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Iodine in PDB 4qx5: Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design

Enzymatic activity of Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design

All present enzymatic activity of Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design:
2.7.11.12;

Protein crystallography data

The structure of Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design, PDB code: 4qx5 was solved by G.Y.Huang, O.O.Gerlits, M.P.Blakeley, B.Sankaran, A.Y.Kovalevsky, C.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.87 / 1.32
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 48.440, 48.440, 103.462, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 22.4

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Iodine atom in the Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design (pdb code 4qx5). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 18 binding sites of Iodine where determined in the Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design, PDB code: 4qx5:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 18 in 4qx5

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Iodine binding site 1 out of 18 in the Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:20.9
occ:0.28
 OD1 A:ASP334 2.6 32.3 1.0
NZ A:LYS337 3.4 19.2 1.0
CG A:ASP334 3.7 34.7 1.0
I A:IOD403 3.7 23.4 0.2
CD A:ARG333 3.8 16.2 1.0
CG A:ARG333 4.0 15.9 1.0
N A:ASP334 4.2 15.9 1.0
CE A:LYS337 4.3 18.6 1.0
CB A:ARG333 4.3 15.1 1.0
CA A:ASP334 4.3 18.2 1.0
CD A:LYS337 4.4 16.4 1.0
I A:IOD411 4.5 28.5 0.2
OD2 A:ASP334 4.5 39.0 1.0
C A:ARG333 4.5 14.6 1.0
CB A:ASP334 4.6 23.9 1.0
O A:ARG333 5.0 14.6 1.0

Iodine binding site 2 out of 18 in 4qx5

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Iodine binding site 2 out of 18 in the Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:23.4
occ:0.25
 I A:IOD411 3.0 28.5 0.2
OD2 A:ASP271 3.7 17.3 1.0
I A:IOD402 3.7 20.9 0.3
CG A:ASP271 3.8 16.4 1.0
CB A:ASP271 4.0 15.6 1.0
CD A:ARG333 4.2 16.2 1.0
CB A:ARG333 4.2 15.1 1.0
NE A:ARG333 4.3 15.5 1.0
O A:HOH531 4.3 29.4 0.8
OD1 A:ASP271 4.4 19.4 1.0
CG A:ARG333 4.8 15.9 1.0
OD1 A:ASP334 4.9 32.3 1.0

Iodine binding site 3 out of 18 in 4qx5

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Iodine binding site 3 out of 18 in the Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I404

b:27.8
occ:0.27
 I A:IOD406 2.2 25.4 0.2
OE1 A:GLU226 3.2 49.1 1.0
CG A:GLU226 3.3 36.4 1.0
O A:HOH594 3.4 52.0 1.0
CD A:GLU226 3.4 50.9 1.0
CD1 A:TYR227 4.0 23.4 1.0
CB A:PHE230 4.0 24.6 1.0
O A:GLU226 4.1 28.3 1.0
C A:GLU226 4.3 27.6 1.0
CG A:PHE230 4.3 23.5 1.0
CE1 A:TYR227 4.4 25.1 1.0
CB A:GLU226 4.4 31.6 1.0
OE2 A:GLU226 4.4 56.1 1.0
CB A:SER277 4.4 21.3 1.0
N A:TYR227 4.5 24.9 1.0
CA A:TYR227 4.6 23.7 1.0
CD2 A:PHE230 4.7 22.4 1.0
OG A:SER277 4.8 21.4 1.0
CD1 A:PHE230 4.9 28.5 1.0
CA A:GLU226 4.9 32.8 1.0

Iodine binding site 4 out of 18 in 4qx5

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Iodine binding site 4 out of 18 in the Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I405

b:29.9
occ:0.26
 O A:GLY341 2.6 22.4 1.0
OE1 A:GLN311 3.1 29.6 1.0
CA A:GLY341 3.3 20.5 1.0
C A:GLY341 3.3 19.1 1.0
CB A:SER347 3.6 35.1 1.0
CA A:SER347 3.6 33.8 1.0
N A:SER347 3.8 28.9 1.0
CG A:GLN311 3.9 22.3 1.0
CD A:GLN311 3.9 27.4 1.0
CG1 A:VAL346 4.0 28.9 1.0
CE2 A:PHE336 4.1 17.6 1.0
CZ A:PHE336 4.1 20.2 1.0
C A:VAL346 4.3 29.0 1.0
CB A:VAL346 4.4 25.4 1.0
O A:VAL346 4.6 37.6 1.0
N A:GLY341 4.6 19.1 1.0
O A:ILE340 4.6 19.4 1.0
N A:GLY342 4.6 18.5 1.0
O A:LEU343 4.7 26.7 1.0
OG A:SER347 4.9 43.9 1.0

Iodine binding site 5 out of 18 in 4qx5

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Iodine binding site 5 out of 18 in the Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I406

b:25.4
occ:0.20
 I A:IOD404 2.2 27.8 0.3
OE2 A:GLU254 3.0 28.3 0.4
OE1 A:GLU226 3.2 49.1 1.0
OG A:SER277 3.6 21.4 1.0
O A:HOH560 3.8 34.6 0.7
CE1 A:TYR227 3.8 25.1 1.0
CB A:SER277 3.9 21.3 1.0
CD A:GLU254 4.0 25.2 0.4
CD A:GLU226 4.1 50.9 1.0
OE2 A:GLU254 4.1 28.6 0.6
CD1 A:TYR227 4.2 23.4 1.0
CD1 A:LEU329 4.2 19.3 1.0
CD A:GLU254 4.4 24.8 0.6
CG A:GLU226 4.7 36.4 1.0
OE1 A:GLU254 4.7 24.9 0.6
OE1 A:GLU254 4.7 25.9 0.4
CG A:GLU254 4.8 23.2 0.4
CG2 A:THR327 4.8 19.4 1.0
OE2 A:GLU226 4.9 56.1 1.0
O A:HOH594 4.9 52.0 1.0
CE A:LYS223 5.0 47.1 1.0

Iodine binding site 6 out of 18 in 4qx5

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Iodine binding site 6 out of 18 in the Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I407

b:34.1
occ:0.21
 O A:HOH561 2.6 33.0 0.7
NZ A:LYS247 3.7 46.5 1.0
CE A:LYS247 3.8 38.1 1.0
OE2 A:GLU243 4.6 30.3 1.0

Iodine binding site 7 out of 18 in 4qx5

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Iodine binding site 7 out of 18 in the Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I408

b:93.2
occ:0.45
 O A:HOH566 2.6 46.3 1.0
O A:HOH607 3.6 22.1 0.7
O A:HOH594 4.6 52.0 1.0

Iodine binding site 8 out of 18 in 4qx5

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Iodine binding site 8 out of 18 in the Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I409

b:24.3
occ:0.41
 O A:HOH602 3.4 29.5 0.6
CD1 A:LEU339 3.8 24.3 1.0
CG A:LEU339 4.0 21.8 1.0
OG A:SER335 4.0 25.6 1.0
CA A:SER335 4.2 16.3 1.0
ND1 A:HIS338 4.2 24.4 1.0
CB A:SER335 4.3 19.7 1.0
CD2 A:LEU339 4.4 23.2 1.0
CB A:HIS338 4.7 22.4 1.0
O A:SER335 4.7 17.5 1.0
O A:ASP334 4.9 19.6 1.0
CG A:HIS338 4.9 21.5 1.0
C A:SER335 5.0 15.1 1.0

Iodine binding site 9 out of 18 in 4qx5

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Iodine binding site 9 out of 18 in the Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I410

b:22.3
occ:0.18
 O A:ILE263 2.8 16.1 1.0
O A:HOH503 3.7 16.9 0.9
C A:ILE263 3.9 15.2 1.0
CG1 A:ILE264 4.0 15.8 1.0
CA A:ILE264 4.2 14.7 1.0
CZ A:PHE274 4.3 14.0 1.0
N A:ILE264 4.5 15.3 1.0
NH2 A:ARG316 4.6 14.2 1.0
CB A:ILE264 4.7 14.5 1.0
OG1 A:THR272 4.8 13.8 1.0
CE1 A:PHE274 4.9 15.1 1.0

Iodine binding site 10 out of 18 in 4qx5

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Iodine binding site 10 out of 18 in the Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Pkg Agonist Design within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I411

b:28.5
occ:0.19
 O A:HOH531 2.7 29.4 0.8
I A:IOD403 3.0 23.4 0.2
N A:ARG333 3.8 16.2 1.0
OD2 A:ASP334 3.8 39.0 1.0
CG A:ASP334 3.9 34.7 1.0
N A:ASP334 3.9 15.9 1.0
CB A:ASP332 3.9 19.9 1.0
CB A:ARG333 4.0 15.1 1.0
OD1 A:ASP334 4.0 32.3 1.0
CG A:ASP332 4.2 23.4 1.0
CA A:ARG333 4.4 15.6 1.0
I A:IOD402 4.5 20.9 0.3
CB A:ASP334 4.5 23.9 1.0
OD2 A:ASP332 4.5 34.2 1.0
O A:ASP271 4.6 16.6 1.0
C A:ARG333 4.6 14.6 1.0
C A:ASP332 4.7 14.3 1.0
OD1 A:ASP332 4.7 23.7 1.0
CB A:ASP271 4.7 15.6 1.0
CA A:ASP334 4.8 18.2 1.0
CA A:ASP332 4.8 15.3 1.0
O A:HOH586 5.0 35.9 0.8

Reference:

G.Y.Huang, O.O.Gerlits, M.P.Blakeley, B.Sankaran, A.Y.Kovalevsky, C.Kim. Neutron Diffraction Reveals Hydrogen Bonds Critical For Cgmp-Selective Activation: Insights For Cgmp-Dependent Protein Kinase Agonist Design. Biochemistry V. 53 6725 2014.
ISSN: ISSN 0006-2960
PubMed: 25271401
DOI: 10.1021/BI501012V
Page generated: Sun Aug 11 19:45:02 2024

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