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Bromine in PDB 5av1: Crystal Structure of DAPK1 in the Presence of Bromide Ions.

Enzymatic activity of Crystal Structure of DAPK1 in the Presence of Bromide Ions.

All present enzymatic activity of Crystal Structure of DAPK1 in the Presence of Bromide Ions.:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of DAPK1 in the Presence of Bromide Ions., PDB code: 5av1 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) 28.57 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.819, 62.279, 88.449, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 21.5

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of DAPK1 in the Presence of Bromide Ions. (pdb code 5av1). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 7 binding sites of Bromine where determined in the Crystal Structure of DAPK1 in the Presence of Bromide Ions., PDB code: 5av1:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7;

Bromine binding site 1 out of 7 in 5av1

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Bromine binding site 1 out of 7 in the Crystal Structure of DAPK1 in the Presence of Bromide Ions.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of DAPK1 in the Presence of Bromide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br301

b:20.5
occ:0.41
 BR A:BR305 1.4 26.5 0.2
O A:HOH647 3.4 38.3 1.0
O A:HOH520 3.4 23.2 1.0
N A:ASP161 3.4 17.4 1.0
NZ A:LYS42 3.6 27.0 1.0
CA A:ASP161 3.7 18.7 1.0
O A:HOH669 3.7 31.6 1.0
CD1 A:LEU93 3.9 24.2 1.0
CD A:LYS42 3.9 24.9 1.0
CB A:ILE160 4.2 19.2 1.0
CE A:LYS42 4.2 27.3 1.0
CB A:ASP161 4.4 22.7 1.0
CD1 A:ILE160 4.4 23.6 1.0
C A:ILE160 4.5 19.5 1.0
CA A:ILE160 4.8 18.7 1.0
CG1 A:ILE160 4.8 18.4 1.0
C A:ASP161 4.9 20.9 1.0
CG A:ASP161 4.9 28.5 1.0
N A:PHE162 4.9 19.4 1.0
OD1 A:ASP161 5.0 26.3 1.0

Bromine binding site 2 out of 7 in 5av1

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Bromine binding site 2 out of 7 in the Crystal Structure of DAPK1 in the Presence of Bromide Ions.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of DAPK1 in the Presence of Bromide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br302

b:33.2
occ:0.28
 O A:HOH642 2.8 37.6 1.0
OE2 A:GLU17 3.4 40.9 1.0
CD A:LYS29 3.5 33.6 1.0
N A:GLU17 3.5 27.4 1.0
CA A:GLY16 3.8 30.6 1.0
CG A:GLU17 3.9 35.1 1.0
CD A:GLU17 4.1 40.4 1.0
CE A:LYS29 4.1 38.7 1.0
CG A:LYS29 4.1 28.5 1.0
C A:GLY16 4.2 28.8 1.0
NZ A:LYS29 4.2 41.0 1.0
CB A:LYS29 4.3 24.5 1.0
CB A:GLU17 4.3 34.5 1.0
O A:HOH569 4.4 35.5 1.0
CA A:GLU17 4.5 29.1 1.0
N A:GLY16 4.7 28.2 1.0

Bromine binding site 3 out of 7 in 5av1

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Bromine binding site 3 out of 7 in the Crystal Structure of DAPK1 in the Presence of Bromide Ions.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of DAPK1 in the Presence of Bromide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br303

b:28.6
occ:0.33
 O A:HOH620 2.5 24.2 1.0
O A:HOH654 2.8 27.7 1.0
ND1 A:HIS131 2.9 17.6 1.0
N A:ILE266 3.0 17.6 1.0
CG2 A:ILE266 3.4 19.3 1.0
CE1 A:HIS131 3.6 17.1 1.0
CB A:ILE266 3.6 16.9 1.0
CA A:THR265 3.9 19.1 1.0
CB A:THR265 3.9 20.0 1.0
CA A:ILE266 3.9 17.1 1.0
C A:THR265 3.9 19.1 1.0
CG A:HIS131 3.9 17.1 1.0
CG A:MET200 4.0 18.8 1.0
O A:HOH586 4.1 22.7 1.0
CB A:LEU196 4.1 18.1 1.0
SD A:MET200 4.2 17.4 1.0
CB A:HIS131 4.3 17.1 1.0
O A:HOH603 4.3 31.5 1.0
O A:HOH672 4.4 36.7 1.0
O A:LEU196 4.5 18.3 1.0
CG2 A:THR265 4.6 21.6 1.0
CD1 A:LEU196 4.6 21.9 1.0
C A:LEU196 4.8 18.9 1.0
NE2 A:HIS131 4.8 17.1 1.0
O A:HOH519 4.8 22.2 1.0
O A:HOH548 5.0 32.7 1.0
CD2 A:HIS131 5.0 17.5 1.0
OG1 A:THR265 5.0 20.7 1.0

Bromine binding site 4 out of 7 in 5av1

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Bromine binding site 4 out of 7 in the Crystal Structure of DAPK1 in the Presence of Bromide Ions.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of DAPK1 in the Presence of Bromide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br304

b:29.1
occ:0.24
 O A:HOH548 2.5 32.7 1.0
NE2 A:GLN267 3.4 31.2 1.0
O A:HOH586 3.4 22.7 1.0
O A:HOH654 3.5 27.7 1.0
OG A:SER132 3.7 22.0 1.0
CG2 A:ILE266 3.8 19.3 1.0
CE1 A:TYR128 4.0 22.6 1.0
N A:SER132 4.1 18.0 1.0
CG A:GLN267 4.1 23.8 1.0
CD1 A:TYR128 4.1 23.0 1.0
CA A:SER132 4.2 18.4 1.0
CD A:GLN267 4.2 30.6 1.0
C A:HIS131 4.3 18.0 1.0
CB A:HIS131 4.4 17.1 1.0
O A:HIS131 4.4 18.7 1.0
CB A:SER132 4.6 19.9 1.0
O A:TYR128 4.6 18.1 1.0
O A:HOH631 4.9 34.5 1.0
CZ A:TYR128 5.0 22.9 1.0
CA A:HIS131 5.0 17.7 1.0

Bromine binding site 5 out of 7 in 5av1

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Bromine binding site 5 out of 7 in the Crystal Structure of DAPK1 in the Presence of Bromide Ions.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of DAPK1 in the Presence of Bromide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br305

b:26.5
occ:0.21
 BR A:BR301 1.4 20.5 0.4
O A:HOH520 2.9 23.2 1.0
N A:ASP161 3.3 17.4 1.0
CD1 A:LEU93 3.6 24.2 1.0
CG2 A:ILE77 3.9 24.0 1.0
CB A:ILE160 3.9 19.2 1.0
CA A:ASP161 3.9 18.7 1.0
O A:HOH669 4.0 31.6 1.0
CD2 A:LEU93 4.2 23.8 1.0
CA A:ILE160 4.2 18.7 1.0
C A:ILE160 4.2 19.5 1.0
CG1 A:ILE77 4.3 24.6 1.0
CG A:LEU93 4.5 19.8 1.0
CB A:ILE77 4.5 21.9 1.0
NZ A:LYS42 4.5 27.0 1.0
CG2 A:ILE160 4.6 20.9 1.0
O A:HOH647 4.7 38.3 1.0
N A:PHE162 4.8 19.4 1.0
CD A:LYS42 4.8 24.9 1.0
CD1 A:ILE160 4.9 23.6 1.0
CG1 A:ILE160 4.9 18.4 1.0
C A:ASP161 4.9 20.9 1.0
CB A:ASP161 5.0 22.7 1.0

Bromine binding site 6 out of 7 in 5av1

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Bromine binding site 6 out of 7 in the Crystal Structure of DAPK1 in the Presence of Bromide Ions.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of DAPK1 in the Presence of Bromide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br306

b:37.1
occ:0.31
 NH2 A:ARG254 3.4 24.8 1.0
NH1 A:ARG254 3.4 24.7 1.0
CZ A:ARG254 3.9 24.3 1.0

Bromine binding site 7 out of 7 in 5av1

Go back to Bromine Binding Sites List in 5av1
Bromine binding site 7 out of 7 in the Crystal Structure of DAPK1 in the Presence of Bromide Ions.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of DAPK1 in the Presence of Bromide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br307

b:53.7
occ:1.00
 O A:HOH619 2.8 39.2 1.0
O A:HOH537 2.9 28.5 1.0
OG1 A:THR225 3.0 19.6 1.0
CB A:THR225 3.5 18.9 1.0
CA A:LYS222 3.6 22.9 1.0
CD1 A:LEU218 3.9 26.2 1.0
O A:THR221 4.0 23.4 1.0
CG2 A:THR225 4.0 18.8 1.0
CB A:PRO181 4.0 23.9 1.0
N A:LYS222 4.0 23.8 1.0
CB A:LYS222 4.1 26.7 1.0
O A:HOH658 4.2 41.0 1.0
C A:THR221 4.2 23.7 1.0
CG A:PRO181 4.4 25.9 1.0
OE2 A:GLU182 4.5 29.7 1.0
CG A:GLU182 4.6 25.8 1.0
C A:LYS222 4.6 24.7 1.0
O A:LYS222 4.6 21.1 1.0
N A:GLU182 4.8 21.6 1.0
O A:GLY219 4.9 24.6 1.0
CA A:THR225 4.9 19.4 1.0
CD A:GLU182 4.9 29.5 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: Mon Jul 7 08:00:37 2025

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