Atomistry » Bromine » PDB 6rqb-6ts9 » 6sye
Atomistry »
  Bromine »
    PDB 6rqb-6ts9 »
      6sye »

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

Go back to Bromine Binding Sites List in 6sye
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

Go back to Bromine Binding Sites List in 6sye
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

Go back to Bromine Binding Sites List in 6sye
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

Go back to Bromine Binding Sites List in 6sye
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

Go back to Bromine Binding Sites List in 6sye
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

Go back to Bromine Binding Sites List in 6sye
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

Go back to Bromine Binding Sites List in 6sye
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

Go back to Bromine Binding Sites List in 6sye
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy