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Bromine in PDB 4ygj: Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein

Enzymatic activity of Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein

All present enzymatic activity of Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein:
4.2.1.1;

Protein crystallography data

The structure of Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein, PDB code: 4ygj was solved by J.M.Fox, K.Kang, W.Sherman, A.Heroux, G.M.Sastry, M.Baghbanzadeh, M.R.Lockett, G.M.Whitesides, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.299, 41.379, 72.460, 90.00, 104.64, 90.00
R / Rfree (%) 12.7 / 14.7

Other elements in 4ygj:

The structure of Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein (pdb code 4ygj). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 10 binding sites of Bromine where determined in the Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein, PDB code: 4ygj:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 10 in 4ygj

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Bromine binding site 1 out of 10 in the Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br302

b:11.5
occ:0.30
 O A:HOH647 1.4 10.5 1.0
BR A:BR303 1.6 14.1 0.3
ZN A:ZN301 2.6 8.0 1.0
OG1 A:THR199 3.4 8.2 1.0
O A:HOH556 3.4 13.1 1.0
ND1 A:HIS119 3.4 7.4 1.0
NE2 A:HIS94 3.7 8.2 1.0
N A:THR199 3.8 8.3 1.0
BR A:BR304 3.9 21.9 0.5
CE1 A:HIS94 3.9 8.0 1.0
CE1 A:HIS119 4.0 7.3 1.0
CB A:THR199 4.2 8.0 1.0
CH2 A:TRP209 4.3 9.1 1.0
CG2 A:THR199 4.3 9.0 1.0
CG A:HIS119 4.3 7.2 1.0
CZ2 A:TRP209 4.3 9.0 1.0
NE2 A:HIS96 4.3 7.8 1.0
CA A:THR199 4.5 8.2 1.0
CB A:HIS119 4.6 7.3 1.0
CA A:LEU198 4.7 9.0 1.0
C A:LEU198 4.7 8.2 1.0
OE1 A:GLU106 4.8 8.1 1.0
CE1 A:HIS96 4.9 8.7 1.0
CD2 A:HIS94 5.0 7.7 1.0

Bromine binding site 2 out of 10 in 4ygj

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Bromine binding site 2 out of 10 in the Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br303

b:14.1
occ:0.30
 BR A:BR302 1.6 11.5 0.3
O A:HOH647 2.9 10.5 1.0
BR A:BR304 3.6 21.9 0.5
CD2 A:LEU198 3.6 15.5 1.0
CA A:LEU198 3.7 9.0 1.0
N A:THR199 3.7 8.3 1.0
CZ2 A:TRP209 4.0 9.0 1.0
ZN A:ZN301 4.1 8.0 1.0
O A:HOH556 4.2 13.1 1.0
CH2 A:TRP209 4.2 9.1 1.0
CG2 A:VAL143 4.2 9.0 1.0
C A:LEU198 4.2 8.2 1.0
CB A:LEU198 4.3 11.1 1.0
OG1 A:THR199 4.5 8.2 1.0
O A:SER197 4.6 7.9 1.0
ND1 A:HIS119 4.6 7.4 1.0
CG1 A:VAL143 4.7 8.8 1.0
CG A:LEU198 4.7 13.9 1.0
CE1 A:HIS94 4.7 8.0 1.0
N A:LEU198 4.8 8.4 1.0
CG2 A:THR199 4.8 9.0 1.0
CG2 A:VAL121 4.8 9.3 1.0
CA A:THR199 4.9 8.2 1.0
NE2 A:HIS94 4.9 8.2 1.0
CB A:THR199 4.9 8.0 1.0
CB A:VAL143 5.0 8.0 1.0

Bromine binding site 3 out of 10 in 4ygj

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Bromine binding site 3 out of 10 in the Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br304

b:21.9
occ:0.50
 O A:HOH640 2.3 26.1 1.0
O A:HOH556 3.1 13.1 1.0
NE2 A:GLN92 3.4 12.8 1.0
BR A:BR303 3.6 14.1 0.3
CE1 A:HIS94 3.7 8.0 1.0
O A:HOH592 3.8 24.1 1.0
BR A:BR302 3.9 11.5 0.3
CG2 A:VAL121 4.0 9.3 1.0
CD2 A:LEU198 4.2 15.5 1.0
O A:HOH647 4.2 10.5 1.0
ND1 A:HIS94 4.4 8.5 1.0
NE2 A:HIS94 4.5 8.2 1.0
O A:HOH568 4.5 23.3 1.0
O A:HOH590 4.5 19.8 1.0
CD A:GLN92 4.6 9.7 1.0
OG1 A:THR200 4.6 11.5 1.0
CG1 A:VAL121 4.6 9.2 1.0
CB A:VAL121 4.9 8.5 1.0
O A:HOH572 4.9 16.6 1.0

Bromine binding site 4 out of 10 in 4ygj

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Bromine binding site 4 out of 10 in the Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br305

b:20.8
occ:0.50
 O A:HOH590 3.1 19.8 1.0
O A:HOH650 3.4 35.3 1.0
CG A:PRO202 3.8 15.6 1.0
CD A:PRO202 3.9 14.2 1.0
CG2 A:VAL135 4.2 11.4 1.0
CD1 A:LEU198 4.2 15.4 1.0
CE2 A:PHE131 4.2 14.5 1.0
CD1 A:LEU204 4.4 14.2 1.0
CG1 A:VAL135 4.4 12.7 1.0
CB A:VAL135 4.6 11.4 1.0
CZ A:PHE131 4.7 14.3 1.0

Bromine binding site 5 out of 10 in 4ygj

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Bromine binding site 5 out of 10 in the Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br306

b:18.2
occ:0.50
 O A:HOH552 3.3 13.4 1.0
CG A:PRO247 3.6 12.2 0.5
NE2 A:GLN249 3.6 11.5 1.0
O A:HOH613 3.6 31.3 1.0
CB A:PRO13 4.0 12.2 1.0
CD A:PRO247 4.0 9.6 0.5
C A:PRO13 4.1 11.3 1.0
N A:GLU14 4.2 12.4 1.0
O A:PRO13 4.2 11.5 1.0
CA A:GLU14 4.3 13.7 1.0
CD A:PRO247 4.3 9.2 0.5
CG A:PRO247 4.3 9.1 0.5
CB A:PRO247 4.5 9.4 0.5
CD A:GLN249 4.5 10.8 1.0
OE1 A:GLN249 4.5 13.2 1.0
CA A:PRO13 4.7 11.2 1.0
CB A:GLU14 4.7 17.7 1.0
CB A:PRO247 5.0 9.2 0.5

Bromine binding site 6 out of 10 in 4ygj

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Bromine binding site 6 out of 10 in the Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br307

b:47.3
occ:0.50
 NZ A:LYS213 3.5 33.7 1.0
CB A:GLU214 3.8 10.4 1.0
CA A:GLU214 3.8 9.9 1.0
CG A:LYS213 4.0 14.9 1.0
CG A:GLU214 4.1 12.1 1.0
N A:GLU214 4.1 9.5 1.0
CD A:LYS213 4.3 19.7 1.0
O A:LYS213 4.3 11.9 1.0
C A:LYS213 4.4 9.6 1.0
CE A:LYS213 4.4 31.5 1.0
CD A:GLU214 4.7 15.4 1.0
CB A:LYS213 4.8 12.1 1.0
CD A:PRO215 4.9 10.3 0.5
CD A:PRO215 4.9 10.9 0.5

Bromine binding site 7 out of 10 in 4ygj

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Bromine binding site 7 out of 10 in the Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br308

b:32.7
occ:0.50
 O A:HOH574 3.3 19.2 1.0
CE2 A:PHE260 3.7 20.2 1.0
CZ A:PHE260 3.9 17.8 1.0
CB A:THR35 3.9 14.7 1.0
CZ2 A:TRP192 4.0 11.9 1.0
O A:HOH456 4.0 24.9 1.0
CG2 A:THR35 4.1 15.4 1.0
CD A:LYS213 4.3 19.7 1.0
O A:HOH663 4.5 30.9 1.0
OG1 A:THR35 4.5 14.6 1.0
CE2 A:TRP192 4.7 10.3 1.0
NE1 A:TRP192 4.7 11.2 1.0
O A:THR35 4.8 17.9 1.0
CH2 A:TRP192 4.9 11.7 1.0
CD2 A:PHE260 4.9 17.7 1.0
CA A:THR35 4.9 13.7 1.0

Bromine binding site 8 out of 10 in 4ygj

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Bromine binding site 8 out of 10 in the Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br309

b:26.2
occ:0.50
 O A:HOH430 3.0 18.8 1.0
O A:HOH463 3.0 32.7 1.0
CE A:LYS257 3.7 21.3 1.0
CD A:LYS257 4.0 18.6 1.0
NZ A:LYS257 4.1 24.8 1.0
OD2 A:ASP41 4.2 16.6 1.0
CG A:LYS257 4.2 13.8 1.0
CG A:ASP41 4.3 15.1 1.0
CB A:ASP41 4.4 14.8 1.0
CD A:LYS39 4.4 30.9 1.0
CB A:LYS39 4.4 22.9 1.0
CG A:LYS39 4.8 31.3 1.0
OE1 A:GLN255 4.8 52.4 0.5
O A:HOH450 4.9 28.0 1.0
OD1 A:ASP41 4.9 16.9 1.0
O A:HOH419 4.9 22.1 1.0
CG A:GLN255 4.9 12.6 0.5

Bromine binding site 9 out of 10 in 4ygj

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Bromine binding site 9 out of 10 in the Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br310

b:25.8
occ:0.50
 O A:HOH661 2.7 29.7 1.0
O A:HOH508 2.9 26.6 1.0
NZ A:LYS154 3.0 17.8 1.0
N A:SER217 3.5 11.4 1.0
CA A:ILE216 3.7 9.9 1.0
O A:HOH467 3.8 25.0 1.0
O A:HOH449 3.8 17.7 1.0
CB A:ILE216 3.9 10.7 1.0
CD A:LYS154 4.0 17.1 1.0
CE A:LYS154 4.0 18.2 1.0
CG2 A:ILE216 4.0 12.0 1.0
C A:ILE216 4.1 10.6 1.0
OG A:SER217 4.1 19.5 0.3
CB A:SER217 4.5 12.0 0.3
O A:PRO215 4.5 12.7 1.0
CB A:SER217 4.5 13.3 0.4
CA A:SER217 4.5 11.3 0.3
CA A:SER217 4.5 11.7 0.4
O A:SER217 4.6 12.3 1.0
CA A:SER217 4.6 12.4 0.3
O A:HOH458 4.6 24.4 1.0
N A:ILE216 4.8 9.7 1.0
OG A:SER217 4.9 11.2 0.3
CB A:SER217 4.9 17.4 0.3
CA A:PRO186 4.9 13.1 1.0
O A:LEU185 5.0 11.6 0.5

Bromine binding site 10 out of 10 in 4ygj

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Bromine binding site 10 out of 10 in the Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Nabr--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br311

b:29.4
occ:0.50
 OD1 A:ASP165 2.4 77.9 1.0
O A:HOH577 3.1 19.2 1.0
CG A:ASP165 3.4 56.2 1.0
O A:HOH446 3.5 25.1 1.0
CE A:LYS228 3.7 28.8 1.0
CD A:LYS228 3.7 22.9 1.0
OD2 A:ASP165 3.8 70.0 1.0
CG A:LYS225 3.9 17.6 1.0
CD A:LYS225 4.2 17.6 1.0
CB A:LYS225 4.2 15.9 1.0
O A:HOH627 4.3 26.4 1.0
CB A:LYS228 4.6 13.3 1.0
CB A:ASP165 4.6 34.4 1.0
CE A:LYS225 4.7 18.9 1.0
CA A:LYS225 4.7 13.5 1.0
N A:ASP165 4.7 16.1 1.0
CG A:LYS228 4.8 15.9 1.0
CA A:ASP165 4.8 20.1 1.0
O A:LYS225 4.8 12.9 1.0
O A:HOH575 4.8 22.3 1.0

Reference:

J.M.Fox, K.Kang, W.Sherman, A.Heroux, M.Sastry, M.Baghbanzadeh, M.R.Lockett, G.M.Whitesides. Interactions Between Hofmeister Anions and the Binding Pocket of A Protein. J.Am.Chem.Soc. 2015.
ISSN: ESSN 1520-5126
PubMed: 25738615
DOI: 10.1021/JACS.5B00187
Page generated: Wed Jul 10 23:05:36 2024

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