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Chlorine in PDB 8rt3: Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions

Enzymatic activity of Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions

All present enzymatic activity of Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions:
3.2.1.17;

Protein crystallography data

The structure of Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions, PDB code: 8rt3 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) 27.45 / 1.09
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.21, 77.21, 39.05, 90, 90, 90
R / Rfree (%) 12.2 / 14.2

Other elements in 8rt3:

The structure of Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions (pdb code 8rt3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions, PDB code: 8rt3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 8rt3

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Chlorine binding site 1 out of 7 in the Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions


Mono view


Stereo pair view

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

b:42.7
occ:0.89
 HE1 A:TRP63 2.2 17.0 1.0
HD21 A:ASN59 2.5 18.9 0.4
O1 A:NO31005 2.7 23.7 0.7
O A:HOH1207 2.8 39.5 0.8
NE1 A:TRP63 3.0 14.1 1.0
HD1 A:TRP62 3.1 24.5 1.0
ND2 A:ASN59 3.2 15.7 0.4
O A:HOH1107 3.2 38.4 1.0
HD22 A:ASN59 3.3 18.9 0.4
O A:HOH1273 3.5 35.8 1.0
N A:NO31005 3.5 21.9 0.7
O A:HOH1122 3.6 34.1 1.0
O2 A:NO31005 3.7 16.6 0.7
HZ2 A:TRP63 3.7 18.0 1.0
HC61 A:DO31002 3.8 22.2 0.7
HB1 A:ALA107 3.9 17.5 1.0
CD1 A:TRP62 3.9 20.4 1.0
CE2 A:TRP63 4.0 13.9 1.0
CD1 A:TRP63 4.0 13.5 1.0
O A:HOH1192 4.0 37.1 0.8
HD1 A:TRP63 4.1 16.2 1.0
CZ2 A:TRP63 4.2 15.0 1.0
HG23 A:ILE98 4.2 16.8 1.0
CG A:ASN59 4.4 15.0 0.4
HC52 A:DO31002 4.4 22.0 0.7
HB3 A:ASN59 4.4 17.2 0.6
HE1 A:TRP62 4.5 27.9 1.0
HG21 A:ILE98 4.5 16.8 1.0
O A:HOH1196 4.5 31.6 0.8
HB2 A:TRP62 4.6 17.9 1.0
C6 A:DO31002 4.6 18.5 0.7
HC62 A:DO31002 4.6 22.2 0.7
NE1 A:TRP62 4.6 23.2 1.0
OD1 A:ASN59 4.7 15.7 0.4
O3 A:NO31005 4.7 24.3 0.7
CB A:ALA107 4.7 14.6 1.0
HC51 A:DO31002 4.8 22.0 0.7
HB2 A:ALA107 4.8 17.5 1.0
C5 A:DO31002 4.8 18.3 0.7
CG2 A:ILE98 4.9 14.0 1.0
HG12 A:ILE98 4.9 15.3 1.0
CG A:TRP62 5.0 17.1 1.0
HD13 A:ILE98 5.0 16.9 1.0

Chlorine binding site 2 out of 7 in 8rt3

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Chlorine binding site 2 out of 7 in the Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1007

b:33.8
occ:0.75
 H A:ASN74 2.4 19.5 1.0
HB3 A:ARG73 2.9 22.8 0.5
HB3 A:ARG73 2.9 22.8 0.5
N A:ASN74 3.2 16.2 1.0
HD23 A:LEU75 3.4 25.9 1.0
HA A:ARG73 3.5 21.3 0.5
HA A:ARG73 3.5 21.3 0.5
HD3 A:ARG73 3.6 28.7 0.5
HD2 A:ARG73 3.6 28.1 0.5
C A:ASN74 3.7 15.6 1.0
CB A:ARG73 3.7 19.0 0.5
CB A:ARG73 3.8 19.0 0.5
HB3 A:ASN74 3.8 18.9 1.0
O A:ASN74 3.8 16.3 1.0
HA A:LEU75 3.9 18.3 1.0
O A:HOH1194 3.9 34.0 1.0
CA A:ARG73 3.9 17.7 0.5
CA A:ARG73 3.9 17.7 0.5
HD3 A:ARG73 4.0 28.1 0.5
CA A:ASN74 4.0 15.5 1.0
HG A:LEU75 4.0 22.4 1.0
C A:ARG73 4.1 16.2 1.0
N A:LEU75 4.2 14.9 1.0
CD A:ARG73 4.2 23.4 0.5
CD2 A:LEU75 4.2 21.6 1.0
CD A:ARG73 4.3 23.9 0.5
O A:HOH1293 4.3 31.7 0.5
HD2 A:ARG73 4.3 28.7 0.5
HD21 A:LEU75 4.4 25.9 1.0
CB A:ASN74 4.4 15.8 1.0
CG A:ARG73 4.4 21.3 0.5
HB2 A:ARG73 4.4 22.8 0.5
HB2 A:ARG73 4.4 22.8 0.5
HG2 A:ARG73 4.4 25.6 0.5
CA A:LEU75 4.5 15.3 1.0
CG A:ARG73 4.5 21.4 0.5
H A:LEU75 4.6 17.9 1.0
CG A:LEU75 4.6 18.6 1.0
HA A:ASN74 4.9 18.6 1.0
O A:HOH1268 4.9 32.3 1.0
HB2 A:ASN74 4.9 18.9 1.0
HG3 A:ARG73 4.9 25.7 0.5
HD22 A:LEU75 5.0 25.9 1.0

Chlorine binding site 3 out of 7 in 8rt3

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Chlorine binding site 3 out of 7 in the Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1009

b:15.8
occ:1.00
 H A:GLY26 2.4 12.8 1.0
HA A:GLN121 2.8 16.1 1.0
HG A:SER24 2.9 17.8 1.0
HA3 A:GLY26 3.0 13.3 1.0
O A:HOH1322 3.0 30.2 0.6
HB2 A:SER24 3.0 16.0 1.0
OG A:SER24 3.1 14.8 1.0
O A:HOH1326 3.1 39.5 1.0
N A:GLY26 3.2 10.7 1.0
HG23 A:VAL120 3.2 17.3 1.0
O A:HOH1302 3.4 24.2 1.0
HD11 A:ILE124 3.5 27.6 1.0
HB2 A:GLN121 3.6 19.3 1.0
CB A:SER24 3.6 13.3 1.0
CA A:GLY26 3.6 11.1 1.0
CA A:GLN121 3.6 13.4 1.0
HG2 A:GLN121 3.7 20.4 1.0
HG12 A:ILE124 3.7 23.4 1.0
HD13 A:ILE124 3.9 27.6 1.0
N A:GLN121 3.9 13.1 1.0
CB A:GLN121 4.0 16.1 1.0
CD1 A:ILE124 4.1 23.0 1.0
H A:ASN27 4.2 12.0 1.0
CG2 A:VAL120 4.2 14.4 1.0
H A:LEU25 4.2 13.6 1.0
HB3 A:SER24 4.2 16.0 1.0
H A:GLN121 4.2 15.7 1.0
HA2 A:GLY26 4.2 13.3 1.0
C A:VAL120 4.2 12.4 1.0
N A:LEU25 4.2 11.3 1.0
O A:VAL120 4.3 12.4 1.0
CG A:GLN121 4.3 17.0 1.0
C A:LEU25 4.4 10.6 1.0
HB3 A:LEU25 4.4 15.0 1.0
C A:SER24 4.4 11.7 1.0
CG1 A:ILE124 4.4 19.5 1.0
HG21 A:VAL120 4.4 17.3 1.0
HG3 A:GLN121 4.5 20.4 1.0
C A:GLY26 4.6 9.7 1.0
CA A:SER24 4.6 11.5 1.0
N A:ASN27 4.7 10.0 1.0
HG22 A:VAL120 4.7 17.3 1.0
CA A:LEU25 4.7 11.6 1.0
HB A:VAL120 4.8 15.9 1.0
O A:SER24 4.8 12.0 1.0
C A:GLN121 4.8 13.0 1.0
O A:HOH1338 4.9 35.2 0.8
HG13 A:ILE124 4.9 23.4 1.0
HB3 A:GLN121 4.9 19.3 1.0
O A:HOH1271 4.9 38.3 1.0
O A:HOH1330 4.9 30.5 0.7
HD12 A:ILE124 4.9 27.6 1.0
HD22 A:ASN27 5.0 14.2 1.0
O A:HOH1162 5.0 16.8 1.0
CB A:VAL120 5.0 13.2 1.0

Chlorine binding site 4 out of 7 in 8rt3

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Chlorine binding site 4 out of 7 in the Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1010

b:17.4
occ:0.76
 H A:THR69 2.5 17.3 1.0
O A:HOH1298 3.0 41.5 1.0
HA2 A:GLY67 3.1 19.9 1.0
H A:GLY67 3.1 17.4 1.0
O A:HOH1198 3.1 14.7 1.0
HG A:SER72 3.3 20.6 1.0
N A:THR69 3.3 14.4 1.0
O A:HOH1253 3.3 28.5 0.8
O A:THR69 3.4 15.4 1.0
H A:ARG68 3.4 17.4 0.5
H A:ARG68 3.5 17.4 0.5
O A:HOH1172 3.5 33.6 1.0
CA A:GLY67 3.5 16.5 1.0
N A:ARG68 3.5 14.5 1.0
C A:GLY67 3.6 16.8 1.0
N A:GLY67 3.6 14.5 1.0
OD1 A:ASN65 3.6 17.1 1.0
C A:THR69 3.6 15.8 1.0
HB A:THR69 3.7 16.7 1.0
OG A:SER72 3.8 17.1 1.0
CA A:THR69 3.9 14.7 1.0
HA A:PRO70 3.9 23.0 1.0
O A:HOH1233 4.0 17.9 1.0
H A:ASP66 4.1 14.7 1.0
O A:GLY67 4.2 20.3 1.0
N A:PRO70 4.2 17.9 1.0
OD1 A:ASP66 4.2 12.7 1.0
CB A:THR69 4.3 13.9 1.0
C A:ARG68 4.3 15.6 1.0
CA A:ARG68 4.3 15.4 0.5
HA A:ARG68 4.4 18.5 0.5
CA A:ARG68 4.4 14.4 0.5
HA3 A:GLY67 4.5 19.9 1.0
HG1 A:THR69 4.5 16.8 1.0
H A:SER72 4.5 22.1 1.0
CA A:PRO70 4.6 19.2 1.0
HA A:ARG68 4.6 17.3 0.5
O A:HOH1203 4.6 38.3 1.0
C A:ASP66 4.7 13.6 1.0
O A:HOH1329 4.7 35.4 1.0
O A:HOH1165 4.7 28.5 1.0
NA A:NA1008 4.8 15.1 1.0
HA A:ASN65 4.8 15.6 1.0
CG A:ASN65 4.8 15.5 1.0
N A:ASP66 4.8 12.3 1.0
HA A:THR69 4.9 17.6 1.0
HD3 A:PRO70 4.9 24.6 1.0
OG1 A:THR69 4.9 14.0 1.0
CB A:SER72 5.0 16.7 1.0
HB3 A:SER72 5.0 20.0 1.0

Chlorine binding site 5 out of 7 in 8rt3

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Chlorine binding site 5 out of 7 in the Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1011

b:24.4
occ:0.77
 H A:GLU7 2.4 16.3 1.0
HA3 A:GLY4 2.7 19.4 1.0
O A:HOH1254 2.8 22.5 1.0
H A:CYS6 2.9 16.9 1.0
O A:HOH1258 3.0 29.6 0.6
HB2 A:GLU7 3.0 17.8 1.0
HB2 A:CYS6 3.1 19.4 1.0
N A:GLU7 3.1 13.6 1.0
N A:CYS6 3.4 14.1 1.0
CA A:GLY4 3.5 16.2 1.0
C A:GLY4 3.5 14.0 1.0
CB A:GLU7 3.7 14.8 1.0
HB3 A:GLU7 3.7 17.8 1.0
N A:ARG5 3.8 15.4 1.0
H A:ARG5 3.8 18.5 1.0
CB A:CYS6 3.9 16.2 1.0
CA A:CYS6 3.9 14.1 1.0
C A:CYS6 3.9 13.4 1.0
CA A:GLU7 4.0 13.7 1.0
O A:GLY4 4.0 14.0 1.0
HA2 A:GLY4 4.2 19.4 1.0
H A:GLY4 4.2 18.2 1.0
C A:ARG5 4.3 14.2 1.0
O A:HOH1346 4.3 37.4 1.0
O A:HOH1270 4.3 17.6 0.3
N A:GLY4 4.4 15.2 1.0
HA A:GLU7 4.4 16.4 1.0
O A:HOH1350 4.5 38.9 0.5
HB3 A:CYS6 4.5 19.4 1.0
CA A:ARG5 4.6 15.4 1.0
HB3 A:ARG5 4.7 21.9 1.0
O A:HOH1307 4.8 36.2 1.0
HA A:CYS6 4.9 17.0 1.0
H A:LEU8 4.9 14.9 1.0
OE1 A:GLU7 4.9 19.3 1.0
CG A:GLU7 5.0 16.5 1.0
SG A:CYS6 5.0 19.1 1.0

Chlorine binding site 6 out of 7 in 8rt3

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Chlorine binding site 6 out of 7 in the Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1012

b:15.0
occ:0.55
 CL A:CL1012 0.0 15.0 0.6
CL A:CL1012 1.1 19.2 0.5
O A:HOH1299 1.8 21.6 0.6
HH A:TYR23 2.2 14.8 1.0
OH A:TYR23 2.9 12.4 1.0
O A:HOH1255 3.0 38.0 0.8
HE2 A:TYR23 3.2 13.7 1.0
O A:HOH1153 3.4 21.0 1.0
HA3 A:GLY104 3.6 15.1 1.0
CZ A:TYR23 3.6 11.0 1.0
CE2 A:TYR23 3.7 11.4 1.0
O A:HOH1159 3.7 21.2 1.0
CA A:GLY104 4.4 12.6 1.0
HA2 A:GLY104 4.5 15.1 1.0
O A:HOH1315 4.6 36.6 1.0
O A:ARG21 4.6 15.5 1.0
CE1 A:TYR23 4.7 11.8 1.0
H A:MET105 4.8 13.0 1.0
O A:HOH1333 4.8 19.5 0.3
HB3 A:ARG21 4.9 20.8 0.5
CD2 A:TYR23 4.9 11.5 1.0
HB3 A:ARG21 4.9 20.1 0.5
HH21 A:ARG21 5.0 30.9 0.5

Chlorine binding site 7 out of 7 in 8rt3

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Chlorine binding site 7 out of 7 in the Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1012

b:19.2
occ:0.45
 CL A:CL1012 0.0 19.2 0.5
CL A:CL1012 1.1 15.0 0.6
HH A:TYR23 2.1 14.8 1.0
O A:HOH1299 2.6 21.6 0.6
HA3 A:GLY104 2.7 15.1 1.0
O A:HOH1159 2.8 21.2 1.0
O A:HOH1255 2.9 38.0 0.8
OH A:TYR23 2.9 12.4 1.0
HE2 A:TYR23 3.0 13.7 1.0
HA2 A:GLY104 3.5 15.1 1.0
CA A:GLY104 3.5 12.6 1.0
CE2 A:TYR23 3.6 11.4 1.0
CZ A:TYR23 3.7 11.0 1.0
O A:HOH1113 4.0 23.8 0.5
N A:GLY104 4.1 12.9 1.0
O A:HOH1153 4.2 21.0 1.0
H A:MET105 4.3 13.0 1.0
H A:GLY104 4.4 15.5 0.4
H A:GLY104 4.4 15.5 0.6
O A:HOH1333 4.4 19.5 0.3
HH21 A:ARG21 4.4 30.9 0.5
HB3 A:ARG21 4.6 20.8 0.5
HE A:ARG21 4.6 28.5 0.5
HB3 A:ARG21 4.6 20.1 0.5
O A:HOH1106 4.7 24.9 0.8
C A:ASN103 4.7 12.4 0.6
HG22 A:VAL99 4.7 16.5 1.0
C A:GLY104 4.7 11.2 1.0
C A:ASN103 4.7 15.4 0.4
O A:VAL99 4.8 14.8 1.0
N A:MET105 4.8 10.8 1.0
O A:ASN103 4.8 11.6 0.6
O A:ARG21 4.8 15.5 1.0
CD2 A:TYR23 4.9 11.5 1.0
CE1 A:TYR23 4.9 11.8 1.0
O A:ASN103 4.9 15.5 0.4

Reference:

C.Maccarthy, E.V.Koudan, S.V.Petrov, A.A.Levin, Y.D.Khesuani, V.Borshchevskiy. Hen Egg White Lysozyme Crystallized with Bioassembler in Space Microgravity Conditions To Be Published.
Page generated: Tue Jul 30 12:19:36 2024

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