Chlorine in PDB 8rt2: Hen Egg White Lysozyme Crystallized with Bioassembler on Earth

Enzymatic activity of Hen Egg White Lysozyme Crystallized with Bioassembler on Earth

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

Protein crystallography data

The structure of Hen Egg White Lysozyme Crystallized with Bioassembler on Earth, PDB code: 8rt2 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 8rt2:

The structure of Hen Egg White Lysozyme Crystallized with Bioassembler on Earth 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 on Earth (pdb code 8rt2). 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 on Earth, PDB code: 8rt2:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 8rt2

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Chlorine binding site 1 out of 7 in the Hen Egg White 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 Hen Egg White 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 8rt2

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Chlorine binding site 2 out of 7 in the Hen Egg White 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 Hen Egg White 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 8rt2

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Chlorine binding site 3 out of 7 in the Hen Egg White 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 Hen Egg White 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 8rt2

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Chlorine binding site 4 out of 7 in the Hen Egg White 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 Hen Egg White 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 8rt2

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Chlorine binding site 5 out of 7 in the Hen Egg White 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 Hen Egg White 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 8rt2

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Chlorine binding site 6 out of 7 in the Hen Egg White 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 Hen Egg White 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 8rt2

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Chlorine binding site 7 out of 7 in the Hen Egg White 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 Hen Egg White 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, S.V.Petrov, A.A.Levin, Y.D.Khesuani, V.Borshchevskiy. Hen Egg White Lysozyme Crystallized with Bioassembler on Earth To Be Published.
Page generated: Tue Jul 30 12:19:37 2024

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