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Bromine in PDB 6yoe: Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging

Enzymatic activity of Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging

All present enzymatic activity of Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging:
3.2.1.17;

Protein crystallography data

The structure of Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging, PDB code: 6yoe was solved by C.-Y.Huang, I.Martiel, P.Villanueva-Perez, E.Panepucci, M.Caffrey, M.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.51 / 1.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.500, 78.500, 40.460, 90.00, 90.00, 90.00
R / Rfree (%) 26.3 / 28.5

Other elements in 6yoe:

The structure of Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging also contains other interesting chemical elements:

Sodium (Na) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging (pdb code 6yoe). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 7 binding sites of Bromine where determined in the Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging, PDB code: 6yoe:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7;

Bromine binding site 1 out of 7 in 6yoe

Go back to Bromine Binding Sites List in 6yoe
Bromine binding site 1 out of 7 in the Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br202

b:48.6
occ:0.90
 OH A:TYR23 3.4 43.7 1.0
O A:HOH317 3.8 40.0 1.0
CA A:GLY104 4.1 43.2 1.0
CE2 A:TYR23 4.2 38.3 1.0
CZ A:TYR23 4.2 42.7 1.0
N A:GLY104 4.7 43.6 1.0
O A:ARG21 4.8 48.2 1.0

Bromine binding site 2 out of 7 in 6yoe

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Bromine binding site 2 out of 7 in the Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br203

b:49.8
occ:0.87
 NH2 A:ARG14 3.7 56.4 1.0
N A:ILE88 3.9 44.7 1.0
CG1 A:ILE88 4.1 42.6 1.0
CA A:ASP87 4.2 45.0 1.0
O A:SER86 4.2 47.5 1.0
CB A:ALA11 4.2 44.3 1.0
OD1 A:ASP87 4.3 50.0 1.0
CZ A:PHE3 4.4 45.7 1.0
CG A:ASP87 4.4 51.8 1.0
CE1 A:HIS15 4.5 49.8 1.0
CG2 A:ILE88 4.5 44.6 1.0
C A:ASP87 4.6 44.8 1.0
CD1 A:ILE88 4.7 44.4 1.0
CB A:ILE88 4.7 45.0 1.0
OD2 A:ASP87 4.8 54.1 1.0
CB A:ASP87 4.8 49.8 1.0
CA A:ILE88 4.9 43.0 1.0
CE2 A:PHE3 4.9 44.0 1.0
CZ A:ARG14 5.0 51.9 1.0

Bromine binding site 3 out of 7 in 6yoe

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Bromine binding site 3 out of 7 in the Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br204

b:51.9
occ:0.96
 N A:GLY26 3.3 45.1 1.0
CG A:GLN121 3.4 62.6 1.0
OG A:SER24 3.5 45.4 1.0
CA A:GLY26 3.6 45.1 1.0
CA A:GLN121 3.7 53.3 1.0
CB A:SER24 3.8 46.1 1.0
CD1 A:ILE124 3.8 52.5 1.0
CB A:GLN121 3.9 58.9 1.0
N A:GLN121 4.2 52.9 1.0
O A:VAL120 4.4 48.9 1.0
N A:LEU25 4.4 45.8 1.0
C A:VAL120 4.5 52.0 1.0
CG2 A:VAL120 4.5 48.7 1.0
C A:LEU25 4.5 43.0 1.0
CG1 A:ILE124 4.6 51.5 1.0
CD A:GLN121 4.7 76.7 1.0
C A:GLY26 4.7 44.9 1.0
C A:SER24 4.8 45.6 1.0
CA A:LEU25 4.9 43.0 1.0
CA A:SER24 5.0 46.7 1.0
N A:ASN27 5.0 42.8 1.0
C A:GLN121 5.0 50.2 1.0

Bromine binding site 4 out of 7 in 6yoe

Go back to Bromine Binding Sites List in 6yoe
Bromine binding site 4 out of 7 in the Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br205

b:48.8
occ:0.54
 O A:HOH325 2.2 42.7 1.0
O A:THR69 3.0 50.6 1.0
N A:THR69 3.4 48.5 1.0
C A:THR69 3.6 50.9 1.0
OD1 A:ASN65 3.6 48.7 1.0
C A:GLY67 3.7 47.3 1.0
CA A:GLY67 3.7 45.2 1.0
N A:ARG68 3.8 42.9 1.0
N A:GLY67 3.9 42.6 1.0
CA A:THR69 3.9 47.0 1.0
O A:HOH331 4.1 46.1 1.0
OG A:SER72 4.1 49.7 1.0
CB A:THR69 4.2 49.3 1.0
O A:GLY67 4.3 49.0 1.0
C A:ARG68 4.4 48.1 1.0
OD1 A:ASP66 4.5 44.1 1.0
N A:PRO70 4.6 51.6 1.0
CA A:ARG68 4.6 45.4 1.0
OG1 A:THR69 4.8 46.5 1.0
CG A:ASN65 4.8 48.1 1.0
CA A:PRO70 5.0 52.2 1.0

Bromine binding site 5 out of 7 in 6yoe

Go back to Bromine Binding Sites List in 6yoe
Bromine binding site 5 out of 7 in the Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br206

b:53.8
occ:0.60
 NH1 A:ARG68 3.3 52.6 1.0
O A:HOH323 3.6 48.4 1.0
CD A:ARG68 4.2 47.4 1.0
CZ A:ARG68 4.4 47.5 1.0
NH1 A:ARG45 4.7 52.9 1.0
NE A:ARG68 4.8 47.6 1.0

Bromine binding site 6 out of 7 in 6yoe

Go back to Bromine Binding Sites List in 6yoe
Bromine binding site 6 out of 7 in the Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br207

b:66.1
occ:0.83
 N A:ASN74 3.5 51.7 1.0
CG A:ARG73 3.6 55.2 1.0
CB A:ARG73 3.6 51.2 1.0
CA A:ARG73 4.0 49.4 1.0
C A:ASN74 4.2 48.0 1.0
CZ A:ARG73 4.2 62.1 1.0
CD2 A:LEU75 4.2 54.5 1.0
NE A:ARG73 4.2 58.8 1.0
O A:ASN74 4.2 47.4 1.0
C A:ARG73 4.3 50.7 1.0
NH1 A:ARG73 4.3 64.1 1.0
CA A:ASN74 4.4 48.3 1.0
N A:LEU75 4.5 49.3 1.0
NH2 A:ARG73 4.5 63.9 1.0
CD A:ARG73 4.5 57.5 1.0
CG A:LEU75 4.6 50.4 1.0
CA A:LEU75 4.8 49.4 1.0
CB A:ASN74 4.9 49.7 1.0

Bromine binding site 7 out of 7 in 6yoe

Go back to Bromine Binding Sites List in 6yoe
Bromine binding site 7 out of 7 in the Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br208

b:67.3
occ:1.00
 NZ A:LYS33 3.4 48.3 1.0
O A:HOH347 3.6 54.5 1.0
CD A:ARG5 4.3 50.5 1.0
CE2 A:PHE38 4.3 48.6 1.0
CE A:LYS33 4.3 44.6 1.0
C5 A:AE3201 4.4 60.1 1.0
CZ3 A:TRP123 4.4 44.0 1.0
CB A:ARG5 4.5 50.3 1.0
CD A:LYS33 4.7 40.9 1.0
NE A:ARG5 4.8 47.4 1.0
CG A:ARG5 4.9 49.2 1.0

Reference:

I.Martiel, C.Y.Huang, P.Villanueva-Perez, E.Panepucci, S.Basu, M.Caffrey, B.Pedrini, O.Bunk, M.Stampanoni, M.Wang. Low-Dose in Situ Prelocation of Protein Microcrystals By 2D X-Ray Phase-Contrast Imaging For Serial Crystallography. Iucrj V. 7 1131 2020.
ISSN: ESSN 2052-2525
PubMed: 33209324
DOI: 10.1107/S2052252520013238
Page generated: Thu Jul 11 03:14:34 2024

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