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Chlorine in PDB 8zst: Lysozyme Crystallized with Bioassembler on Earth

Enzymatic activity of Lysozyme Crystallized with Bioassembler on Earth

All present enzymatic activity of Lysozyme Crystallized with Bioassembler on Earth:
3.2.1.17;

Protein crystallography data

The structure of Lysozyme Crystallized with Bioassembler on Earth, PDB code: 8zst was solved by C.Maccarthy, E.V.Koudan, S.V.Petrov, A.A.Levin, Y.D.Khesuani, V.Borshchevskiy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.73 / 0.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.03, 77.03, 38.97, 90, 90, 90
R / Rfree (%) 12.1 / 13.3

Other elements in 8zst:

The structure of Lysozyme Crystallized with Bioassembler on Earth also contains other interesting chemical elements:

Gadolinium (Gd) 4 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Lysozyme Crystallized with Bioassembler on Earth (pdb code 8zst). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Lysozyme Crystallized with Bioassembler on Earth, PDB code: 8zst:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 8zst

Go back to Chlorine Binding Sites List in 8zst
Chlorine binding site 1 out of 7 in the Lysozyme Crystallized with Bioassembler on Earth


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Lysozyme Crystallized with Bioassembler on Earth within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1006

b:10.8
occ:0.85
CL A:CL1006 0.0 10.8 0.8
CL A:CL1006 0.9 13.4 0.1
HH A:TYR23 2.3 11.9 1.0
OH A:TYR23 3.0 9.0 1.0
O A:HOH1294 3.1 25.8 1.0
HE2 A:TYR23 3.2 11.1 1.0
O A:HOH1198 3.2 11.3 1.0
HA3 A:GLY104 3.4 12.4 1.0
CZ A:TYR23 3.6 8.1 1.0
CE2 A:TYR23 3.7 8.2 1.0
O A:HOH1216 3.8 31.9 0.8
HA2 A:GLY104 4.1 12.4 1.0
CA A:GLY104 4.2 9.8 1.0
O A:ARG21 4.6 10.4 1.0
H A:MET105 4.7 10.7 1.0
O A:HOH1264 4.7 26.7 1.0
CE1 A:TYR23 4.8 8.0 1.0
HE A:ARG21 4.8 20.2 0.5
N A:GLY104 4.8 10.9 1.0
HH22 A:ARG21 4.9 21.8 0.5
HB3 A:ARG21 4.9 15.0 0.5
CD2 A:TYR23 4.9 8.0 1.0
HB3 A:ARG21 4.9 15.0 0.5

Chlorine binding site 2 out of 7 in 8zst

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Chlorine binding site 2 out of 7 in the Lysozyme Crystallized with Bioassembler on Earth


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Lysozyme Crystallized with Bioassembler on Earth within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1006

b:13.4
occ:0.15
CL A:CL1006 0.0 13.4 0.1
CL A:CL1006 0.9 10.8 0.8
HH A:TYR23 2.3 11.9 1.0
HA3 A:GLY104 2.8 12.4 1.0
O A:HOH1294 2.8 25.8 1.0
O A:HOH1216 3.0 31.9 0.8
HE2 A:TYR23 3.0 11.1 1.0
OH A:TYR23 3.1 9.0 1.0
HA2 A:GLY104 3.3 12.4 1.0
CA A:GLY104 3.5 9.8 1.0
CE2 A:TYR23 3.6 8.2 1.0
CZ A:TYR23 3.8 8.1 1.0
O A:HOH1198 3.9 11.3 1.0
N A:GLY104 4.0 10.9 1.0
O A:HOH1128 4.1 12.8 0.9
H A:GLY104 4.2 13.4 1.0
HH22 A:ARG21 4.3 21.8 0.5
H A:MET105 4.4 10.7 1.0
HE A:ARG21 4.5 20.2 0.5
HE A:ARG21 4.5 20.2 0.5
HB3 A:ARG21 4.5 15.0 0.5
HB3 A:ARG21 4.5 15.0 0.5
O A:ARG21 4.7 10.4 1.0
O A:HOH1346 4.7 29.0 1.0
C A:GLY104 4.7 8.7 1.0
HD3 A:ARG21 4.8 18.7 0.5
C A:ASN103 4.8 13.6 1.0
N A:MET105 4.9 7.6 1.0
CD2 A:TYR23 4.9 8.0 1.0
O A:VAL99 4.9 10.5 1.0
HG22 A:VAL99 4.9 11.4 1.0
O A:HOH1264 4.9 26.7 1.0
O A:ASN103 5.0 13.8 1.0

Chlorine binding site 3 out of 7 in 8zst

Go back to Chlorine Binding Sites List in 8zst
Chlorine binding site 3 out of 7 in the Lysozyme Crystallized with Bioassembler on Earth


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Lysozyme Crystallized with Bioassembler on Earth within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1007

b:12.6
occ:0.73
H A:THR69 2.4 12.9 0.3
H A:THR69 2.4 12.9 0.7
O A:HOH1320 3.1 37.8 1.0
H A:GLY67 3.1 13.9 1.0
HA2 A:GLY67 3.1 14.8 1.0
O A:HOH1232 3.1 10.7 1.0
N A:THR69 3.3 10.1 1.0
O A:HOH1306 3.3 33.8 1.0
O A:THR69 3.4 10.7 1.0
H A:ARG68 3.4 14.4 0.7
H A:ARG68 3.5 14.4 0.3
N A:ARG68 3.5 10.5 0.7
C A:GLY67 3.5 12.6 1.0
CA A:GLY67 3.5 12.9 1.0
N A:ARG68 3.5 12.5 0.3
N A:GLY67 3.5 10.9 1.0
OD1 A:ASN65 3.6 13.2 1.0
C A:THR69 3.6 10.9 1.0
O A:HOH1186 3.7 33.0 1.0
HB A:THR69 3.7 12.5 1.0
OG A:SER72 3.8 12.1 1.0
CA A:THR69 3.9 10.2 1.0
HA A:PRO70 4.0 15.5 0.3
O A:HOH1269 4.1 13.0 1.0
HA A:PRO70 4.1 15.5 0.7
H A:ASP66 4.1 12.1 1.0
O A:GLY67 4.2 16.4 1.0
OD1 A:ASP66 4.2 8.9 1.0
C A:ARG68 4.2 11.2 0.7
N A:PRO70 4.2 12.8 1.0
C A:ARG68 4.3 10.6 0.3
CB A:THR69 4.3 10.1 1.0
CA A:ARG68 4.3 11.2 0.7
CA A:ARG68 4.4 12.1 0.3
HA A:ARG68 4.4 14.0 0.7
HG1 A:THR69 4.5 12.1 1.0
HA3 A:GLY67 4.5 14.8 1.0
HA A:ARG68 4.5 14.0 0.3
H A:SER72 4.6 14.4 1.0
CA A:PRO70 4.6 14.4 0.3
C A:ASP66 4.6 10.1 1.0
CA A:PRO70 4.7 14.0 0.7
O A:HOH1193 4.7 35.7 1.0
O A:HOH1217 4.7 21.9 1.0
NA A:NA1012 4.8 10.4 1.0
HD3 A:PRO70 4.8 16.0 0.3
HA A:ASN65 4.8 12.4 1.0
CG A:ASN65 4.8 12.2 1.0
N A:ASP66 4.8 9.2 1.0
HA A:THR69 4.8 12.9 1.0
OG1 A:THR69 4.9 9.6 1.0
HD3 A:PRO70 4.9 16.0 0.7

Chlorine binding site 4 out of 7 in 8zst

Go back to Chlorine Binding Sites List in 8zst
Chlorine binding site 4 out of 7 in the Lysozyme Crystallized with Bioassembler on Earth


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Lysozyme Crystallized with Bioassembler on Earth within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1008

b:27.2
occ:0.80
HE1 A:TRP63 2.3 12.9 1.0
HD21 A:ASN59 2.7 12.9 0.3
HD1 A:TRP62 3.0 16.4 1.0
O3 A:NO31005 3.0 14.3 0.8
NE1 A:TRP63 3.1 9.9 1.0
ND2 A:ASN59 3.4 12.3 0.3
HD22 A:ASN59 3.5 12.9 0.3
HZ2 A:TRP63 3.6 12.9 1.0
HC62 A:DO31002 3.6 15.3 0.8
O A:HOH1135 3.6 28.4 1.0
O A:HOH1119 3.7 23.3 1.0
CD1 A:TRP62 3.8 15.0 1.0
N A:NO31005 3.9 13.8 0.8
CE2 A:TRP63 4.0 9.8 1.0
O1 A:NO31005 4.0 11.5 0.8
CZ2 A:TRP63 4.1 10.7 1.0
HB1 A:ALA107 4.2 13.2 1.0
CD1 A:TRP63 4.2 9.5 1.0
HG22 A:ILE98 4.2 12.6 1.0
HC52 A:DO31002 4.2 15.1 0.8
HE1 A:TRP62 4.3 17.1 1.0
HD1 A:TRP63 4.3 12.4 1.0
NE1 A:TRP62 4.4 16.6 1.0
C6 A:DO31002 4.4 14.7 0.8
HB2 A:TRP62 4.5 13.3 1.0
HB3 A:ASN59 4.5 12.5 0.4
CG A:ASN59 4.6 11.1 0.3
HB3 A:ASN59 4.6 12.5 0.3
O A:HOH1349 4.6 31.1 0.9
HC61 A:DO31002 4.6 15.3 0.8
O A:HOH1295 4.6 32.1 1.0
HC51 A:DO31002 4.6 15.1 0.8
C5 A:DO31002 4.7 14.0 0.8
HB2 A:ALA107 4.7 13.2 1.0
CG A:TRP62 4.8 12.1 1.0
HG23 A:ILE98 4.8 12.6 1.0
CB A:ALA107 4.9 12.4 1.0
OD1 A:ASN59 4.9 10.3 0.3
CG2 A:ILE98 5.0 10.7 1.0

Chlorine binding site 5 out of 7 in 8zst

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Chlorine binding site 5 out of 7 in the Lysozyme Crystallized with Bioassembler on Earth


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Lysozyme Crystallized with Bioassembler on Earth within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1009

b:18.9
occ:0.70
H A:GLU7 2.4 13.1 1.0
HA3 A:GLY4 2.7 13.4 1.0
O A:HOH1296 2.8 17.1 1.0
O A:HOH1290 2.9 37.9 1.0
HB2 A:GLU7 2.9 13.4 1.0
H A:CYS6 3.0 13.7 1.0
HB2 A:CYS6 3.1 14.9 1.0
N A:GLU7 3.2 10.1 1.0
CA A:GLY4 3.5 12.4 1.0
N A:CYS6 3.5 10.9 1.0
C A:GLY4 3.6 10.8 1.0
HB3 A:GLU7 3.6 13.4 1.0
CB A:GLU7 3.6 10.9 1.0
H A:ARG5 3.8 14.0 0.3
N A:ARG5 3.8 12.6 0.3
N A:ARG5 3.8 11.1 0.7
H A:ARG5 3.8 14.0 0.7
CB A:CYS6 3.9 12.9 1.0
CA A:CYS6 4.0 11.0 1.0
CA A:GLU7 4.0 10.1 1.0
C A:CYS6 4.0 10.3 1.0
O A:GLY4 4.0 10.0 1.0
HA2 A:GLY4 4.1 13.4 1.0
H A:GLY4 4.2 13.3 1.0
C A:ARG5 4.3 10.2 0.7
O A:HOH1304 4.3 30.3 1.0
N A:GLY4 4.4 11.2 1.0
HA A:GLU7 4.4 13.1 1.0
C A:ARG5 4.4 11.7 0.3
O A:HOH1379 4.4 37.1 1.0
O A:HOH1390 4.4 29.9 0.8
HB3 A:CYS6 4.5 14.9 1.0
CA A:ARG5 4.6 11.5 0.7
CA A:ARG5 4.7 13.3 0.3
HB3 A:ARG5 4.7 14.9 0.7
H A:LEU8 4.9 12.0 1.0
OE1 A:GLU7 4.9 13.9 1.0
CG A:GLU7 4.9 12.0 1.0
HA A:CYS6 4.9 13.7 1.0
HG2 A:ARG5 4.9 15.4 0.3

Chlorine binding site 6 out of 7 in 8zst

Go back to Chlorine Binding Sites List in 8zst
Chlorine binding site 6 out of 7 in the Lysozyme Crystallized with Bioassembler on Earth


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Lysozyme Crystallized with Bioassembler on Earth within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1010

b:29.9
occ:0.70
H A:ASN74 2.3 13.9 1.0
N A:ASN74 3.1 11.8 1.0
HA A:ARG73 3.4 14.4 1.0
HD22 A:LEU75 3.4 16.0 1.0
CB A:ARG73 3.6 17.9 0.7
CB A:ARG73 3.7 18.8 0.3
HB3 A:ASN74 3.7 13.7 1.0
C A:ASN74 3.8 10.7 1.0
CA A:ARG73 3.8 13.8 0.3
CA A:ARG73 3.8 13.1 0.7
O A:ASN74 3.9 11.4 1.0
CA A:ASN74 3.9 10.7 1.0
CD A:ARG73 4.0 27.9 0.3
C A:ARG73 4.0 11.7 1.0
O A:HOH1121 4.0 33.7 1.0
HA A:LEU75 4.1 13.6 1.0
HG A:LEU75 4.1 15.6 1.0
N A:LEU75 4.2 10.6 1.0
CD2 A:LEU75 4.3 16.3 1.0
CB A:ASN74 4.3 11.5 1.0
CG A:ARG73 4.3 23.8 0.7
CG A:ARG73 4.4 24.1 0.3
CD A:ARG73 4.4 27.9 0.7
O A:HOH1303 4.6 27.9 1.0
H A:LEU75 4.6 13.4 1.0
CA A:LEU75 4.7 11.2 1.0
CG A:LEU75 4.7 13.5 1.0
HB2 A:ASN74 4.8 13.7 1.0
HA A:ASN74 4.8 13.5 1.0
HD21 A:LEU75 4.8 16.0 1.0
HD23 A:LEU75 4.8 16.0 1.0

Chlorine binding site 7 out of 7 in 8zst

Go back to Chlorine Binding Sites List in 8zst
Chlorine binding site 7 out of 7 in the Lysozyme Crystallized with Bioassembler on Earth


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Lysozyme Crystallized with Bioassembler on Earth within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1011

b:11.2
occ:1.00
H A:GLY26 2.4 10.6 1.0
HA A:GLN121 2.8 15.1 1.0
HB2 A:SER24 3.0 12.3 1.0
HA3 A:GLY26 3.0 10.7 1.0
HD12 A:ILE124 3.1 17.1 1.0
O A:HOH1359 3.1 31.1 0.7
OG A:SER24 3.1 10.9 1.0
N A:GLY26 3.2 7.6 1.0
O A:HOH1362 3.2 21.0 1.0
HG23 A:VAL120 3.2 12.4 1.0
O A:HOH1341 3.3 14.8 0.8
HG A:SER24 3.3 13.1 1.0
CB A:SER24 3.5 9.8 1.0
HB2 A:GLN121 3.5 15.1 1.0
CA A:GLY26 3.6 7.8 1.0
CA A:GLN121 3.6 9.5 1.0
HG12 A:ILE124 3.7 16.8 1.0
HG2 A:GLN121 3.7 15.1 1.0
N A:GLN121 3.9 8.9 1.0
CB A:GLN121 3.9 11.4 1.0
CD1 A:ILE124 4.0 16.8 1.0
HB3 A:SER24 4.1 12.3 1.0
H A:LEU25 4.1 10.9 1.0
CG2 A:VAL120 4.1 10.9 1.0
H A:ASN27 4.2 10.2 1.0
C A:VAL120 4.2 8.8 1.0
H A:GLN121 4.2 15.1 1.0
N A:LEU25 4.2 8.0 1.0
O A:VAL120 4.2 8.9 1.0
HA2 A:GLY26 4.2 10.7 1.0
HG21 A:VAL120 4.3 12.4 1.0
CG A:GLN121 4.3 12.0 1.0
HD11 A:ILE124 4.3 17.1 1.0
CG1 A:ILE124 4.3 14.8 1.0
HB3 A:LEU25 4.4 11.3 1.0
C A:LEU25 4.4 7.7 1.0
C A:SER24 4.4 7.8 1.0
HG3 A:GLN121 4.5 15.1 1.0
CA A:SER24 4.6 8.2 1.0
C A:GLY26 4.6 7.3 1.0
HD13 A:ILE124 4.6 17.1 1.0
N A:ASN27 4.7 7.2 1.0
HB A:VAL120 4.7 12.4 1.0
HG22 A:VAL120 4.7 12.4 1.0
CA A:LEU25 4.7 7.8 1.0
C A:GLN121 4.8 9.1 1.0
O A:SER24 4.8 8.4 1.0
HG13 A:ILE124 4.8 16.8 1.0
HB3 A:GLN121 4.9 15.1 1.0
O A:HOH1307 4.9 17.8 1.0
CB A:VAL120 4.9 9.6 1.0
HG22 A:ILE124 5.0 16.4 1.0
O A:HOH1167 5.0 12.5 1.0
O A:HOH1259 5.0 11.3 1.0

Reference:

C.Maccarthy, E.V.Koudan, M.Shevtsov, V.Parfenov, S.Petrov, A.Levin, F.Senatov, N.Sykilinda, S.Ostrovskiy, S.Pekov, I.Gushchin, I.Popov, E.Zinovev, A.Bogorodskiy, A.Mishin, V.Ivanovich, A.Rogachev, Y.Khesuani, V.Borshchevskiy. Exploring the Potential of A Bioassembler For Protein Crystallization in Space. Npj Microgravity 2025.
DOI: 10.1038/S41526-025-00477-W
Page generated: Sun Jul 13 15:55:22 2025

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