A:HOH684 3.6 30.4 1.0
N A:ALA103 3.6 15.1 1.0
CA A:GLY102 3.9 13.0 1.0
C A:GLY102 4.0 13.6 1.0
CB A:ASP104 4.0 20.5 1.0
O A:HOH650 4.1 33.3 1.0
CA A:ASP104 4.1 18.1 1.0
CB A:LYS100 4.3 12.7 1.0
N A:GLY102 4.3 12.0 1.0
CD A:LYS100 4.3 16.6 1.0
C A:ALA103 4.4 16.6 1.0
C A:ASP104 4.4 16.4 1.0
O A:ASP104 4.4 14.1 1.0
CA A:ALA103 4.5 16.7 1.0
OD2 A:ASP104 4.6 28.6 1.0
CB A:ALA103 4.8 17.3 1.0
CG A:ASP104 4.8 24.3 1.0
CG A:LYS100 4.9 15.2 1.0
O A:GLY102 4.9 14.4 1.0

Iodine binding site 4 out of 14 in 8d8w

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Iodine binding site 4 out of 14 in the Crystal Structure of Choe with SER38 Adopting Alternative Conformations


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 Choe with SER38 Adopting Alternative Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I405

b:40.5
occ:0.50
 NE2 A:GLN46 3.4 28.7 1.0
O A:HOH686 3.5 28.0 1.0
N A:GLY65 3.6 26.2 1.0
O A:LEU63 3.7 24.3 1.0
O A:GLY65 3.8 27.9 1.0
C A:LEU63 4.0 25.0 1.0
CA A:GLY65 4.0 27.5 1.0
C A:GLY65 4.1 28.6 1.0
N A:PRO64 4.1 22.7 1.0
CD A:PRO64 4.1 22.4 1.0
O A:HOH682 4.2 30.9 1.0
CG A:GLN46 4.3 26.3 1.0
CD A:GLN46 4.4 26.7 1.0
N A:LEU63 4.6 26.5 1.0
C A:PRO64 4.7 23.4 1.0
CB A:ALA62 4.8 29.7 1.0
C A:ALA62 4.8 28.9 1.0
CA A:LEU63 4.8 24.7 1.0
CG A:PRO64 4.8 21.6 1.0
CB A:GLN46 4.9 23.4 1.0
N A:GLU66 5.0 31.3 1.0
CA A:PRO64 5.0 21.9 1.0

Iodine binding site 5 out of 14 in 8d8w

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Iodine binding site 5 out of 14 in the Crystal Structure of Choe with SER38 Adopting Alternative Conformations


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 Choe with SER38 Adopting Alternative Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I406

b:48.9
occ:0.50
 NE A:ARG114 2.7 35.9 1.0
O A:HOH505 2.8 40.1 1.0
NH2 A:ARG114 3.4 37.1 1.0
O A:HIS115 3.4 17.4 1.0
CZ A:ARG114 3.5 38.4 1.0
CD A:ARG114 3.7 33.8 1.0
O A:HOH584 3.8 22.0 1.0
O A:GLY120 4.0 17.6 1.0
CG A:ARG114 4.0 29.4 1.0
CA A:THR116 4.0 15.5 1.0
CG2 A:THR116 4.1 16.5 1.0
CA A:GLN121 4.1 14.1 1.0
CB A:ALA124 4.2 20.0 1.0
C A:GLY120 4.2 16.5 1.0
CG A:GLN121 4.3 12.9 1.0
N A:GLN121 4.3 14.2 1.0
C A:HIS115 4.4 18.1 1.0
CB A:THR116 4.5 15.4 1.0
N A:THR116 4.6 16.4 1.0
O A:HOH561 4.7 18.9 1.0
NH1 A:ARG114 4.8 41.3 1.0
CB A:GLN121 4.8 12.9 1.0
O A:HOH644 4.8 29.7 1.0
CG2 A:VAL96 4.9 14.3 1.0

Iodine binding site 6 out of 14 in 8d8w

Go back to Iodine Binding Sites List in 8d8w
Iodine binding site 6 out of 14 in the Crystal Structure of Choe with SER38 Adopting Alternative Conformations


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 Choe with SER38 Adopting Alternative Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I407

b:48.1
occ:0.50
 OG A:SER23 3.2 19.6 0.5
O A:HOH687 3.3 33.5 1.0
N A:SER23 3.3 18.9 1.0
CA A:THR22 3.8 21.9 1.0
CB A:THR22 3.9 20.4 1.0
OG A:SER23 4.1 18.5 0.5
CB A:SER23 4.1 17.4 0.5
C A:THR22 4.1 19.9 1.0
CB A:SER23 4.2 18.1 0.5
CD A:ARG304 4.3 18.1 0.5
CA A:SER23 4.3 17.3 0.5
CG2 A:THR22 4.3 20.7 1.0
CA A:SER23 4.3 17.6 0.5
NH1 A:ARG304 4.3 17.6 0.5
NE A:ARG304 4.5 18.4 0.5
CZ A:ARG304 4.5 19.6 0.5
O A:SER23 4.5 15.8 1.0
C A:SER23 4.9 15.5 1.0

Iodine binding site 7 out of 14 in 8d8w

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Iodine binding site 7 out of 14 in the Crystal Structure of Choe with SER38 Adopting Alternative Conformations


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 Choe with SER38 Adopting Alternative Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I402

b:19.4
occ:0.60
 O B:HOH565 3.2 24.2 1.0
O B:HOH892 3.4 40.5 1.0
O B:HOH783 3.5 43.9 1.0
O B:HOH869 3.7 29.6 1.0
CB B:GLN268 3.8 22.7 1.0
CA B:ALA200 3.9 8.3 1.0
CG B:GLN268 4.0 23.1 1.0
CG B:GLU286 4.0 10.1 1.0
CB B:ALA200 4.1 8.4 1.0
CB B:ALA203 4.1 10.0 1.0
CB B:GLU286 4.3 9.3 1.0
N B:ALA200 4.8 8.0 1.0
O B:HOH763 4.8 41.2 1.0
O B:ALA200 4.8 8.3 1.0
CD B:GLU286 4.9 11.0 1.0
C B:ALA200 4.9 8.3 1.0

Iodine binding site 8 out of 14 in 8d8w

Go back to Iodine Binding Sites List in 8d8w
Iodine binding site 8 out of 14 in the Crystal Structure of Choe with SER38 Adopting Alternative Conformations


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 Choe with SER38 Adopting Alternative Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I403

b:22.6
occ:0.50
 O B:HOH734 2.6 33.8 1.0
I B:IOD404 2.9 36.3 0.5
N B:GLY102 3.5 7.5 1.0
ND2 B:ASN171 3.8 9.2 1.0
CA B:GLY102 3.9 8.1 1.0
CB B:LYS100 3.9 7.6 1.0
OG B:SER101 4.1 6.8 1.0
CD B:LYS100 4.1 11.0 1.0
OD1 B:ASP148 4.2 9.3 1.0
O B:HOH641 4.3 27.5 1.0
O B:HOH718 4.3 21.1 1.0
CE B:LYS100 4.3 13.3 1.0
NZ B:LYS100 4.3 15.6 1.0
N B:SER101 4.4 6.8 1.0
CG B:ASP148 4.5 9.0 1.0
OD2 B:ASP148 4.5 9.7 1.0
C B:SER101 4.5 7.5 1.0
CG B:LYS100 4.6 9.2 1.0
O B:HOH730 4.8 21.5 1.0
C B:GLY102 4.8 8.2 1.0
CA B:SER101 4.9 6.9 1.0
C B:LYS100 4.9 6.8 1.0
CA B:LYS100 5.0 6.8 1.0

Iodine binding site 9 out of 14 in 8d8w

Go back to Iodine Binding Sites List in 8d8w
Iodine binding site 9 out of 14 in the Crystal Structure of Choe with SER38 Adopting Alternative Conformations


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 Choe with SER38 Adopting Alternative Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I404

b:36.3
occ:0.50
 I B:IOD403 2.9 22.6 0.5
NZ B:LYS100 3.3 15.6 1.0
N B:ASP104 3.4 10.4 1.0
CE B:LYS100 3.4 13.3 1.0
N B:ALA103 3.6 9.4 1.0
O B:HOH730 3.7 21.5 1.0
O B:HOH734 3.8 33.8 1.0
CA B:GLY102 3.9 8.1 1.0
C B:GLY102 4.0 8.2 1.0
CB B:ASP104 4.0 13.1 1.0
CA B:ASP104 4.1 10.9 1.0
CD B:LYS100 4.2 11.0 1.0
CB B:LYS100 4.2 7.6 1.0
N B:GLY102 4.3 7.5 1.0
O B:ASP104 4.4 8.4 1.0
C B:ASP104 4.4 9.2 1.0
C B:ALA103 4.4 10.1 1.0
CA B:ALA103 4.5 9.6 1.0
OD2 B:ASP104 4.6 21.6 1.0
CG B:ASP104 4.8 16.4 1.0
CG B:LYS100 4.8 9.2 1.0
O B:GLY102 4.9 8.7 1.0
CB B:ALA103 4.9 10.6 1.0

Iodine binding site 10 out of 14 in 8d8w

Go back to Iodine Binding Sites List in 8d8w
Iodine binding site 10 out of 14 in the Crystal Structure of Choe with SER38 Adopting Alternative Conformations


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 Choe with SER38 Adopting Alternative Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I405

b:32.0
occ:0.50
 O B:HOH743 3.2 38.6 1.0
NE2 B:GLN46 3.2 19.6 1.0
N B:GLY65 3.5 13.5 1.0
O B:HOH703 3.7 16.1 1.0
O B:LEU63 3.7 15.1 1.0
O B:GLY65 3.8 16.1 1.0
CA B:GLY65 3.8 14.9 1.0
O B:HOH680 3.8 29.8 1.0
C B:GLY65 3.9 16.5 1.0
C B:LEU63 4.0 13.6 1.0
O B:HOH879 4.0 40.3 1.0
N B:PRO64 4.1 11.8 1.0
O B:HOH712 4.1 22.3 1.0
CD B:GLN46 4.2 15.8 1.0
CD B:PRO64 4.2 11.8 1.0
CG B:GLN46 4.3 13.2 1.0
C B:PRO64 4.7 12.4 1.0
N B:GLU66 4.7 18.5 1.0
CB B:ALA62 4.7 15.2 1.0
N B:LEU63 4.8 13.0 1.0
C B:ALA62 4.8 14.3 1.0
CG B:PRO64 4.9 11.6 1.0
CA B:LEU63 4.9 12.6 1.0

Reference:

V.D.Pham, M.Couture, L.-A.Lortie, M.-E.Picard, S.Charette, R.Levesque, R.Shi. Crystal Structures of Bacterial Acetylcholinesterase Choe Provide Insights Into the Plasticity of Catalytic Ser in Regulating the Active Site Geometry and the Functional State of the Sgnh Hydrolases To Be Published.
Page generated: Thu Jul 27 17:46:25 2023

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