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Bromine in PDB 6sye: Crystal Structure of Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0

Enzymatic activity of Crystal Structure of Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0

All present enzymatic activity of Crystal Structure of Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0, PDB code: 6sye was solved by A.Camara-Artigas, M.Plaza-Garrido, M.C.Salinas-Garcia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.60 / 0.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 30.206, 55.235, 71.576, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 19.8

Other elements in 6sye:

The structure of Crystal Structure of Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0 (pdb code 6sye). 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 Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0, PDB code: 6sye:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 6sye

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Bromine binding site 1 out of 8 in the Crystal Structure of Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0


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 Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br202

b:12.5
occ:1.00
 BR3 A:LYE202 0.0 12.5 1.0
C13 A:LYE202 1.9 12.1 1.0
H061 A:LYE203 2.8 13.4 1.0
C11 A:LYE202 2.8 13.3 1.0
C14 A:LYE202 2.9 12.2 1.0
H141 A:LYE202 3.0 14.6 1.0
O12 A:LYE202 3.0 14.1 1.0
C06 A:LYE203 3.8 11.2 1.0
C14 A:LYE203 3.9 11.7 1.0
C08 A:LYE203 3.9 10.6 1.0
C13 A:LYE203 3.9 12.6 1.0
C09 A:LYE203 3.9 10.9 1.0
C11 A:LYE203 4.0 12.6 1.0
C10 A:LYE203 4.0 11.9 1.0
C10 A:LYE202 4.1 15.1 1.0
C08 A:LYE202 4.2 12.4 1.0
H141 A:LYE203 4.3 14.1 1.0
H011 A:LYE203 4.3 14.2 1.0
H091 A:LYE203 4.4 13.1 1.0
C01 A:LYE203 4.5 11.9 1.0
C07 A:LYE203 4.5 9.9 1.0
C05 A:LYE203 4.6 10.0 1.0
O12 A:LYE203 4.7 13.7 1.0
C09 A:LYE202 4.7 13.6 1.0
H181 A:LYE202 4.7 16.3 1.0
BR3 A:LYE203 4.9 15.3 1.0

Bromine binding site 2 out of 8 in 6sye

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Bromine binding site 2 out of 8 in the Crystal Structure of Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0


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 Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br202

b:19.2
occ:1.00
 BR4 A:LYE202 0.0 19.2 1.0
C10 A:LYE202 1.9 15.1 1.0
C11 A:LYE202 2.8 13.3 1.0
C09 A:LYE202 2.9 13.6 1.0
H091 A:LYE202 3.0 16.4 1.0
O12 A:LYE202 3.0 14.1 1.0
O A:HOH449 3.5 25.5 1.0
O A:HOH303 3.9 31.6 1.0
O A:HOH341 4.0 25.1 1.0
C13 A:LYE202 4.1 12.1 1.0
C08 A:LYE202 4.2 12.4 1.0
C14 A:LYE202 4.7 12.2 1.0
O12 A:LYE203 4.8 13.7 1.0
BR4 A:LYE203 4.9 14.0 1.0

Bromine binding site 3 out of 8 in 6sye

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Bromine binding site 3 out of 8 in the Crystal Structure of Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0


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 Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br202

b:15.3
occ:1.00
 BR2 A:LYE202 0.0 15.3 1.0
C21 A:LYE202 1.9 14.0 1.0
C22 A:LYE202 2.9 13.0 1.0
C20 A:LYE202 2.9 14.7 1.0
H221 A:LYE202 3.0 15.7 1.0
O24 A:LYE202 3.1 15.5 1.0
HG3 A:ARG128 3.2 13.4 1.0
HD2 A:ARG128 3.5 14.2 1.0
O A:HOH375 3.5 21.7 1.0
H A:ARG128 3.6 12.0 1.0
O A:GLY126 3.6 14.0 1.0
H021 A:LYE203 3.6 14.2 1.0
HA A:CYS127 3.6 11.8 1.0
O A:HOH407 3.8 30.4 1.0
CG A:ARG128 3.9 11.2 1.0
HB2 A:ARG128 4.0 12.6 1.0
CD A:ARG128 4.0 11.8 1.0
O A:HOH332 4.1 18.1 1.0
HH11 A:ARG128 4.1 16.0 1.0
N A:ARG128 4.2 10.0 1.0
NE A:ARG128 4.2 12.2 1.0
C19 A:LYE202 4.2 15.3 1.0
C17 A:LYE202 4.2 13.0 1.0
NH1 A:ARG128 4.3 13.3 1.0
CZ A:ARG128 4.3 12.9 1.0
C02 A:LYE203 4.4 11.8 1.0
CB A:ARG128 4.4 10.5 1.0
H031 A:LYE203 4.5 13.5 1.0
CA A:CYS127 4.5 9.8 1.0
HE A:ARG128 4.6 14.7 1.0
O A:HOH415 4.6 32.8 1.0
C A:GLY126 4.7 12.6 1.0
C18 A:LYE202 4.7 13.6 1.0
HH12 A:ARG128 4.7 16.0 1.0
HG2 A:ARG128 4.7 13.4 1.0
C A:CYS127 4.7 10.0 1.0
C03 A:LYE203 4.8 11.2 1.0
HD3 A:ARG128 4.9 14.2 1.0
SG A:CYS6 4.9 9.8 1.0
CA A:ARG128 5.0 10.1 1.0

Bromine binding site 4 out of 8 in 6sye

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Bromine binding site 4 out of 8 in the Crystal Structure of Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0


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 Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br202

b:17.9
occ:1.00
 BR1 A:LYE202 0.0 17.9 1.0
C19 A:LYE202 1.9 15.3 1.0
C18 A:LYE202 2.8 13.6 1.0
C20 A:LYE202 2.9 14.7 1.0
H181 A:LYE202 2.9 16.3 1.0
O24 A:LYE202 3.1 15.5 1.0
H011 A:LYE203 3.3 14.2 1.0
C17 A:LYE202 4.1 13.0 1.0
C21 A:LYE202 4.2 14.0 1.0
H021 A:LYE203 4.2 14.2 1.0
C01 A:LYE203 4.3 11.9 1.0
H141 A:LYE202 4.4 14.6 1.0
HH12 A:ARG128 4.4 16.0 1.0
C22 A:LYE202 4.7 13.0 1.0
C02 A:LYE203 4.7 11.8 1.0
HH11 A:ARG128 5.0 16.0 1.0
NH1 A:ARG128 5.0 13.3 1.0

Bromine binding site 5 out of 8 in 6sye

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Bromine binding site 5 out of 8 in the Crystal Structure of Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0


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 Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br203

b:15.3
occ:1.00
 BR3 A:LYE203 0.0 15.3 1.0
C13 A:LYE203 1.9 12.6 1.0
C11 A:LYE203 2.8 12.6 1.0
C14 A:LYE203 2.9 11.7 1.0
H141 A:LYE203 3.0 14.1 1.0
O12 A:LYE203 3.0 13.7 1.0
O A:HOH391 3.5 34.4 1.0
O A:HOH321 3.8 12.8 1.0
O A:HOH341 3.9 25.1 1.0
HZ1 A:LYS1 3.9 19.8 1.0
OE1 A:GLU7 3.9 12.7 1.0
C10 A:LYE203 4.1 11.9 1.0
C08 A:LYE203 4.2 10.6 1.0
CD A:GLU7 4.3 11.2 1.0
OE2 A:GLU7 4.3 10.9 1.0
HZ2 A:LYS1 4.5 19.8 1.0
H221 A:LYE203 4.5 13.2 1.0
NZ A:LYS1 4.5 16.5 1.0
HZ3 A:LYS1 4.6 19.8 1.0
C09 A:LYE203 4.7 10.9 1.0
O12 A:LYE202 4.9 14.1 1.0
O A:HOH402 4.9 25.9 1.0
BR3 A:LYE202 4.9 12.5 1.0

Bromine binding site 6 out of 8 in 6sye

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Bromine binding site 6 out of 8 in the Crystal Structure of Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0


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 Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br203

b:14.0
occ:1.00
 BR4 A:LYE203 0.0 14.0 1.0
C10 A:LYE203 1.9 11.9 1.0
C09 A:LYE203 2.8 10.9 1.0
C11 A:LYE203 2.8 12.6 1.0
H091 A:LYE203 2.9 13.1 1.0
O12 A:LYE203 3.0 13.7 1.0
H061 A:LYE202 3.1 15.8 1.0
HG3 A:GLU7 3.1 12.1 1.0
O A:HOH303 3.3 31.6 1.0
O A:HOH446 3.4 18.9 1.0
HA A:GLU7 3.5 10.7 1.0
HB2 A:GLU7 3.6 11.5 1.0
O A:HOH449 3.7 25.5 1.0
O A:HOH384 3.8 15.9 1.0
C09 A:LYE202 3.9 13.6 1.0
C08 A:LYE202 3.9 12.4 1.0
C10 A:LYE202 3.9 15.1 1.0
C14 A:LYE202 4.0 12.2 1.0
CG A:GLU7 4.0 10.0 1.0
C11 A:LYE202 4.0 13.3 1.0
C13 A:LYE202 4.0 12.1 1.0
CB A:GLU7 4.1 9.6 1.0
C06 A:LYE202 4.1 13.2 1.0
C13 A:LYE203 4.1 12.6 1.0
C08 A:LYE203 4.2 10.6 1.0
CA A:GLU7 4.2 8.9 1.0
H091 A:LYE202 4.4 16.4 1.0
O A:HOH351 4.4 21.7 1.0
H141 A:LYE202 4.5 14.6 1.0
C07 A:LYE202 4.6 12.6 1.0
HG2 A:GLU7 4.6 12.1 1.0
C14 A:LYE203 4.7 11.7 1.0
O12 A:LYE202 4.7 14.1 1.0
N A:GLU7 4.8 8.9 1.0
CD A:GLU7 4.8 11.2 1.0
C05 A:LYE202 4.9 12.8 1.0
H A:GLU7 4.9 10.7 1.0
BR4 A:LYE202 4.9 19.2 1.0
H011 A:LYE202 4.9 16.3 1.0

Bromine binding site 7 out of 8 in 6sye

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Bromine binding site 7 out of 8 in the Crystal Structure of Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0


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 Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br203

b:13.7
occ:1.00
 BR2 A:LYE203 0.0 13.7 1.0
C21 A:LYE203 1.9 11.8 1.0
C22 A:LYE203 2.8 11.0 1.0
C20 A:LYE203 2.9 12.0 1.0
H221 A:LYE203 2.9 13.2 1.0
O24 A:LYE203 3.1 13.6 1.0
O A:VAL2 3.4 9.9 1.0
O A:HOH358 3.5 23.0 1.0
HG12 A:VAL2 3.6 13.5 1.0
O A:HOH321 3.6 12.8 1.0
N A:GLY4 3.7 8.9 1.0
H A:GLY4 3.7 10.7 1.0
C A:PHE3 3.8 8.6 1.0
HA2 A:GLY4 3.8 11.2 1.0
O A:PHE3 4.0 9.5 1.0
HA3 A:GLY4 4.1 11.2 1.0
CA A:GLY4 4.1 9.3 1.0
O A:HOH329 4.1 13.8 1.0
C17 A:LYE203 4.2 10.4 1.0
C19 A:LYE203 4.2 12.3 1.0
C A:VAL2 4.2 9.1 1.0
HA A:PHE3 4.4 10.4 1.0
H141 A:LYE203 4.4 14.1 1.0
CG1 A:VAL2 4.5 11.2 1.0
HB A:VAL2 4.5 12.5 1.0
CA A:PHE3 4.5 8.7 1.0
C18 A:LYE203 4.7 11.1 1.0
OE2 A:GLU7 4.7 10.9 1.0
N A:PHE3 4.7 8.7 1.0
HG11 A:VAL2 4.8 13.5 1.0
CB A:VAL2 4.9 10.4 1.0

Bromine binding site 8 out of 8 in 6sye

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Bromine binding site 8 out of 8 in the Crystal Structure of Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0


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 Orthorhombic Lysozyme in Presence of the Dye Bromophenol Blue at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br203

b:13.9
occ:1.00
 BR1 A:LYE203 0.0 13.9 1.0
C19 A:LYE203 1.9 12.3 1.0
C18 A:LYE203 2.8 11.1 1.0
C20 A:LYE203 2.9 12.0 1.0
H181 A:LYE203 2.9 13.3 1.0
O24 A:LYE203 3.1 13.6 1.0
C17 A:LYE203 4.2 10.4 1.0
C21 A:LYE203 4.2 11.8 1.0
O28 A:LYE203 4.6 10.1 1.0
C22 A:LYE203 4.7 11.0 1.0

Reference:

M.Plaza-Garrido, M.C.Salinas-Garcia, D.Alba-Elena, J.C.Martinez, A.Camara-Artigas. Lysozyme Crystals Dyed with Bromophenol Blue: Where Has the Dye Gone? Acta Crystallogr D Struct V. 76 845 2020BIOL.
ISSN: ISSN 2059-7983
PubMed: 32876060
DOI: 10.1107/S2059798320008803
Page generated: Thu Jul 11 02:40:02 2024

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