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Bromine in PDB 3x42: Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide

Enzymatic activity of Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide

All present enzymatic activity of Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide:
1.4.3.21;

Protein crystallography data

The structure of Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide, PDB code: 3x42 was solved by T.Okajima, S.Nakanishi, T.Murakawa, M.Kataoka, H.Hayashi, A.Hamaguchi, T.Nakai, Y.Kawano, H.Yamaguchi, K.Tanizawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.74 / 1.88
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 192.684, 63.508, 158.099, 90.00, 117.55, 90.00
R / Rfree (%) 15.8 / 19

Other elements in 3x42:

The structure of Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide also contains other interesting chemical elements:

Potassium (K) 2 atoms
Copper (Cu) 2 atoms
Sodium (Na) 2 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide (pdb code 3x42). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide, PDB code: 3x42:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 3x42

Go back to Bromine Binding Sites List in 3x42
Bromine binding site 1 out of 8 in the Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide


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 Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br702

b:36.9
occ:1.00
 OG A:SER529 3.3 17.3 1.0
NH1 A:ARG532 3.4 24.7 1.0
NE A:ARG532 3.5 19.6 1.0
CA A:SER562 3.6 16.1 1.0
CB A:SER562 3.7 18.8 1.0
CZ A:ARG532 3.9 25.4 1.0
N A:GLY563 3.9 14.7 1.0
CB A:SER529 4.0 13.6 1.0
CG A:ARG533 4.0 14.9 1.0
CA A:SER529 4.1 15.4 1.0
O A:HOH1047 4.2 30.4 1.0
CD A:ARG533 4.2 12.1 1.0
O A:SER529 4.3 13.9 1.0
C A:SER562 4.3 13.4 1.0
CB A:VAL141 4.4 20.0 1.0
CG1 A:VAL141 4.5 21.6 1.0
CB A:ARG532 4.6 12.6 1.0
O A:VAL141 4.6 19.5 1.0
CD A:ARG532 4.6 16.2 1.0
C A:SER529 4.6 14.8 1.0
N A:SER562 4.8 17.1 1.0

Bromine binding site 2 out of 8 in 3x42

Go back to Bromine Binding Sites List in 3x42
Bromine binding site 2 out of 8 in the Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide


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 Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br703

b:48.7
occ:1.00
 O A:HOH1010 3.2 24.4 1.0
OG A:SER374 3.2 17.1 1.0
CE1 A:HIS345 3.3 24.0 1.0
O A:HOH1065 3.4 25.8 1.0
O A:HOH1288 3.4 40.0 1.0
O A:HOH1442 3.5 42.6 1.0
O A:HOH1162 3.7 37.8 1.0
CE2 A:TYR387 3.8 9.5 1.0
ND1 A:HIS345 3.9 22.0 1.0
CG1 A:VAL372 4.1 13.0 1.0
SG A:CYS317 4.1 21.3 1.0
CB A:SER374 4.2 12.8 1.0
NE2 A:HIS345 4.3 24.9 1.0
CD2 A:TYR387 4.4 13.7 1.0
CB A:CYS343 4.4 19.7 1.0
O A:ASP316 4.5 21.2 1.0
CB A:CYS317 4.5 25.7 1.0
CA A:CYS317 4.6 18.8 1.0
CZ A:TYR387 4.8 15.3 1.0
OH A:TYR387 4.9 15.9 1.0
CB A:VAL372 4.9 14.8 1.0

Bromine binding site 3 out of 8 in 3x42

Go back to Bromine Binding Sites List in 3x42
Bromine binding site 3 out of 8 in the Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide


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 Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br704

b:76.5
occ:1.00
 O A:HOH1271 2.7 47.5 1.0
N A:ASP128 3.2 24.8 1.0
O A:HOH1459 3.5 48.1 1.0
O A:HOH1039 3.6 44.1 1.0
CA A:LEU127 3.7 18.3 1.0
CB A:ASP128 3.9 28.4 1.0
C A:LEU127 3.9 21.9 1.0
CA A:ASP128 4.1 25.4 1.0
CD A:LYS131 4.1 36.8 1.0
CD2 A:LEU127 4.1 17.9 1.0
CG1 A:VAL159 4.2 20.2 1.0
CB A:LEU127 4.2 17.4 1.0
CB A:LYS131 4.3 18.8 1.0
O A:ASN126 4.4 19.8 1.0
O A:ASP128 4.4 18.7 1.0
O A:HOH1192 4.5 42.9 0.5
O3 A:GOL711 4.6 48.5 1.0
CG A:LYS131 4.7 28.1 1.0
C A:ASP128 4.8 19.2 1.0
CG A:LEU127 4.8 17.6 1.0
O A:HOH1258 4.9 43.5 1.0
N A:LEU127 4.9 18.9 1.0

Bromine binding site 4 out of 8 in 3x42

Go back to Bromine Binding Sites List in 3x42
Bromine binding site 4 out of 8 in the Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide


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 Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br705

b:56.9
occ:1.00
 N A:GLU36 3.3 16.1 1.0
CA A:GLY34 3.6 18.6 1.0
CB A:GLU36 3.6 22.9 1.0
C A:GLY34 3.6 16.3 1.0
CG A:GLU36 3.6 36.9 1.0
N A:PRO35 3.7 16.6 1.0
O A:HOH1106 3.7 24.6 1.0
CD A:PRO35 3.8 17.3 1.0
O A:HOH1379 3.8 38.5 1.0
CA A:GLU36 3.9 20.4 1.0
O A:GLY34 4.1 15.9 1.0
N A:GLY34 4.2 16.3 1.0
CG A:LYS37 4.2 17.1 1.0
CE A:LYS37 4.3 22.9 1.0
N A:LYS37 4.4 14.8 1.0
C A:PRO35 4.4 19.2 1.0
CG A:PRO35 4.4 24.7 1.0
C A:GLU36 4.5 20.8 1.0
CD A:LYS37 4.6 17.1 1.0
CA A:PRO35 4.6 21.8 1.0
CD A:GLU36 4.9 49.1 1.0
OD2 A:ASP66 4.9 24.1 1.0

Bromine binding site 5 out of 8 in 3x42

Go back to Bromine Binding Sites List in 3x42
Bromine binding site 5 out of 8 in the Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide


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 Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br702

b:0.7
occ:1.00
 NH1 B:ARG532 3.0 49.4 1.0
OG B:SER529 3.1 23.6 1.0
N B:GLY563 3.6 42.8 1.0
NE B:ARG532 3.7 48.0 1.0
CZ B:ARG532 3.8 49.5 1.0
CA B:SER562 4.0 38.5 1.0
CB B:SER529 4.0 26.6 1.0
O B:VAL141 4.1 36.2 1.0
CB B:VAL141 4.1 34.2 1.0
CG1 B:VAL141 4.2 32.7 1.0
CA B:SER529 4.2 21.7 1.0
C B:SER562 4.3 41.4 1.0
CG B:ARG533 4.3 22.9 1.0
CB B:SER562 4.3 41.3 1.0
CD B:ARG533 4.4 22.9 1.0
O B:SER529 4.5 23.8 1.0
CA B:GLY563 4.5 35.9 1.0
C B:SER529 4.8 23.1 1.0
C B:VAL141 4.8 36.2 1.0
O B:HIS561 4.9 29.3 1.0
CB B:ARG532 4.9 27.9 1.0
CG2 B:VAL141 5.0 29.2 1.0

Bromine binding site 6 out of 8 in 3x42

Go back to Bromine Binding Sites List in 3x42
Bromine binding site 6 out of 8 in the Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide


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 Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br703

b:53.2
occ:1.00
 O B:HOH1045 3.2 24.9 1.0
OG B:SER374 3.2 19.1 1.0
CE1 B:HIS345 3.3 25.0 1.0
O B:HOH1244 3.3 50.6 1.0
O B:HOH898 3.3 24.3 1.0
O B:HOH1063 3.5 29.6 1.0
CE2 B:TYR387 3.8 16.9 1.0
O B:HOH1295 3.8 42.7 1.0
ND1 B:HIS345 3.9 21.6 1.0
SG B:CYS317 4.0 24.0 1.0
CG1 B:VAL372 4.1 14.3 1.0
CB B:SER374 4.1 16.3 1.0
NE2 B:HIS345 4.4 27.3 1.0
CD2 B:TYR387 4.4 16.9 1.0
CB B:CYS343 4.4 19.4 1.0
CB B:CYS317 4.5 30.6 1.0
O B:ASP316 4.5 25.9 1.0
CA B:CYS317 4.6 23.6 1.0
CZ B:TYR387 4.8 17.7 1.0
OH B:TYR387 4.9 18.4 1.0

Bromine binding site 7 out of 8 in 3x42

Go back to Bromine Binding Sites List in 3x42
Bromine binding site 7 out of 8 in the Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide


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 Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br704

b:85.2
occ:1.00
 N B:GLU36 3.4 37.4 1.0
CA B:GLY34 3.5 45.8 1.0
CD B:PRO35 3.6 43.7 1.0
C B:GLY34 3.6 46.1 1.0
CB B:GLU36 3.7 46.7 1.0
N B:PRO35 3.7 36.3 1.0
CG B:GLU36 3.8 49.8 1.0
CA B:GLU36 4.0 42.2 1.0
CE B:LYS37 4.2 45.6 1.0
CG B:LYS37 4.2 37.2 1.0
O B:GLY34 4.2 46.7 1.0
CG B:PRO35 4.2 44.1 1.0
N B:GLY34 4.3 44.9 1.0
N B:LYS37 4.3 32.0 1.0
C B:PRO35 4.5 36.3 1.0
C B:GLU36 4.5 38.2 1.0
CD B:LYS37 4.5 39.1 1.0
OD2 B:ASP66 4.6 33.6 1.0
CA B:PRO35 4.6 37.1 1.0

Bromine binding site 8 out of 8 in 3x42

Go back to Bromine Binding Sites List in 3x42
Bromine binding site 8 out of 8 in the Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in the Presence of Sodium Bromide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br705

b:0.5
occ:1.00
 O B:HOH1298 3.0 53.1 1.0
N B:ASP128 3.4 29.3 1.0
O B:HOH1260 3.8 60.7 1.0
CA B:LEU127 3.9 27.7 1.0
O B:HOH1232 3.9 55.0 1.0
CB B:ASP128 4.0 37.1 1.0
C B:LEU127 4.2 28.2 1.0
CD2 B:LEU127 4.2 25.9 1.0
CD B:LYS131 4.2 43.9 1.0
O B:ASN126 4.3 28.8 1.0
CA B:ASP128 4.3 32.7 1.0
CG1 B:VAL159 4.3 24.2 1.0
O B:HOH1254 4.3 45.0 1.0
CB B:LEU127 4.5 26.7 1.0
CB B:LYS131 4.6 33.1 1.0
O B:HOH980 4.6 36.5 0.5
CG B:LYS131 4.8 41.0 1.0
O B:ASP128 4.9 28.3 1.0

Reference:

T.Murakawa, A.Hamaguchi, S.Nakanishi, M.Kataoka, T.Nakai, Y.Kawano, H.Yamaguchi, H.Hayashi, K.Tanizawa, T.Okajima. Probing the Catalytic Mechanism of Copper Amine Oxidase From Arthrobacter Globiformis with Halide Ions J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M115.662726
Page generated: Wed Jul 10 20:42:09 2024

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