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Bromine in PDB 5av2: Crystal Structure of DAPK1-Kaempferol Complex in the Presence of Bromide Ions.

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

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

Protein crystallography data

The structure of Crystal Structure of DAPK1-Kaempferol Complex in the Presence of Bromide Ions., PDB code: 5av2 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) 31.17 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.830, 62.329, 88.377, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 20.9

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of DAPK1-Kaempferol Complex in the Presence of Bromide Ions. (pdb code 5av2). 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-Kaempferol Complex in the Presence of Bromide Ions., PDB code: 5av2:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7;

Bromine binding site 1 out of 7 in 5av2

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Bromine binding site 1 out of 7 in the Crystal Structure of DAPK1-Kaempferol Complex 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-Kaempferol Complex in the Presence of Bromide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br301

b:21.8
occ:0.55
 O A:HOH487 3.3 21.6 1.0
N A:ASP161 3.3 17.4 1.0
NZ A:LYS42 3.5 25.0 1.0
CD1 A:LEU93 3.6 22.0 1.0
CA A:ASP161 3.7 17.4 1.0
C5 A:KMP300 3.8 23.5 1.0
O12 A:KMP300 3.9 23.2 1.0
CD A:LYS42 4.0 23.4 1.0
C15 A:KMP300 4.0 21.1 1.0
CB A:ILE160 4.1 16.4 1.0
CE A:LYS42 4.2 26.1 1.0
C4 A:KMP300 4.4 25.2 1.0
C A:ILE160 4.4 20.5 1.0
CB A:ASP161 4.5 18.8 1.0
C16 A:KMP300 4.6 22.9 1.0
CD1 A:ILE160 4.6 20.0 1.0
CA A:ILE160 4.6 18.8 1.0
OE2 A:GLU64 4.8 23.9 1.0
N A:PHE162 4.8 18.0 1.0
CG1 A:ILE160 4.8 18.2 1.0
C A:ASP161 4.9 17.8 1.0
CG2 A:ILE160 4.9 19.3 1.0
C6 A:KMP300 4.9 26.8 1.0
CG2 A:ILE77 4.9 23.7 1.0
CG A:LEU93 4.9 18.4 1.0
O29 A:KMP300 5.0 26.1 1.0
CD2 A:LEU93 5.0 21.1 1.0

Bromine binding site 2 out of 7 in 5av2

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Bromine binding site 2 out of 7 in the Crystal Structure of DAPK1-Kaempferol Complex 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-Kaempferol Complex in the Presence of Bromide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br302

b:30.0
occ:0.33
 N A:GLU143 3.0 19.8 1.0
O A:HOH656 3.3 31.8 1.0
CG A:GLU143 3.4 32.2 1.0
CD A:PRO142 3.5 19.3 1.0
CB A:GLU143 3.5 28.0 1.0
N A:PRO142 3.6 20.0 1.0
OE1 A:GLU143 3.8 47.5 1.0
CD A:GLU143 3.8 42.7 1.0
CB A:LYS141 3.8 17.8 1.0
CB A:PRO142 3.8 22.8 1.0
CA A:GLU143 3.9 23.7 1.0
C A:PRO142 3.9 20.4 1.0
CG A:LYS141 4.0 19.6 1.0
CD A:LYS141 4.0 22.3 1.0
CA A:PRO142 4.0 20.4 1.0
CD1 A:PHE102 4.1 34.5 1.0
CG A:PRO142 4.1 20.3 1.0
CE2 A:PHE183 4.1 23.7 1.0
C A:LYS141 4.2 20.8 1.0
CZ A:PHE183 4.2 19.9 1.0
CB A:PHE102 4.3 28.9 1.0
CG A:PHE102 4.4 32.8 1.0
CA A:LYS141 4.6 17.8 1.0
OE2 A:GLU143 4.7 47.5 1.0
CE1 A:PHE102 4.9 37.4 1.0
O A:LYS141 5.0 18.1 1.0

Bromine binding site 3 out of 7 in 5av2

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Bromine binding site 3 out of 7 in the Crystal Structure of DAPK1-Kaempferol Complex 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-Kaempferol Complex in the Presence of Bromide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br303

b:23.6
occ:0.27
 O A:HOH614 2.6 22.9 1.0
O A:HOH649 2.8 25.8 1.0
ND1 A:HIS131 2.9 16.6 1.0
N A:ILE266 3.0 16.6 1.0
CG2 A:ILE266 3.4 16.7 1.0
CB A:ILE266 3.6 17.1 1.0
CE1 A:HIS131 3.7 14.9 1.0
CA A:ILE266 3.8 15.9 1.0
CB A:THR265 3.9 19.9 1.0
CA A:THR265 3.9 18.4 1.0
C A:THR265 3.9 16.7 1.0
CG A:HIS131 3.9 15.9 1.0
O A:HOH589 4.0 21.6 1.0
CG A:MET200 4.0 15.8 1.0
SD A:MET200 4.2 16.9 1.0
CB A:LEU196 4.2 16.4 1.0
CB A:HIS131 4.2 17.0 1.0
O A:HOH601 4.3 30.0 1.0
O A:HOH666 4.3 34.4 1.0
CG2 A:THR265 4.6 20.5 1.0
CD1 A:LEU196 4.6 19.3 1.0
O A:LEU196 4.6 17.7 1.0
C A:LEU196 4.8 20.2 1.0
NE2 A:HIS131 4.9 14.8 1.0
O A:HOH516 4.9 19.7 1.0
O A:HOH585 4.9 30.4 1.0
OG1 A:THR265 5.0 19.6 1.0
C A:ILE266 5.0 18.3 1.0
N A:GLN267 5.0 18.4 1.0

Bromine binding site 4 out of 7 in 5av2

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Bromine binding site 4 out of 7 in the Crystal Structure of DAPK1-Kaempferol Complex 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-Kaempferol Complex in the Presence of Bromide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br304

b:28.8
occ:0.24
 O A:HOH585 2.5 30.4 1.0
NE2 A:GLN267 3.2 31.7 1.0
O A:HOH589 3.4 21.6 1.0
O A:HOH649 3.5 25.8 1.0
OG A:SER132 3.7 20.6 1.0
CG2 A:ILE266 3.7 16.7 1.0
N A:SER132 4.0 15.6 1.0
CE1 A:TYR128 4.0 24.2 1.0
CG A:GLN267 4.1 24.1 1.0
CA A:SER132 4.1 18.1 1.0
CD A:GLN267 4.1 30.2 1.0
CD1 A:TYR128 4.1 22.3 1.0
C A:HIS131 4.2 17.0 1.0
CB A:HIS131 4.3 17.0 1.0
O A:HIS131 4.4 17.3 1.0
CB A:SER132 4.5 19.8 1.0
O A:TYR128 4.5 17.0 1.0
O A:HOH623 4.8 34.0 1.0
CA A:HIS131 4.9 17.0 1.0
CZ A:TYR128 4.9 26.3 1.0

Bromine binding site 5 out of 7 in 5av2

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Bromine binding site 5 out of 7 in the Crystal Structure of DAPK1-Kaempferol Complex 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-Kaempferol Complex in the Presence of Bromide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br305

b:30.8
occ:0.32
 OG1 A:THR225 2.9 18.7 1.0
O A:HOH599 3.2 36.5 1.0
O A:HOH558 3.3 28.2 1.0
CB A:THR225 3.5 19.1 1.0
CA A:LYS222 3.6 24.1 1.0
CD1 A:LEU218 3.8 22.7 1.0
CG2 A:THR225 3.9 17.6 1.0
CB A:LYS222 4.0 27.5 1.0
N A:LYS222 4.0 22.2 1.0
O A:THR221 4.1 22.7 1.0
CB A:PRO181 4.1 21.8 1.0
C A:THR221 4.2 24.5 1.0
C A:LYS222 4.6 23.4 1.0
O A:LYS222 4.6 19.7 1.0
CG A:PRO181 4.7 23.6 1.0
OE2 A:GLU182 4.7 31.3 1.0
O A:HOH418 4.7 40.2 1.0
CG A:GLU182 4.7 26.4 1.0
CA A:THR225 4.9 19.1 1.0
N A:GLU182 4.9 19.2 1.0
O A:GLY219 4.9 24.2 1.0

Bromine binding site 6 out of 7 in 5av2

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Bromine binding site 6 out of 7 in the Crystal Structure of DAPK1-Kaempferol Complex 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-Kaempferol Complex in the Presence of Bromide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br306

b:32.3
occ:0.27
 O A:HOH635 2.9 32.7 1.0
CE A:LYS29 3.2 38.4 1.0
N A:GLU17 3.3 26.5 1.0
CD A:LYS29 3.7 32.3 1.0
CA A:GLY16 3.7 30.0 1.0
CB A:GLU17 3.9 34.6 1.0
C A:GLY16 4.0 27.5 1.0
NZ A:LYS29 4.2 38.5 1.0
CG A:LYS29 4.2 29.8 1.0
CB A:LYS29 4.2 22.3 1.0
CA A:GLU17 4.2 27.9 1.0
OE2 A:GLU17 4.7 45.5 1.0
N A:GLY16 4.7 23.4 1.0
O A:HOH514 4.7 35.1 1.0

Bromine binding site 7 out of 7 in 5av2

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Bromine binding site 7 out of 7 in the Crystal Structure of DAPK1-Kaempferol Complex 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-Kaempferol Complex in the Presence of Bromide Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br307

b:44.3
occ:0.40
 NH2 A:ARG254 3.4 25.1 1.0
NH1 A:ARG254 3.4 22.6 1.0
CZ A:ARG254 3.9 25.0 1.0
O A:HOH634 4.9 38.8 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: Wed Jul 10 23:17:22 2024

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