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

Enzymatic activity of Structure of Lysozyme From Sin Imisx Setup Collected By Rotation 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 Rotation 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 Rotation Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase- Contrast Imaging, PDB code: 6yod 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) 39.50 / 1.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.990, 78.990, 38.190, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 21.1

Other elements in 6yod:

The structure of Structure of Lysozyme From Sin Imisx Setup Collected By Rotation 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 Rotation Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase- Contrast Imaging (pdb code 6yod). 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 Rotation Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase- Contrast Imaging, PDB code: 6yod:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7;

Bromine binding site 1 out of 7 in 6yod

Go back to Bromine Binding Sites List in 6yod
Bromine binding site 1 out of 7 in the Structure of Lysozyme From Sin Imisx Setup Collected By Rotation 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 Rotation Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase- Contrast Imaging within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br201

b:27.8
occ:0.67
 OH A:TYR23 3.2 24.2 1.0
O A:HOH332 3.5 28.5 0.9
CE2 A:TYR23 3.9 24.6 1.0
CZ A:TYR23 3.9 25.4 1.0
CA A:GLY104 4.1 22.6 1.0
O A:ARG21 4.6 29.0 1.0
N A:GLY104 4.7 27.0 1.0
O A:HOH328 4.9 34.4 0.9

Bromine binding site 2 out of 7 in 6yod

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Bromine binding site 2 out of 7 in the Structure of Lysozyme From Sin Imisx Setup Collected By Rotation 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 Rotation 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:32.5
occ:0.65
 O A:HOH321 3.5 33.3 0.7
N A:ILE88 3.5 30.1 1.0
CG1 A:ILE88 3.8 28.3 1.0
NH2 A:ARG14 3.9 40.7 1.0
CA A:ASP87 4.0 28.4 1.0
CE1 A:HIS15 4.1 36.4 1.0
C A:ASP87 4.2 32.7 1.0
CG A:ASP87 4.3 48.8 1.0
CZ A:PHE3 4.3 32.0 1.0
CB A:ALA11 4.3 27.4 1.0
O A:SER86 4.4 33.6 1.0
OD1 A:ASP87 4.4 38.3 1.0
CB A:ILE88 4.4 25.3 1.0
CG2 A:ILE88 4.4 29.0 1.0
OD2 A:ASP87 4.5 59.7 1.0
CA A:ILE88 4.5 27.1 1.0
CB A:ASP87 4.6 36.5 1.0
CD1 A:ILE88 4.7 30.6 1.0
CE2 A:PHE3 4.8 26.9 1.0
ND1 A:HIS15 4.9 38.5 1.0
NE2 A:HIS15 4.9 43.0 1.0

Bromine binding site 3 out of 7 in 6yod

Go back to Bromine Binding Sites List in 6yod
Bromine binding site 3 out of 7 in the Structure of Lysozyme From Sin Imisx Setup Collected By Rotation 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 Rotation 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:35.9
occ:0.78
 OG A:SER24 3.2 31.4 1.0
N A:GLY26 3.3 27.1 1.0
CB A:SER24 3.6 30.5 1.0
CA A:GLN121 3.7 33.1 1.0
CA A:GLY26 3.7 28.8 1.0
CD1 A:ILE124 3.8 39.7 1.0
CB A:GLN121 4.0 36.5 1.0
CG A:GLN121 4.1 34.3 1.0
N A:GLN121 4.1 33.4 1.0
N A:LEU25 4.3 28.1 1.0
CG1 A:ILE124 4.3 30.6 1.0
C A:SER24 4.4 26.9 1.0
C A:LEU25 4.5 26.4 1.0
O A:VAL120 4.5 29.9 1.0
C A:VAL120 4.5 29.9 1.0
CG2 A:VAL120 4.6 33.9 1.0
CA A:SER24 4.6 26.9 1.0
C A:GLY26 4.8 27.1 1.0
CA A:LEU25 4.8 25.9 1.0
N A:ASN27 4.9 24.4 1.0
O A:SER24 4.9 26.8 1.0
C A:GLN121 4.9 30.4 1.0

Bromine binding site 4 out of 7 in 6yod

Go back to Bromine Binding Sites List in 6yod
Bromine binding site 4 out of 7 in the Structure of Lysozyme From Sin Imisx Setup Collected By Rotation 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 Rotation 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:38.3
occ:0.48
 O A:HOH360 2.8 33.6 1.0
N A:THR69 3.3 31.3 1.0
O A:THR69 3.4 33.6 1.0
O A:HOH350 3.4 44.4 0.8
O A:HOH386 3.4 44.5 1.0
ND2 A:ASN65 3.6 31.9 1.0
N A:ARG68 3.7 29.0 1.0
C A:THR69 3.7 30.6 1.0
C A:GLY67 3.8 34.9 1.0
N A:GLY67 3.9 29.7 1.0
CA A:GLY67 4.0 31.2 1.0
O A:HOH367 4.0 33.3 1.0
CA A:THR69 4.0 29.4 1.0
OG A:SER72 4.1 35.0 1.0
C A:ARG68 4.3 29.5 1.0
CB A:THR69 4.3 29.1 1.0
O A:GLY67 4.4 32.9 1.0
CA A:ARG68 4.4 25.5 1.0
N A:PRO70 4.5 38.6 1.0
OD1 A:ASP66 4.5 28.6 1.0
CA A:PRO70 4.9 36.1 1.0
O A:HOH307 4.9 37.8 0.8
CG A:ASN65 4.9 37.5 1.0
OG1 A:THR69 4.9 29.6 1.0
NA A:NA208 4.9 26.9 1.0
N A:ASP66 5.0 26.6 1.0

Bromine binding site 5 out of 7 in 6yod

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Bromine binding site 5 out of 7 in the Structure of Lysozyme From Sin Imisx Setup Collected By Rotation 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 Rotation 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:38.1
occ:0.47
 NH1 A:ARG68 3.1 36.0 1.0
CD A:ARG68 4.0 31.5 1.0
CZ A:ARG68 4.2 38.5 1.0
NE A:ARG68 4.5 38.7 1.0
NH1 A:ARG45 4.8 44.7 1.0

Bromine binding site 6 out of 7 in 6yod

Go back to Bromine Binding Sites List in 6yod
Bromine binding site 6 out of 7 in the Structure of Lysozyme From Sin Imisx Setup Collected By Rotation 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 Rotation 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:41.7
occ:0.60
 O A:HOH389 2.8 55.0 1.0
N A:ASN74 3.4 32.6 1.0
CB A:ARG73 3.6 36.6 1.0
NE A:ARG73 3.6 50.9 1.0
C A:ASN74 3.9 27.2 1.0
CA A:ARG73 4.0 30.9 1.0
NH2 A:ARG73 4.0 58.6 1.0
O A:ASN74 4.0 27.2 1.0
CD2 A:LEU75 4.1 44.4 1.0
CA A:ASN74 4.2 28.4 1.0
C A:ARG73 4.2 31.8 1.0
CZ A:ARG73 4.2 55.3 1.0
N A:LEU75 4.2 30.8 1.0
CG A:ARG73 4.5 35.5 1.0
CA A:LEU75 4.6 31.7 1.0
CD A:ARG73 4.6 47.2 1.0
CG A:LEU75 4.6 32.7 1.0
CB A:ASN74 4.6 25.7 1.0

Bromine binding site 7 out of 7 in 6yod

Go back to Bromine Binding Sites List in 6yod
Bromine binding site 7 out of 7 in the Structure of Lysozyme From Sin Imisx Setup Collected By Rotation 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 Rotation 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:53.9
occ:1.00
 NZ A:LYS33 3.5 39.0 1.0
O A:HOH374 3.8 40.9 1.0
CE2 A:PHE38 3.9 33.1 1.0
CZ3 A:TRP123 4.1 32.0 1.0
CE A:LYS33 4.1 37.1 1.0
CD A:ARG5 4.2 31.1 1.0
CB A:ARG5 4.4 33.4 1.0
CD A:LYS33 4.4 32.6 1.0
CZ A:PHE38 4.5 29.1 1.0
CG A:ARG5 4.7 33.2 1.0
NE A:ARG5 4.7 39.4 1.0
C5 A:AE3211 4.7 42.5 1.0
CD2 A:PHE38 4.8 26.5 1.0
CE3 A:TRP123 4.9 34.1 1.0
CH2 A:TRP123 5.0 37.4 1.0
C6 A:AE3211 5.0 49.4 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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