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

Enzymatic activity of Structure of Lysozyme From Coc 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 Coc 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 Coc Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging, PDB code: 6yoc 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) 55.98 / 1.86
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 (%) 22 / 24.2

Other elements in 6yoc:

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

Bromine binding site 1 out of 7 in 6yoc

Go back to Bromine Binding Sites List in 6yoc
Bromine binding site 1 out of 7 in the Structure of Lysozyme From Coc 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 Coc 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:Br201

b:28.2
occ:0.75
 OH A:TYR23 3.2 24.8 1.0
O A:HOH324 3.5 27.3 1.0
CE2 A:TYR23 3.9 30.1 1.0
CZ A:TYR23 3.9 21.1 1.0
CA A:GLY104 4.1 29.3 1.0
N A:GLY104 4.6 31.7 1.0
O A:ARG21 4.7 31.1 1.0

Bromine binding site 2 out of 7 in 6yoc

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Bromine binding site 2 out of 7 in the Structure of Lysozyme From Coc 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 Coc 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:35.0
occ:0.76
 O A:HOH322 3.3 38.8 1.0
N A:ILE88 3.6 32.1 1.0
CG1 A:ILE88 3.8 32.6 1.0
CA A:ASP87 3.9 29.1 1.0
CE1 A:HIS15 4.0 34.3 1.0
CB A:ALA11 4.2 31.1 1.0
O A:SER86 4.3 35.4 1.0
CG A:ASP87 4.3 43.1 1.0
C A:ASP87 4.3 30.8 1.0
NH2 A:ARG14 4.3 50.3 1.0
OD1 A:ASP87 4.3 42.8 1.0
CZ A:PHE3 4.4 36.1 1.0
CG2 A:ILE88 4.4 29.2 1.0
CB A:ILE88 4.5 29.5 1.0
OD2 A:ASP87 4.6 43.9 1.0
CB A:ASP87 4.6 38.3 1.0
CD1 A:ILE88 4.6 25.1 1.0
CA A:ILE88 4.6 28.7 1.0
ND1 A:HIS15 4.7 38.7 1.0
CE2 A:PHE3 4.8 32.1 1.0
NE2 A:HIS15 4.9 41.9 1.0
N A:ASP87 5.0 33.9 1.0

Bromine binding site 3 out of 7 in 6yoc

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Bromine binding site 3 out of 7 in the Structure of Lysozyme From Coc 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 Coc 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:31.8
occ:0.73
 OG A:SER24 3.2 29.5 1.0
N A:GLY26 3.4 29.1 1.0
CB A:SER24 3.6 30.5 1.0
CA A:GLN121 3.6 33.3 1.0
CA A:GLY26 3.6 32.5 1.0
CD1 A:ILE124 3.8 33.1 1.0
N A:GLN121 4.0 29.9 1.0
CB A:GLN121 4.0 40.7 1.0
CG A:GLN121 4.1 41.4 1.0
O A:VAL120 4.3 33.2 1.0
C A:VAL120 4.3 34.2 1.0
CG1 A:ILE124 4.4 30.2 1.0
N A:LEU25 4.4 29.2 1.0
C A:SER24 4.6 30.5 1.0
C A:LEU25 4.6 34.4 1.0
CG2 A:VAL120 4.7 32.0 1.0
C A:GLY26 4.7 31.1 1.0
CA A:SER24 4.7 26.6 1.0
C A:GLN121 4.8 31.5 1.0
N A:ASN27 4.9 25.5 1.0
CA A:LEU25 5.0 26.1 1.0

Bromine binding site 4 out of 7 in 6yoc

Go back to Bromine Binding Sites List in 6yoc
Bromine binding site 4 out of 7 in the Structure of Lysozyme From Coc 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 Coc 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:38.9
occ:0.64
 O A:HOH319 3.0 35.1 1.0
N A:THR69 3.2 32.8 1.0
O A:THR69 3.3 42.1 1.0
N A:ARG68 3.6 29.5 1.0
C A:THR69 3.6 42.0 1.0
CA A:GLY67 3.7 34.7 1.0
C A:GLY67 3.7 37.3 1.0
N A:GLY67 3.8 34.4 1.0
ND2 A:ASN65 3.8 34.0 1.0
CA A:THR69 3.9 39.3 1.0
OG A:SER72 4.0 44.1 1.0
O A:HOH342 4.2 31.0 1.0
C A:ARG68 4.2 36.2 1.0
CB A:THR69 4.2 37.2 1.0
N A:PRO70 4.3 40.5 1.0
CA A:ARG68 4.3 32.1 1.0
OD1 A:ASP66 4.4 32.6 1.0
O A:GLY67 4.5 44.7 1.0
CA A:PRO70 4.8 45.4 1.0
OG1 A:THR69 4.9 30.5 1.0
C A:ASP66 4.9 28.7 1.0

Bromine binding site 5 out of 7 in 6yoc

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Bromine binding site 5 out of 7 in the Structure of Lysozyme From Coc 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 Coc 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:38.6
occ:0.31
 NH1 A:ARG68 3.1 33.0 1.0
CD A:ARG68 3.9 33.4 1.0
CZ A:ARG68 4.2 39.1 1.0
NH1 A:ARG45 4.5 47.2 1.0
NE A:ARG68 4.5 32.5 1.0

Bromine binding site 6 out of 7 in 6yoc

Go back to Bromine Binding Sites List in 6yoc
Bromine binding site 6 out of 7 in the Structure of Lysozyme From Coc 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 Coc 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:52.6
occ:0.55
 N A:ASN74 3.4 37.5 1.0
NE A:ARG73 3.8 53.4 1.0
CB A:ARG73 3.8 36.6 1.0
C A:ASN74 3.8 29.7 1.0
NH2 A:ARG73 4.0 55.3 1.0
O A:ASN74 4.0 32.5 1.0
N A:LEU75 4.1 32.3 1.0
CA A:ASN74 4.1 29.5 1.0
CA A:ARG73 4.1 41.5 1.0
CD2 A:LEU75 4.1 46.0 1.0
C A:ARG73 4.3 36.9 1.0
CZ A:ARG73 4.3 55.1 1.0
CA A:LEU75 4.3 35.1 1.0
CG A:LEU75 4.4 34.2 1.0
CB A:ASN74 4.6 32.3 1.0
CD A:ARG73 4.7 51.9 1.0
CG A:ARG73 4.9 44.2 1.0
CB A:LEU75 5.0 33.3 1.0

Bromine binding site 7 out of 7 in 6yoc

Go back to Bromine Binding Sites List in 6yoc
Bromine binding site 7 out of 7 in the Structure of Lysozyme From Coc 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 Coc 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:50.9
occ:1.00
 NZ A:LYS33 3.6 39.3 1.0
CZ3 A:TRP123 3.9 32.3 1.0
CE2 A:PHE38 3.9 33.6 1.0
CE A:LYS33 4.1 29.9 1.0
CD A:ARG5 4.4 33.3 1.0
CD A:LYS33 4.4 29.9 1.0
CB A:ARG5 4.5 35.7 1.0
O4 A:PE5210 4.5 58.3 1.0
CZ A:PHE38 4.6 30.6 1.0
CH2 A:TRP123 4.6 35.2 1.0
CE3 A:TRP123 4.7 29.6 1.0
CD2 A:PHE38 4.7 25.1 1.0
NE A:ARG5 4.8 35.8 1.0
CG A:ARG5 4.9 36.9 1.0
C7 A:PE5210 5.0 41.5 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 03:12:31 2024

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