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Chlorine in PDB 6qqd: Cryogenic Temperature Structure of Hen Egg White Lysozyme Recorded After An Accumulated Dose of 10 Mgy

Enzymatic activity of Cryogenic Temperature Structure of Hen Egg White Lysozyme Recorded After An Accumulated Dose of 10 Mgy

All present enzymatic activity of Cryogenic Temperature Structure of Hen Egg White Lysozyme Recorded After An Accumulated Dose of 10 Mgy:
3.2.1.17;

Protein crystallography data

The structure of Cryogenic Temperature Structure of Hen Egg White Lysozyme Recorded After An Accumulated Dose of 10 Mgy, PDB code: 6qqd was solved by G.Gotthard, S.Aumonier, A.Royant, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.71 / 1.92
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.960, 77.960, 37.380, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 21.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Cryogenic Temperature Structure of Hen Egg White Lysozyme Recorded After An Accumulated Dose of 10 Mgy (pdb code 6qqd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Cryogenic Temperature Structure of Hen Egg White Lysozyme Recorded After An Accumulated Dose of 10 Mgy, PDB code: 6qqd:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6qqd

Go back to Chlorine Binding Sites List in 6qqd
Chlorine binding site 1 out of 6 in the Cryogenic Temperature Structure of Hen Egg White Lysozyme Recorded After An Accumulated Dose of 10 Mgy


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Cryogenic Temperature Structure of Hen Egg White Lysozyme Recorded After An Accumulated Dose of 10 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:61.5
occ:1.00
 N A:ASN59 3.3 29.9 1.0
CA A:ILE58 3.6 32.9 1.0
ND2 A:ASN59 3.6 35.9 0.3
O A:GLN57 3.6 30.4 1.0
CB A:ASN59 3.8 33.4 0.7
CD1 A:ILE98 3.9 33.4 1.0
CD1 A:TRP63 3.9 30.9 1.0
C A:ILE58 3.9 32.9 1.0
CB A:ASN59 4.0 51.3 0.3
O A:HOH332 4.1 59.1 1.0
CG A:ASN59 4.1 36.7 0.3
NE1 A:TRP63 4.1 32.2 1.0
CA A:ASN59 4.2 35.8 0.7
CA A:ASN59 4.2 34.1 0.3
C A:GLN57 4.4 32.2 1.0
N A:ILE58 4.4 23.4 1.0
CB A:ILE58 4.5 31.3 1.0
NE1 A:TRP108 4.6 27.2 1.0
CG2 A:ILE58 4.6 34.8 1.0
CG1 A:ILE58 4.7 29.9 1.0
O A:HOH387 4.8 51.5 1.0
CG2 A:ILE98 4.9 32.5 1.0
CG1 A:ILE98 4.9 28.0 1.0
O A:HOH304 5.0 53.6 1.0
CE2 A:TRP108 5.0 30.1 1.0

Chlorine binding site 2 out of 6 in 6qqd

Go back to Chlorine Binding Sites List in 6qqd
Chlorine binding site 2 out of 6 in the Cryogenic Temperature Structure of Hen Egg White Lysozyme Recorded After An Accumulated Dose of 10 Mgy


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Cryogenic Temperature Structure of Hen Egg White Lysozyme Recorded After An Accumulated Dose of 10 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:64.2
occ:1.00
 O A:HOH381 2.9 43.5 1.0
ND2 A:ASN65 3.3 40.7 1.0
CB A:ASN65 3.7 33.1 1.0
CB A:PRO79 3.8 39.7 1.0
CA A:PRO79 3.9 34.2 1.0
CG A:ASN65 4.0 34.3 1.0
N A:PRO79 4.1 31.4 1.0
O A:ASN65 4.4 30.4 1.0
CD A:PRO79 4.4 44.8 1.0
CG A:PRO79 4.5 45.2 1.0
C A:ILE78 4.7 43.8 1.0
ND2 A:ASN74 4.8 36.1 1.0
O A:HOH358 4.8 34.1 1.0
O A:ILE78 4.9 33.2 1.0
CA A:ASN65 4.9 33.6 1.0
C A:ASN65 5.0 29.5 1.0

Chlorine binding site 3 out of 6 in 6qqd

Go back to Chlorine Binding Sites List in 6qqd
Chlorine binding site 3 out of 6 in the Cryogenic Temperature Structure of Hen Egg White Lysozyme Recorded After An Accumulated Dose of 10 Mgy


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Cryogenic Temperature Structure of Hen Egg White Lysozyme Recorded After An Accumulated Dose of 10 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:68.9
occ:1.00
 N A:ILE88 3.1 35.9 1.0
OD1 A:ASP87 3.4 0.5 1.0
CG1 A:ILE88 3.6 44.8 1.0
NH1 A:ARG14 3.8 64.4 1.0
CA A:ASP87 3.8 46.0 1.0
CE1 A:HIS15 3.8 47.8 1.0
C A:ASP87 3.9 33.6 1.0
O A:HOH309 4.0 53.4 1.0
CG2 A:ILE88 4.1 50.5 1.0
CB A:ILE88 4.1 33.2 1.0
CA A:ILE88 4.2 34.2 1.0
O A:SER86 4.2 42.9 0.5
O A:SER86 4.2 49.0 0.5
CB A:ALA11 4.2 30.4 1.0
CG A:ASP87 4.3 69.5 1.0
CZ A:PHE3 4.4 53.1 1.0
CB A:ASP87 4.5 42.8 1.0
ND1 A:HIS15 4.6 44.4 1.0
CD1 A:ILE88 4.6 45.8 1.0
NE2 A:HIS15 4.8 48.3 1.0
N A:ASP87 4.8 47.5 1.0
CE2 A:PHE3 4.8 36.7 1.0
N A:THR89 4.9 32.0 1.0
C A:ILE88 4.9 36.3 1.0
C A:SER86 4.9 45.7 0.5
CZ A:ARG14 5.0 47.4 1.0
C A:SER86 5.0 45.3 0.5

Chlorine binding site 4 out of 6 in 6qqd

Go back to Chlorine Binding Sites List in 6qqd
Chlorine binding site 4 out of 6 in the Cryogenic Temperature Structure of Hen Egg White Lysozyme Recorded After An Accumulated Dose of 10 Mgy


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Cryogenic Temperature Structure of Hen Egg White Lysozyme Recorded After An Accumulated Dose of 10 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:37.7
occ:1.00
 OH A:TYR23 2.9 26.9 1.0
CZ A:TYR23 3.6 26.8 1.0
CE2 A:TYR23 3.7 23.8 1.0
CA A:GLY104 4.1 31.4 1.0
O A:ARG21 4.6 32.4 1.0
N A:GLY104 4.7 25.1 1.0
CE1 A:TYR23 4.8 26.1 1.0
CD2 A:TYR23 4.9 26.2 1.0

Chlorine binding site 5 out of 6 in 6qqd

Go back to Chlorine Binding Sites List in 6qqd
Chlorine binding site 5 out of 6 in the Cryogenic Temperature Structure of Hen Egg White Lysozyme Recorded After An Accumulated Dose of 10 Mgy


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Cryogenic Temperature Structure of Hen Egg White Lysozyme Recorded After An Accumulated Dose of 10 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:44.7
occ:1.00
 O A:HOH390 2.7 60.8 1.0
OG A:SER24 3.0 28.8 1.0
N A:GLY26 3.1 27.7 1.0
CA A:GLY26 3.5 29.3 1.0
CB A:SER24 3.5 36.4 1.0
CA A:GLN121 3.8 45.9 1.0
CD1 A:ILE124 3.9 49.4 1.0
N A:GLN121 4.1 38.1 1.0
N A:LEU25 4.1 26.4 1.0
CB A:GLN121 4.1 50.1 1.0
CG A:GLN121 4.2 84.8 1.0
CG2 A:VAL120 4.2 30.9 1.0
C A:SER24 4.2 32.2 1.0
C A:LEU25 4.3 26.5 1.0
CG1 A:ILE124 4.3 41.3 1.0
O A:VAL120 4.4 32.4 1.0
C A:VAL120 4.4 33.1 1.0
CA A:SER24 4.5 28.3 1.0
C A:GLY26 4.6 30.1 1.0
O A:HOH364 4.6 22.7 0.5
CA A:LEU25 4.6 29.1 1.0
O A:SER24 4.7 25.4 1.0
N A:ASN27 4.7 26.4 1.0
CB A:LEU25 4.9 29.0 1.0

Chlorine binding site 6 out of 6 in 6qqd

Go back to Chlorine Binding Sites List in 6qqd
Chlorine binding site 6 out of 6 in the Cryogenic Temperature Structure of Hen Egg White Lysozyme Recorded After An Accumulated Dose of 10 Mgy


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Cryogenic Temperature Structure of Hen Egg White Lysozyme Recorded After An Accumulated Dose of 10 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:53.1
occ:1.00
 O A:HOH353 2.9 34.6 1.0
O A:THR69 3.1 37.6 1.0
N A:THR69 3.1 37.5 1.0
O A:HOH395 3.3 52.5 1.0
OG A:SER72 3.5 34.4 0.5
N A:ARG68 3.5 31.4 1.0
OD1 A:ASN65 3.5 39.4 1.0
C A:THR69 3.6 45.4 1.0
C A:GLY67 3.6 46.0 1.0
OG A:SER72 3.7 52.4 0.5
CA A:GLY67 3.7 35.5 1.0
N A:GLY67 3.7 34.7 1.0
O A:HOH306 3.8 39.2 1.0
CA A:THR69 3.8 41.9 1.0
CB A:THR69 4.1 46.9 1.0
C A:ARG68 4.1 36.9 1.0
OD1 A:ASP66 4.2 30.9 1.0
CA A:ARG68 4.3 31.7 1.0
O A:GLY67 4.3 47.0 1.0
CB A:SER72 4.4 0.2 0.5
N A:PRO70 4.5 78.1 0.5
O A:HOH302 4.6 35.4 1.0
N A:PRO70 4.6 30.7 0.5
OG1 A:THR69 4.7 36.4 1.0
CG A:ASN65 4.7 34.3 1.0
CB A:SER72 4.8 55.5 0.5
C A:ASP66 4.8 33.9 1.0
N A:ASP66 4.9 30.6 1.0

Reference:

G.Gotthard, S.Aumonier, D.De Sanctis, G.Leonard, D.Von Stetten, A.Royant. Specific Radiation Damage Is A Lesser Concern at Room Temperature. Iucrj V. 6 665 2019.
ISSN: ESSN 2052-2525
PubMed: 31316810
DOI: 10.1107/S205225251900616X
Page generated: Mon Jul 29 14:06:44 2024

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