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

Enzymatic activity of Structure of Lysozyme From Coc 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 Coc 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 Coc Imisx Setup Collected By Rotation Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase- Contrast Imaging, PDB code: 6yob 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) 39.58 / 1.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.170, 79.170, 38.240, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 23.9

Other elements in 6yob:

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

Bromine binding site 1 out of 7 in 6yob

Go back to Bromine Binding Sites List in 6yob
Bromine binding site 1 out of 7 in the Structure of Lysozyme From Coc 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 Coc 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:29.2
occ:0.74
 OH A:TYR23 3.2 24.0 1.0
CE2 A:TYR23 3.8 26.3 1.0
CZ A:TYR23 3.9 24.6 1.0
CA A:GLY104 4.1 28.5 1.0
N A:GLY104 4.7 28.9 1.0
O A:ARG21 4.7 30.5 1.0
O A:HOH328 4.9 33.6 1.0

Bromine binding site 2 out of 7 in 6yob

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Bromine binding site 2 out of 7 in the Structure of Lysozyme From Coc 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 Coc 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:38.0
occ:0.70
 O A:HOH323 3.5 37.1 0.7
N A:ILE88 3.5 35.3 1.0
CG1 A:ILE88 3.8 30.6 1.0
NH2 A:ARG14 4.0 45.5 1.0
CE1 A:HIS15 4.0 36.9 1.0
OD1 A:ASP87 4.0 44.8 1.0
CA A:ASP87 4.0 36.2 1.0
CZ A:PHE3 4.2 35.2 1.0
CG A:ASP87 4.2 46.1 1.0
O A:SER86 4.2 37.8 1.0
CB A:ALA11 4.2 30.0 1.0
C A:ASP87 4.3 36.6 1.0
CG2 A:ILE88 4.4 31.4 1.0
CB A:ILE88 4.5 28.8 1.0
CA A:ILE88 4.6 31.3 1.0
CB A:ASP87 4.7 39.5 1.0
OD2 A:ASP87 4.7 54.5 1.0
NE2 A:HIS15 4.7 38.7 1.0
CD1 A:ILE88 4.7 28.4 1.0
CE2 A:PHE3 4.8 34.8 1.0
ND1 A:HIS15 4.8 34.6 1.0
N A:ASP87 5.0 35.4 1.0

Bromine binding site 3 out of 7 in 6yob

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Bromine binding site 3 out of 7 in the Structure of Lysozyme From Coc 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 Coc 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:31.5
occ:0.69
 N A:GLY26 3.3 25.3 1.0
OG A:SER24 3.3 29.6 1.0
CB A:SER24 3.6 30.5 1.0
CA A:GLN121 3.7 36.4 1.0
CA A:GLY26 3.7 26.9 1.0
CD1 A:ILE124 3.9 38.5 1.0
N A:GLN121 4.0 33.6 1.0
CB A:GLN121 4.1 39.6 1.0
N A:LEU25 4.2 29.5 1.0
CG A:GLN121 4.3 41.2 1.0
CG2 A:VAL120 4.3 31.4 1.0
CG1 A:ILE124 4.4 35.7 1.0
C A:VAL120 4.4 33.3 1.0
O A:VAL120 4.4 31.8 1.0
C A:LEU25 4.4 27.4 1.0
C A:SER24 4.5 29.3 1.0
CA A:SER24 4.7 29.1 1.0
CA A:LEU25 4.8 27.6 1.0
C A:GLY26 4.8 28.8 1.0
C A:GLN121 4.9 36.4 1.0
N A:ASN27 4.9 26.8 1.0

Bromine binding site 4 out of 7 in 6yob

Go back to Bromine Binding Sites List in 6yob
Bromine binding site 4 out of 7 in the Structure of Lysozyme From Coc 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 Coc 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:38.9
occ:0.51
 O A:HOH329 3.2 34.0 1.0
O A:THR69 3.2 42.0 1.0
N A:THR69 3.2 37.7 1.0
N A:ARG68 3.6 34.7 1.0
C A:THR69 3.6 43.5 1.0
ND2 A:ASN65 3.7 35.1 1.0
OG A:SER72 3.7 39.4 1.0
CA A:GLY67 3.7 33.8 1.0
N A:GLY67 3.7 32.7 1.0
C A:GLY67 3.8 36.3 1.0
CA A:THR69 3.9 40.1 1.0
O A:HOH344 4.1 36.7 1.0
CB A:THR69 4.2 38.9 1.0
OD1 A:ASP66 4.2 32.9 1.0
C A:ARG68 4.3 37.9 1.0
CA A:ARG68 4.4 35.4 1.0
N A:PRO70 4.4 44.8 1.0
O A:GLY67 4.6 39.2 1.0
OG1 A:THR69 4.7 35.1 1.0
C A:ASP66 4.8 33.8 1.0
CA A:PRO70 4.9 46.6 1.0
N A:ASP66 4.9 33.0 1.0
CB A:SER72 5.0 41.4 1.0
CG A:ASN65 5.0 36.0 1.0

Bromine binding site 5 out of 7 in 6yob

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Bromine binding site 5 out of 7 in the Structure of Lysozyme From Coc 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 Coc 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:39.3
occ:0.30
 NH1 A:ARG68 3.1 40.1 1.0
CD A:ARG68 3.7 37.7 1.0
CZ A:ARG68 4.2 38.8 1.0
NE A:ARG68 4.4 38.9 1.0
NH1 A:ARG45 4.8 44.2 1.0
CG A:ARG68 5.0 36.0 1.0

Bromine binding site 6 out of 7 in 6yob

Go back to Bromine Binding Sites List in 6yob
Bromine binding site 6 out of 7 in the Structure of Lysozyme From Coc 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 Coc 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:52.2
occ:0.51
 N A:ASN74 3.3 36.6 1.0
CB A:ARG73 3.7 43.1 1.0
C A:ASN74 3.8 35.1 1.0
CD2 A:LEU75 4.0 44.9 1.0
O A:ASN74 4.0 35.1 1.0
CA A:ARG73 4.0 39.1 1.0
CA A:ASN74 4.1 32.9 1.0
NE A:ARG73 4.1 55.7 1.0
N A:LEU75 4.1 35.2 1.0
C A:ARG73 4.2 38.1 1.0
NH2 A:ARG73 4.2 56.7 1.0
CA A:LEU75 4.4 36.5 1.0
CG A:LEU75 4.5 40.1 1.0
CZ A:ARG73 4.6 59.6 1.0
CB A:ASN74 4.6 34.6 1.0
O A:HOH304 4.6 49.6 0.9
CG A:ARG73 4.9 45.4 1.0

Bromine binding site 7 out of 7 in 6yob

Go back to Bromine Binding Sites List in 6yob
Bromine binding site 7 out of 7 in the Structure of Lysozyme From Coc 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 Coc 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:59.9
occ:1.00
 NZ A:LYS33 3.7 41.1 1.0
CZ3 A:TRP123 3.8 35.0 1.0
CE2 A:PHE38 4.0 31.1 1.0
CD A:ARG5 4.1 36.2 1.0
CE A:LYS33 4.4 37.4 1.0
CB A:ARG5 4.4 34.5 1.0
CD A:LYS33 4.4 32.7 1.0
NE A:ARG5 4.6 38.8 1.0
C2 A:PG0210 4.6 48.1 1.0
CZ A:PHE38 4.6 29.5 1.0
CH2 A:TRP123 4.7 38.1 1.0
CE3 A:TRP123 4.7 35.7 1.0
CG A:ARG5 4.7 35.3 1.0
CD2 A:PHE38 4.9 31.4 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: Sat Dec 12 02:42:28 2020

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