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Iodine in PDB 3lr0: Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH

Enzymatic activity of Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH

All present enzymatic activity of Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH:
2.7.13.3;

Protein crystallography data

The structure of Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH, PDB code: 3lr0 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.10 / 1.90
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 58.360, 58.360, 75.690, 90.00, 90.00, 120.00
R / Rfree (%) 21.1 / 25.4

Iodine Binding Sites:

The binding sites of Iodine atom in the Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH (pdb code 3lr0). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH, PDB code: 3lr0:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 3lr0

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Iodine binding site 1 out of 7 in the Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1

b:60.9
occ:0.70
 NE A:ARG109 3.8 25.7 0.5
CB A:ASP105 3.9 19.3 1.0
OG A:SER108 4.0 22.9 1.0
CG A:ASP105 4.1 21.7 1.0
O A:ASP105 4.3 18.4 1.0
OD1 A:ASP105 4.3 22.2 1.0
NH1 A:ARG109 4.3 28.3 0.5
CZ A:ARG109 4.3 27.3 0.5
CA A:ASP105 4.3 18.8 1.0
CD2 A:LEU45 4.4 26.9 1.0
CD A:ARG109 4.5 23.7 0.5
OD2 A:ASP105 4.5 21.9 1.0
CG A:ARG109 4.6 20.8 0.5
CB A:GLN41 4.6 25.8 1.0
C A:ASP105 4.7 17.9 1.0
CG A:ARG109 4.7 22.3 0.5
CG A:LEU45 4.8 23.4 1.0
CA A:GLN41 5.0 25.5 1.0

Iodine binding site 2 out of 7 in 3lr0

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Iodine binding site 2 out of 7 in the Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2

b:42.9
occ:0.27
 OE1 A:GLN46 3.4 17.9 0.5
CB A:ALA49 4.2 13.3 1.0
CA A:GLN46 4.4 17.2 0.5
O A:LEU45 4.4 18.1 1.0
CA A:GLN46 4.5 17.7 0.5
CD A:GLN46 4.6 17.6 0.5
N A:GLN46 4.6 17.5 1.0
C A:LEU45 4.7 18.7 1.0
CG A:GLN46 4.8 20.1 0.5
O A:HOH174 4.9 20.2 1.0
CB A:GLN46 5.0 17.1 0.5

Iodine binding site 3 out of 7 in 3lr0

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Iodine binding site 3 out of 7 in the Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I3

b:34.5
occ:0.50
 O A:HOH174 3.1 20.2 1.0
O A:HOH212 3.7 32.6 1.0
CD A:LYS52 3.8 15.0 1.0
CA A:ALA49 3.9 14.0 1.0
CB A:ALA49 4.2 13.3 1.0
NZ A:LYS52 4.2 19.8 1.0
CE A:LYS52 4.3 18.2 1.0
N A:ALA49 4.4 13.9 1.0
CG1 A:VAL48 4.5 13.1 1.0
CB A:LYS52 4.7 10.5 1.0
C A:VAL48 4.7 13.3 1.0
O A:VAL48 4.8 13.4 1.0
CG A:LYS52 4.8 12.5 1.0

Iodine binding site 4 out of 7 in 3lr0

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Iodine binding site 4 out of 7 in the Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I4

b:29.5
occ:1.00
 OG A:SER119 3.4 12.8 1.0
N A:ASP122 3.5 16.4 1.0
CE A:LYS89 3.7 19.3 1.0
CG A:LYS89 3.9 14.7 1.0
N A:ASN121 3.9 12.6 1.0
CA A:PHE90 4.0 9.4 1.0
N A:LYS91 4.0 10.5 1.0
CB A:SER119 4.0 12.3 1.0
C A:PHE90 4.0 10.5 1.0
O A:SER119 4.0 12.9 1.0
O A:LYS89 4.1 8.8 1.0
CA A:ASP122 4.1 18.2 1.0
CD A:LYS89 4.2 18.9 1.0
C A:SER119 4.2 12.0 1.0
N A:PHE90 4.2 9.4 1.0
C A:LYS89 4.2 10.5 1.0
CB A:LYS91 4.3 10.0 1.0
C A:VAL120 4.3 11.6 1.0
CA A:ASN121 4.4 14.9 1.0
CA A:VAL120 4.4 9.7 1.0
C A:ASN121 4.4 16.0 1.0
N A:VAL120 4.5 10.4 1.0
OD1 A:ASP122 4.6 28.9 1.0
O A:PHE90 4.6 9.6 1.0
O A:HOH210 4.7 33.5 1.0
CB A:LYS89 4.7 12.3 1.0
O A:HOH167 4.7 26.4 1.0
NZ A:LYS89 4.7 26.8 1.0
CA A:LYS91 4.7 11.1 1.0
CA A:SER119 4.8 11.6 1.0
CG A:ASP122 4.9 23.8 1.0

Iodine binding site 5 out of 7 in 3lr0

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Iodine binding site 5 out of 7 in the Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I5

b:50.5
occ:0.50
 I A:IOD5 0.0 50.5 0.5
I A:IOD5 2.0 45.1 0.5
NH1 A:ARG67 3.3 32.8 1.0
O A:HOH207 3.8 36.5 1.0
O A:HOH208 3.9 42.5 1.0
CD1 A:LEU70 3.9 20.9 1.0
NE A:ARG66 4.0 23.2 0.5
CE1 A:TYR137 4.4 19.2 1.0
NH2 A:ARG66 4.4 21.8 0.5
CZ A:ARG67 4.5 30.3 1.0
CG A:ARG66 4.6 20.8 0.5
CZ A:ARG66 4.7 24.1 0.5
CD A:ARG67 4.8 23.2 1.0
CD A:ARG66 4.9 23.2 0.5
OH A:TYR137 4.9 23.3 1.0
CG A:LEU70 5.0 15.7 1.0

Iodine binding site 6 out of 7 in 3lr0

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Iodine binding site 6 out of 7 in the Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I5

b:45.1
occ:0.50
 I A:IOD5 0.0 45.1 0.5
I A:IOD5 2.0 50.5 0.5
CD A:PRO83 3.5 18.4 1.0
N A:PRO83 3.7 17.4 1.0
NH1 A:ARG67 3.7 32.8 1.0
CE1 A:TYR137 3.8 19.2 1.0
CD1 A:LEU70 3.8 20.9 1.0
CG A:PRO83 4.0 19.2 1.0
CD1 A:TYR137 4.1 18.7 1.0
O A:HOH208 4.1 42.5 1.0
C A:TYR82 4.2 16.9 1.0
CB A:PRO83 4.4 17.2 1.0
CA A:PRO83 4.4 17.2 1.0
CA A:TYR82 4.6 16.3 1.0
CG1 A:VAL81 4.6 13.2 1.0
O A:TYR82 4.9 16.9 1.0
O A:VAL81 4.9 15.3 1.0
CZ A:ARG67 4.9 30.3 1.0
CZ A:TYR137 5.0 21.3 1.0

Iodine binding site 7 out of 7 in 3lr0

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Iodine binding site 7 out of 7 in the Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Periplasmic Domain of the Riss Sensor Protein From Burkholderia Pseudomallei, Iodide Phased at Low pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I6

b:48.6
occ:0.22
 O A:HOH198 3.1 33.8 1.0
NZ A:LYS131 3.3 32.9 1.0
CE A:LYS131 3.7 30.7 1.0
CB A:ASP113 3.8 17.7 1.0
OD2 A:ASP113 4.0 29.4 1.0
CA A:GLY111 4.1 18.2 1.0
N A:ASP113 4.2 16.0 1.0
CG A:ASP113 4.2 22.2 1.0
O A:LEU110 4.2 21.1 1.0
O A:HOH168 4.4 32.0 1.0
C A:GLY111 4.5 17.7 1.0
CA A:ASP113 4.5 16.4 1.0
N A:ASP112 4.7 17.3 1.0
C A:ASP113 4.8 14.5 1.0
N A:THR114 4.9 13.8 1.0
O A:GLY111 5.0 15.3 1.0

Reference:

T.E.Edwards, J.Abendroth, B.L.Staker, I.Phan, P.Myler, R.Stacy, L.Stewart, S.I.Miller, Seattle Structural Genomics Center For Infectious Disease(Ssgcid). Structural Basis For pH Sensing By the Periplasmic Domain of the Riss Histidine Kinase From Bukholderia Pseudomallei To Be Published.
Page generated: Sun Aug 11 15:37:34 2024

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