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Chlorine in PDB 5fst: Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure

Enzymatic activity of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure

All present enzymatic activity of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure:
3.2.1.17;

Protein crystallography data

The structure of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure, PDB code: 5fst was solved by B.Lafumat, C.Mueller-Dieckmann, N.Colloc'h, T.Prange, A.Royant, P.Van Derlinden, P.Carpentier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.86 / 1.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.001, 79.001, 37.053, 90.00, 90.00, 90.00
R / Rfree (%) 10.9 / 13.4

Other elements in 5fst:

The structure of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure also contains other interesting chemical elements:

Krypton (Kr) 5 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure (pdb code 5fst). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure, PDB code: 5fst:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5fst

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Chlorine binding site 1 out of 8 in the Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:14.8
occ:1.00
HH A:TYR23 2.9 10.6 0.0
OH A:TYR23 3.0 10.6 1.0
O A:HOH2042 3.2 30.8 1.0
HE2 A:TYR23 3.2 9.0 1.0
O A:HOH2041 3.2 13.5 1.0
HA3 A:GLY104 3.4 10.4 1.0
O A:HOH2162 3.6 45.8 1.0
CZ A:TYR23 3.7 9.1 1.0
CE2 A:TYR23 3.7 9.0 1.0
HA2 A:GLY104 4.2 10.4 1.0
CA A:GLY104 4.2 10.4 1.0
H A:MET105 4.5 8.4 1.0
O A:ARG21 4.6 12.6 1.0
N A:GLY104 4.8 11.7 1.0
CE1 A:TYR23 4.9 8.9 1.0
CD2 A:TYR23 4.9 8.8 1.0
HB3 A:ARG21 4.9 13.5 1.0

Chlorine binding site 2 out of 8 in 5fst

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Chlorine binding site 2 out of 8 in the Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:17.7
occ:1.00
H A:GLY26 2.3 9.5 1.0
HG A:SER24 2.7 15.7 0.0
O A:HOH2047 2.8 38.3 1.0
HA A:GLN121 2.8 14.2 1.0
HB2 A:SER24 2.9 12.5 1.0
HA3 A:GLY26 3.0 9.8 1.0
OG A:SER24 3.0 15.7 1.0
N A:GLY26 3.2 9.5 1.0
HG21 A:VAL120 3.4 13.8 1.0
HD12 A:ILE124 3.4 23.3 1.0
CB A:SER24 3.4 12.5 1.0
HB2 A:GLN121 3.5 19.9 1.0
HG2 A:GLN121 3.6 24.0 1.0
CA A:GLY26 3.6 9.8 1.0
CA A:GLN121 3.6 14.2 1.0
HG12 A:ILE124 3.6 17.1 1.0
HD11 A:ILE124 3.7 23.3 1.0
CB A:GLN121 3.9 19.9 1.0
CD1 A:ILE124 3.9 23.3 1.0
H A:ASN27 3.9 9.0 1.0
N A:GLN121 3.9 13.5 1.0
HB3 A:SER24 4.1 12.5 1.0
H A:LEU25 4.1 11.0 1.0
CG A:GLN121 4.1 24.0 1.0
N A:LEU25 4.1 11.0 1.0
HA2 A:GLY26 4.2 9.8 1.0
CG1 A:ILE124 4.3 17.1 1.0
CG2 A:VAL120 4.3 13.8 1.0
C A:SER24 4.3 9.9 1.0
C A:VAL120 4.3 12.0 1.0
C A:LEU25 4.3 9.8 1.0
O A:VAL120 4.3 12.4 1.0
HB3 A:LEU25 4.3 11.4 1.0
H A:GLN121 4.4 13.5 1.0
HG3 A:GLN121 4.4 24.0 1.0
CA A:SER24 4.5 10.5 1.0
HG22 A:VAL120 4.5 13.8 1.0
C A:GLY26 4.5 8.9 1.0
N A:ASN27 4.6 9.0 1.0
CA A:LEU25 4.7 10.6 1.0
O A:SER24 4.7 11.1 1.0
HG13 A:ILE124 4.8 17.1 1.0
HG23 A:VAL120 4.8 13.8 1.0
HD13 A:ILE124 4.8 23.3 1.0
C A:GLN121 4.8 12.8 1.0
HB3 A:GLN121 4.8 19.9 1.0
HB A:VAL120 4.9 12.1 1.0
HD21 A:ASN27 4.9 10.8 1.0
O A:HOH2032 5.0 24.8 1.0
HG22 A:ILE124 5.0 14.6 1.0
O A:HOH2049 5.0 28.0 1.0
HA A:SER24 5.0 10.5 1.0

Chlorine binding site 3 out of 8 in 5fst

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Chlorine binding site 3 out of 8 in the Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:15.1
occ:1.00
H A:THR69 2.3 11.0 1.0
O A:HOH2117 3.1 11.1 1.0
O A:HOH2125 3.2 25.8 1.0
O A:HOH2124 3.2 33.5 1.0
N A:THR69 3.2 11.0 1.0
HA2 A:GLY67 3.3 12.5 1.0
H A:GLY67 3.3 10.5 1.0
O A:THR69 3.3 12.9 1.0
O A:HOH2119 3.4 32.3 1.0
H A:ARG68 3.4 11.3 1.0
HG A:SER72 3.5 14.4 0.0
N A:ARG68 3.5 11.3 1.0
C A:GLY67 3.5 12.2 1.0
HB A:THR69 3.6 10.8 1.0
CA A:GLY67 3.7 12.5 1.0
C A:THR69 3.7 10.6 1.0
OG A:SER72 3.7 14.4 1.0
N A:GLY67 3.7 10.5 1.0
OD1 A:ASN65 3.7 13.6 1.0
CA A:THR69 3.9 10.9 1.0
O A:HOH2118 4.0 14.7 1.0
H A:ASP66 4.2 9.1 1.0
O A:GLY67 4.2 15.4 1.0
CB A:THR69 4.2 10.8 1.0
C A:ARG68 4.2 12.8 1.0
OD1 A:ASP66 4.3 9.6 1.0
CA A:ARG68 4.3 12.0 0.5
CA A:ARG68 4.4 12.5 0.5
HA A:ARG68 4.5 12.0 0.5
HA A:PRO70 4.5 13.1 1.0
N A:PRO70 4.5 12.3 1.0
HA A:ARG68 4.6 12.5 0.5
HA3 A:GLY67 4.6 12.5 1.0
H A:SER72 4.6 15.9 1.0
NA A:NA209 4.7 11.9 1.0
C A:ASP66 4.8 9.1 1.0
HA A:THR69 4.8 10.9 1.0
OG1 A:THR69 4.9 10.6 1.0
HA A:ASN65 4.9 9.5 1.0
CB A:SER72 4.9 14.4 1.0
O A:HOH2128 4.9 24.5 0.5
HB3 A:SER72 4.9 14.4 1.0
CG A:ASN65 4.9 12.9 1.0
N A:ASP66 4.9 9.1 1.0

Chlorine binding site 4 out of 8 in 5fst

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Chlorine binding site 4 out of 8 in the Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:29.8
occ:1.00
H A:ILE88 2.3 11.2 1.0
O A:HOH2009 2.6 38.5 1.0
HG12 A:ILE88 2.7 11.8 1.0
O A:HOH2025 2.9 43.5 1.0
HA A:ASP87 3.0 12.2 1.0
HE1 A:HIS15 3.2 17.9 1.0
N A:ILE88 3.3 11.2 1.0
HZ A:PHE3 3.4 12.9 1.0
O A:HOH2004 3.5 28.1 1.0
O A:HOH2023 3.5 25.4 1.0
HG21 A:ILE88 3.5 12.2 1.0
HB2 A:ALA11 3.6 12.1 1.0
CG1 A:ILE88 3.7 11.8 1.0
CA A:ASP87 3.9 12.2 1.0
O A:SER86 3.9 14.5 1.0
CE1 A:HIS15 4.0 17.9 1.0
C A:ASP87 4.1 11.7 1.0
HG13 A:ILE88 4.1 11.8 1.0
CB A:ILE88 4.2 11.0 1.0
OD1 A:ASP87 4.2 16.4 1.0
CG2 A:ILE88 4.2 12.2 1.0
CZ A:PHE3 4.2 12.9 1.0
CA A:ILE88 4.3 10.3 1.0
HH21 A:ARG14 4.3 58.5 1.0
HE2 A:PHE3 4.4 12.3 1.0
HB3 A:ALA11 4.4 12.1 1.0
CB A:ALA11 4.5 12.1 1.0
HD11 A:ILE88 4.5 13.6 1.0
H A:THR89 4.5 10.7 1.0
CD1 A:ILE88 4.5 13.6 1.0
HG22 A:ILE88 4.5 12.2 1.0
HD12 A:ILE88 4.5 13.6 1.0
CG A:ASP87 4.7 17.9 1.0
CB A:ASP87 4.7 14.1 1.0
HD1 A:HIS15 4.8 17.5 1.0
C A:SER86 4.8 12.4 1.0
ND1 A:HIS15 4.8 17.5 1.0
CE2 A:PHE3 4.8 12.3 1.0
N A:ASP87 4.8 11.7 1.0
NE2 A:HIS15 4.8 24.8 1.0
HE2 A:HIS15 4.8 24.8 1.0
HB2 A:ASP87 4.9 14.1 1.0
HB1 A:ALA11 4.9 12.1 1.0
HZ1 A:LYS1 5.0 17.5 0.5
HG23 A:ILE88 5.0 12.2 1.0

Chlorine binding site 5 out of 8 in 5fst

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Chlorine binding site 5 out of 8 in the Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:26.9
occ:1.00
HZ1 A:LYS33 2.6 20.2 1.0
HE2 A:PHE38 2.8 11.0 1.0
HZ3 A:TRP123 3.0 17.1 1.0
O A:HOH2067 3.3 53.8 1.0
HD3 A:ARG5 3.3 14.7 1.0
HB2 A:ARG5 3.4 13.3 1.0
HD3 A:LYS33 3.4 12.9 1.0
NZ A:LYS33 3.5 20.2 1.0
CE2 A:PHE38 3.7 11.0 1.0
HE2 A:LYS33 3.8 15.9 1.0
CZ3 A:TRP123 3.9 17.1 1.0
O A:HOH2014 3.9 0.6 1.0
HZ2 A:LYS33 3.9 20.2 1.0
CE A:LYS33 4.0 15.9 1.0
HZ A:PHE38 4.1 10.1 1.0
HZ3 A:LYS33 4.2 20.2 1.0
CD A:LYS33 4.2 12.9 1.0
O A:HOH2064 4.2 32.0 1.0
CD A:ARG5 4.2 14.7 1.0
CZ A:PHE38 4.3 10.1 1.0
CB A:ARG5 4.3 13.3 1.0
HE A:ARG5 4.5 16.5 1.0
HG3 A:ARG5 4.6 13.4 1.0
HE3 A:TRP123 4.6 13.4 1.0
CD2 A:PHE38 4.6 9.9 1.0
HD2 A:PHE38 4.6 9.9 1.0
HH2 A:TRP123 4.6 18.7 1.0
CG A:ARG5 4.7 13.4 1.0
HB3 A:ARG5 4.7 13.3 1.0
HD2 A:LYS33 4.7 12.9 1.0
CE3 A:TRP123 4.7 13.4 1.0
CH2 A:TRP123 4.8 18.7 1.0
HD2 A:ARG5 4.8 14.7 1.0
NE A:ARG5 4.9 16.5 1.0
HG2 A:LYS33 5.0 11.2 1.0
HE3 A:LYS33 5.0 15.9 1.0

Chlorine binding site 6 out of 8 in 5fst

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Chlorine binding site 6 out of 8 in the Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:18.4
occ:0.80
HD21 A:ASN65 2.3 15.3 1.0
HB3 A:PRO79 2.9 10.8 1.0
HB3 A:ASN65 3.0 10.9 1.0
O A:HOH2135 3.1 20.5 1.0
HA A:PRO79 3.2 10.3 1.0
ND2 A:ASN65 3.2 15.3 1.0
CB A:PRO79 3.7 10.8 1.0
CA A:PRO79 3.7 10.3 1.0
HD22 A:ASN65 3.8 15.3 1.0
HD3 A:PRO79 3.9 12.3 1.0
CB A:ASN65 3.9 10.9 1.0
N A:PRO79 3.9 11.0 1.0
CG A:ASN65 4.0 12.9 1.0
O A:ASN65 4.3 9.3 1.0
CD A:PRO79 4.3 12.3 1.0
HB2 A:ASN65 4.3 10.9 1.0
HB2 A:PRO79 4.4 10.8 1.0
CG A:PRO79 4.5 14.2 1.0
C A:ILE78 4.5 10.4 1.0
HG3 A:PRO79 4.5 14.2 1.0
HD22 A:ASN74 4.5 14.1 1.0
O A:ILE78 4.7 11.0 1.0
HD21 A:ASN74 4.9 14.1 1.0
C A:ASN65 4.9 8.7 1.0
CA A:ASN65 4.9 9.5 1.0
ND2 A:ASN74 5.0 14.1 1.0
H A:ASN65 5.0 9.4 1.0

Chlorine binding site 7 out of 8 in 5fst

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Chlorine binding site 7 out of 8 in the Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:35.5
occ:1.00
H A:ASN74 2.2 13.0 1.0
HE A:ARG73 2.2 22.6 1.0
HB3 A:ARG73 3.0 15.6 1.0
NE A:ARG73 3.2 22.6 1.0
N A:ASN74 3.2 13.0 1.0
HA A:ARG73 3.4 14.8 1.0
HD21 A:LEU75 3.4 20.8 1.0
HH21 A:ARG73 3.5 23.9 1.0
O A:HOH2134 3.5 70.1 1.0
HD2 A:ARG73 3.5 22.3 1.0
HB3 A:ASN74 3.6 12.4 1.0
C A:ASN74 3.8 13.1 1.0
CB A:ARG73 3.8 15.6 1.0
CD A:ARG73 3.8 22.3 1.0
O A:ASN74 3.9 13.8 1.0
CA A:ASN74 3.9 11.9 1.0
CA A:ARG73 3.9 14.8 1.0
C A:ARG73 4.1 13.1 1.0
CZ A:ARG73 4.1 22.4 1.0
NH2 A:ARG73 4.1 23.9 1.0
HA A:LEU75 4.2 13.9 1.0
CB A:ASN74 4.2 12.4 1.0
HD22 A:LEU75 4.2 20.8 1.0
CD2 A:LEU75 4.2 20.8 1.0
N A:LEU75 4.3 12.6 1.0
CG A:ARG73 4.4 18.5 1.0
HG A:LEU75 4.5 16.2 1.0
HB2 A:ARG73 4.6 15.6 1.0
HD3 A:ARG73 4.7 22.3 1.0
HB2 A:ASN74 4.7 12.4 1.0
H A:LEU75 4.8 12.6 1.0
CA A:LEU75 4.8 13.9 1.0
O A:HOH2130 4.8 47.4 1.0
HG3 A:ARG73 4.8 18.5 1.0
HA A:ASN74 4.9 11.9 1.0
CG A:LEU75 4.9 16.2 1.0
HH22 A:ARG73 5.0 23.9 1.0
HD23 A:LEU75 5.0 20.8 1.0

Chlorine binding site 8 out of 8 in 5fst

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Chlorine binding site 8 out of 8 in the Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:32.0
occ:0.00
O A:HOH2123 0.1 23.1 1.0
HH11 A:ARG68 2.1 13.5 0.5
HH11 A:ARG68 2.2 11.4 0.5
HD2 A:ARG68 2.9 11.8 0.5
NH1 A:ARG68 2.9 13.5 0.5
NH1 A:ARG68 2.9 11.4 0.5
HD3 A:ARG68 3.1 15.6 0.5
HH12 A:ARG68 3.1 13.5 0.5
HH12 A:ARG68 3.2 11.4 0.5
HD2 A:ARG68 3.2 15.6 0.5
CD A:ARG68 3.6 15.6 0.5
CD A:ARG68 3.8 11.8 0.5
CZ A:ARG68 4.0 11.5 0.5
CZ A:ARG68 4.0 10.8 0.5
HH12 A:ARG45 4.2 14.5 0.2
NE A:ARG68 4.2 13.0 0.5
HD3 A:ARG68 4.3 11.8 0.5
NE A:ARG68 4.3 11.4 0.5
HB2 A:ARG68 4.4 13.7 0.5
HB3 A:ARG68 4.4 13.7 0.5
HH22 A:ARG45 4.5 19.2 0.2
HB2 A:ARG68 4.5 12.2 0.5
HH21 A:ARG45 4.5 37.0 0.5
HB3 A:ARG68 4.7 12.2 0.5
HH22 A:ARG45 4.7 37.0 0.5
NH2 A:ARG45 4.7 37.0 0.5
CG A:ARG68 4.8 13.8 0.5
CB A:ARG68 4.8 13.7 0.5
CG A:ARG68 4.8 13.9 0.5
CB A:ARG68 4.9 12.2 0.5
NH1 A:ARG45 4.9 14.5 0.2
HG2 A:ARG68 4.9 13.8 0.5
NH2 A:ARG45 5.0 19.2 0.2
HH22 A:ARG45 5.0 9.5 0.2

Reference:

B.Lafumat, C.Mueller-Dieckmann, N.Colloc'h, T.Prange, A.Royant, P.Van Der Linden, P.Carpentier. Gas-Sensitive Biological Crystals Processed in Pressurized Oxygen and Krypton Atmospheres: Deciphering Gas Channels in Proteins Using A Novel `Soak-and-Freeze' Methodology. J.Appl.Crystallogr. V. 49 1478 2016.
ISSN: ISSN 0021-8898
DOI: 10.1107/S1600576716010992
Page generated: Sat Dec 12 11:45:30 2020

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