Iodine in PDB 5av3: Crystal Structure of DAPK1-Kaempferol Complex in the Presence of Iodide Ions.

Enzymatic activity of Crystal Structure of DAPK1-Kaempferol Complex in the Presence of Iodide Ions.

All present enzymatic activity of Crystal Structure of DAPK1-Kaempferol Complex in the Presence of Iodide Ions.:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of DAPK1-Kaempferol Complex in the Presence of Iodide Ions., PDB code: 5av3 was solved by T.Yokoyama, M.Mizuguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.16 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.884, 62.357, 88.329, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23.3

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of DAPK1-Kaempferol Complex in the Presence of Iodide Ions. (pdb code 5av3). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Crystal Structure of DAPK1-Kaempferol Complex in the Presence of Iodide Ions., PDB code: 5av3:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 5av3

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Iodine binding site 1 out of 9 in the Crystal Structure of DAPK1-Kaempferol Complex in the Presence of Iodide Ions.


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 DAPK1-Kaempferol Complex in the Presence of Iodide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I301

b:23.6
occ:0.42
 I A:IOD302 1.7 23.1 0.4
NZ A:LYS42 3.1 33.9 1.0
N A:ASP161 3.4 23.2 1.0
CA A:ASP161 3.7 23.6 1.0
N A:PHE162 3.8 20.3 1.0
CE A:LYS42 3.8 31.5 1.0
OE2 A:GLU64 3.8 28.5 1.0
CD1 A:LEU93 4.1 27.2 1.0
C A:ASP161 4.3 23.3 1.0
CG2 A:ILE77 4.3 22.8 1.0
CD2 A:LEU93 4.3 23.9 1.0
CD1 A:LEU68 4.3 21.8 1.0
CD2 A:LEU68 4.4 21.9 1.0
C A:ILE160 4.5 21.2 1.0
CD1 A:PHE162 4.6 22.0 1.0
CG A:LEU93 4.9 22.9 1.0
CD A:LYS42 4.9 27.3 1.0
CA A:ILE160 4.9 21.9 1.0
CB A:ILE160 4.9 22.5 1.0
CA A:PHE162 4.9 23.8 1.0
CG A:LEU68 4.9 22.2 1.0
CB A:ASP161 5.0 24.8 1.0
CB A:PHE162 5.0 22.8 1.0

Iodine binding site 2 out of 9 in 5av3

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Iodine binding site 2 out of 9 in the Crystal Structure of DAPK1-Kaempferol Complex in the Presence of Iodide Ions.


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 DAPK1-Kaempferol Complex in the Presence of Iodide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:23.1
occ:0.41
 I A:IOD301 1.7 23.6 0.4
NZ A:LYS42 3.2 33.9 1.0
CE A:LYS42 3.3 31.5 1.0
N A:ASP161 3.5 23.2 1.0
CD1 A:LEU93 3.5 27.2 1.0
CA A:ASP161 3.9 23.6 1.0
C15 A:KMP300 4.0 24.3 1.0
C5 A:KMP300 4.0 28.3 1.0
O12 A:KMP300 4.1 25.2 1.0
CB A:ILE160 4.2 22.5 1.0
C16 A:KMP300 4.5 25.3 1.0
C A:ILE160 4.6 21.2 1.0
C4 A:KMP300 4.6 28.3 1.0
CD2 A:LEU93 4.6 23.9 1.0
CD A:LYS42 4.6 27.3 1.0
CG A:LEU93 4.6 22.9 1.0
CA A:ILE160 4.7 21.9 1.0
CG2 A:ILE77 4.7 22.8 1.0
CD1 A:ILE160 4.7 24.8 1.0
CB A:ASP161 4.9 24.8 1.0
CG2 A:ILE160 5.0 21.7 1.0
N A:PHE162 5.0 20.3 1.0
CG1 A:ILE160 5.0 22.7 1.0

Iodine binding site 3 out of 9 in 5av3

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Iodine binding site 3 out of 9 in the Crystal Structure of DAPK1-Kaempferol Complex in the Presence of Iodide Ions.


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 DAPK1-Kaempferol Complex in the Presence of Iodide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:30.8
occ:0.31
 I A:IOD304 3.3 32.5 0.1
CG A:GLU143 3.4 34.4 1.0
N A:GLU143 3.5 25.9 1.0
OE1 A:GLU143 3.7 43.6 1.0
CD1 A:PHE102 3.7 37.4 1.0
CB A:GLU143 3.8 31.4 1.0
CD A:PRO142 3.9 23.1 1.0
CD A:GLU143 3.9 39.7 1.0
N A:PRO142 4.0 24.0 1.0
CB A:PRO142 4.0 26.7 1.0
CE1 A:PHE183 4.1 25.6 1.0
CB A:LYS141 4.1 22.9 1.0
CZ A:PHE183 4.2 24.2 1.0
CA A:GLU143 4.2 28.3 1.0
CD A:LYS141 4.2 25.9 1.0
CG A:PRO142 4.3 26.2 1.0
CG A:LYS141 4.3 23.8 1.0
C A:PRO142 4.3 25.4 1.0
CE1 A:PHE102 4.3 39.8 1.0
CA A:PRO142 4.4 24.4 1.0
CG A:PHE102 4.4 35.8 1.0
CB A:PHE102 4.5 32.2 1.0
C A:LYS141 4.6 23.3 1.0
CA A:LYS141 4.9 22.8 1.0

Iodine binding site 4 out of 9 in 5av3

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Iodine binding site 4 out of 9 in the Crystal Structure of DAPK1-Kaempferol Complex in the Presence of Iodide Ions.


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 DAPK1-Kaempferol Complex in the Presence of Iodide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:32.5
occ:0.15
 CG A:PRO142 3.3 26.2 1.0
I A:IOD303 3.3 30.8 0.3
CD1 A:PHE102 3.4 37.4 1.0
CB A:PRO142 3.7 26.7 1.0
CE1 A:PHE102 3.8 39.8 1.0
CZ A:PHE183 3.8 24.2 1.0
CD A:PRO142 3.9 23.1 1.0
CD1 A:ILE209 4.1 20.9 1.0
CE1 A:PHE183 4.5 25.6 1.0
CG A:PHE102 4.5 35.8 1.0
CG2 A:ILE209 4.5 23.7 1.0
O A:HOH518 4.6 38.8 1.0
CE2 A:PHE183 4.8 24.2 1.0
O A:HOH602 4.8 46.0 1.0
N A:PRO142 4.9 24.0 1.0
CB A:PHE102 4.9 32.2 1.0
CA A:PRO142 5.0 24.4 1.0

Iodine binding site 5 out of 9 in 5av3

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Iodine binding site 5 out of 9 in the Crystal Structure of DAPK1-Kaempferol Complex in the Presence of Iodide Ions.


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 DAPK1-Kaempferol Complex in the Presence of Iodide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:32.2
occ:0.21
 OG1 A:THR225 3.2 22.7 1.0
O A:HOH542 3.2 30.1 1.0
O A:HOH572 3.2 39.9 1.0
CA A:LYS222 3.7 29.6 1.0
CB A:THR225 3.8 22.6 1.0
O A:THR221 4.0 26.4 1.0
CD1 A:LEU218 4.1 28.8 1.0
CB A:PRO181 4.1 26.5 1.0
N A:LYS222 4.2 28.2 1.0
CG2 A:THR225 4.2 21.6 1.0
C A:THR221 4.3 28.5 1.0
CB A:LYS222 4.3 32.4 1.0
O A:HOH415 4.5 43.2 1.0
CG A:PRO181 4.5 28.4 1.0
OE2 A:GLU182 4.6 35.4 1.0
CG A:GLU182 4.6 27.9 1.0
O A:LYS222 4.7 24.2 1.0
C A:LYS222 4.7 28.4 1.0

Iodine binding site 6 out of 9 in 5av3

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Iodine binding site 6 out of 9 in the Crystal Structure of DAPK1-Kaempferol Complex in the Presence of Iodide Ions.


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 DAPK1-Kaempferol Complex in the Presence of Iodide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I306

b:23.3
occ:0.39
 O A:HOH598 3.2 27.1 1.0
O A:HOH565 3.4 26.1 1.0
NE2 A:GLN267 3.7 31.0 1.0
CG2 A:ILE266 3.9 19.6 1.0
N A:SER132 3.9 20.5 1.0
OG A:SER132 4.0 23.3 1.0
C A:HIS131 4.0 20.5 1.0
CA A:SER132 4.1 20.7 1.0
O A:HIS131 4.1 20.6 1.0
CB A:HIS131 4.2 19.1 1.0
CE1 A:TYR128 4.4 26.7 1.0
CG A:GLN267 4.4 28.0 1.0
CD A:GLN267 4.5 30.9 1.0
CD1 A:TYR128 4.5 25.2 1.0
CB A:SER132 4.6 22.1 1.0
O A:TYR128 4.7 19.8 1.0
CA A:HIS131 4.8 20.2 1.0

Iodine binding site 7 out of 9 in 5av3

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Iodine binding site 7 out of 9 in the Crystal Structure of DAPK1-Kaempferol Complex in the Presence of Iodide Ions.


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 DAPK1-Kaempferol Complex in the Presence of Iodide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I307

b:27.2
occ:0.19
 O A:HOH598 3.0 27.1 1.0
ND1 A:HIS131 3.1 19.7 1.0
N A:ILE266 3.3 21.6 1.0
CE1 A:HIS131 3.7 21.9 1.0
CA A:THR265 3.8 21.9 1.0
CG A:MET200 3.8 20.6 1.0
CB A:THR265 3.9 24.4 1.0
O A:HOH578 3.9 33.5 1.0
CG2 A:ILE266 3.9 19.6 1.0
CB A:LEU196 3.9 21.4 1.0
C A:THR265 4.0 22.1 1.0
CB A:ILE266 4.1 20.1 1.0
O A:LEU196 4.2 20.7 1.0
SD A:MET200 4.2 20.1 1.0
CG A:HIS131 4.2 19.4 1.0
CA A:ILE266 4.3 21.4 1.0
O A:HOH486 4.3 20.1 1.0
O A:HOH565 4.3 26.1 1.0
C A:LEU196 4.4 21.9 1.0
CG2 A:THR265 4.5 25.1 1.0
O A:HOH609 4.5 38.9 1.0
CD1 A:LEU196 4.6 21.9 1.0
CB A:HIS131 4.7 19.1 1.0
CA A:LEU196 4.8 22.4 1.0
N A:GLU197 4.8 23.1 1.0
NE2 A:HIS131 4.9 21.1 1.0
CG A:LEU196 4.9 22.4 1.0

Iodine binding site 8 out of 9 in 5av3

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Iodine binding site 8 out of 9 in the Crystal Structure of DAPK1-Kaempferol Complex in the Presence of Iodide Ions.


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 DAPK1-Kaempferol Complex in the Presence of Iodide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I308

b:31.7
occ:0.43
 CE A:LYS29 3.7 38.1 1.0
C A:CYS30 4.0 25.9 1.0
CA A:CYS30 4.0 25.2 1.0
N A:CYS30 4.1 23.8 1.0
C A:LYS29 4.2 26.1 1.0
N A:GLY16 4.2 30.2 1.0
N A:ARG31 4.2 25.4 1.0
CB A:LYS29 4.2 29.7 1.0
CA A:GLY16 4.3 31.7 1.0
O A:CYS30 4.3 24.8 1.0
CB A:ARG31 4.3 26.7 1.0
O A:LYS29 4.3 26.5 1.0
OE1 A:GLN38 4.4 34.9 1.0
O A:ASP14 4.5 28.3 1.0
CG A:LYS29 4.6 34.1 1.0
NZ A:LYS29 4.6 41.0 1.0
CD A:LYS29 4.7 35.8 1.0
C A:THR15 4.7 32.7 1.0
CA A:ARG31 4.8 25.3 1.0
CA A:LYS29 4.9 27.6 1.0
CG A:GLN38 4.9 29.6 1.0

Iodine binding site 9 out of 9 in 5av3

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Iodine binding site 9 out of 9 in the Crystal Structure of DAPK1-Kaempferol Complex in the Presence of Iodide Ions.


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 DAPK1-Kaempferol Complex in the Presence of Iodide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I309

b:45.7
occ:0.29
 NH2 A:ARG254 3.5 27.9 1.0
NH1 A:ARG254 3.7 28.2 1.0
CZ A:ARG254 4.0 29.1 1.0

Reference:

T.Yokoyama, Y.Kosaka, M.Mizuguchi. Structural Insight Into the Interactions Between Death-Associated Protein Kinase 1 and Natural Flavonoids. J.Med.Chem. V. 58 7400 2015.
ISSN: ISSN 0022-2623
PubMed: 26322379
DOI: 10.1021/ACS.JMEDCHEM.5B00893
Page generated: Sun Dec 13 19:38:26 2020

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