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Chlorine in PDB 6lfh: X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme

Enzymatic activity of X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme

All present enzymatic activity of X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme, PDB code: 6lfh was solved by A.Kar, A.Das, K.Mandal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.61 / 1.46
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 32.950, 56.410, 61.220, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.6

Other elements in 6lfh:

The structure of X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme (pdb code 6lfh). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme, PDB code: 6lfh:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6lfh

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Chlorine binding site 1 out of 6 in the X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cl201

b:13.6
occ:1.00
 O X:HOH343 3.2 11.3 1.0
O X:HOH380 3.2 18.9 1.0
ND2 X:ASN66 3.3 13.6 1.0
CA X:SER80 3.7 12.4 1.0
CB X:ASN66 3.8 13.7 1.0
CB X:SER80 3.8 13.1 1.0
N X:SER80 3.9 11.9 1.0
CG X:ASN66 4.1 15.4 1.0
O X:ASN66 4.2 11.8 1.0
O X:HOH454 4.3 25.1 1.0
OG X:SER80 4.4 13.1 1.0
C X:LEU79 4.5 13.8 1.0
O X:LEU79 4.5 16.3 1.0
ND2 X:ASN75 4.8 20.0 1.0
C X:ASN66 4.8 13.2 1.0
CA X:ASN66 4.8 12.5 1.0
O X:HOH426 4.9 23.5 1.0

Chlorine binding site 2 out of 6 in 6lfh

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Chlorine binding site 2 out of 6 in the X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cl202

b:24.2
occ:1.00
 O X:HOH454 3.1 25.1 1.0
O X:HOH458 3.3 27.4 1.0
ND2 X:ASN75 3.4 20.0 1.0
CB X:ASN66 3.7 13.7 1.0
CG X:ASN66 3.8 15.4 1.0
CB X:ASN75 3.8 16.9 1.0
ND2 X:ASN66 3.9 13.6 1.0
CG X:ASN75 4.1 17.4 1.0
OD1 X:ASN66 4.3 16.7 1.0
O X:HOH496 4.5 34.2 1.0
O X:HOH363 4.5 19.5 1.0
O X:HOH380 4.6 18.9 1.0
O X:HOH318 5.0 33.2 1.0

Chlorine binding site 3 out of 6 in 6lfh

Go back to Chlorine Binding Sites List in 6lfh
Chlorine binding site 3 out of 6 in the X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cl203

b:31.4
occ:1.00
 NZ X:LYS97 3.1 14.2 1.0
O X:HOH484 3.3 45.6 1.0
CE X:LYS97 3.8 12.3 1.0
O X:HOH330 3.9 24.9 1.0
CE1 X:TYR20 4.0 13.8 1.0
CD X:LYS97 4.1 13.6 1.0
CD1 X:TYR20 4.2 12.2 1.0
O X:HOH355 4.5 37.0 1.0
O X:HOH396 4.7 14.0 1.0
O X:GLY16 4.8 13.7 1.0

Chlorine binding site 4 out of 6 in 6lfh

Go back to Chlorine Binding Sites List in 6lfh
Chlorine binding site 4 out of 6 in the X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cl204

b:18.6
occ:1.00
 O X:HOH446 2.8 58.3 1.0
O X:HOH513 3.2 33.7 1.0
O X:HOH511 3.2 38.2 1.0
O X:HOH331 3.2 33.6 1.0
N X:ALA26 3.3 10.1 1.0
N X:LEU25 3.6 10.3 1.0
CB X:ALA26 3.8 14.1 1.0
CB X:SER24 3.8 13.5 1.0
CB X:LEU25 3.8 12.8 1.0
CA X:LEU25 4.1 11.0 1.0
OG X:SER24 4.1 11.5 1.0
CA X:ALA26 4.1 13.2 1.0
C X:LEU25 4.1 10.0 1.0
O X:HOH338 4.2 28.4 1.0
CG2 X:VAL125 4.2 15.2 1.0
OD1 X:ASP18 4.3 18.4 1.0
C X:SER24 4.4 10.1 1.0
CG1 X:VAL125 4.5 18.3 1.0
CA X:SER24 4.6 10.7 1.0
CB X:VAL125 4.9 13.8 1.0

Chlorine binding site 5 out of 6 in 6lfh

Go back to Chlorine Binding Sites List in 6lfh
Chlorine binding site 5 out of 6 in the X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cl205

b:20.3
occ:1.00
 O X:HOH387 3.1 25.8 1.0
N X:GLY129 3.2 15.4 1.0
CA X:GLY129 3.6 18.6 1.0
C X:GLY127 3.7 16.5 1.0
O X:HOH356 3.7 20.1 1.0
CA X:GLY127 3.8 18.0 1.0
N X:CYS128 3.9 15.3 1.0
O X:GLY127 4.0 16.8 1.0
N X:GLY127 4.1 17.8 1.0
C X:CYS128 4.3 14.7 1.0
C X:GLY129 4.6 20.4 1.0
CA X:CYS128 4.7 13.9 1.0
N X:VAL130 4.8 15.7 1.0
O X:HOH333 5.0 16.0 1.0

Chlorine binding site 6 out of 6 in 6lfh

Go back to Chlorine Binding Sites List in 6lfh
Chlorine binding site 6 out of 6 in the X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of X-Ray Crystal Structure of Chemically Synthesized Human Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cl206

b:15.0
occ:1.00
 O X:HOH389 3.1 16.2 1.0
O X:HOH316 3.2 28.4 1.0
NH2 X:ARG107 3.3 19.2 1.0
NH1 X:ARG107 3.5 16.6 1.0
CH2 X:TRP112 3.8 13.6 1.0
CZ X:ARG107 3.9 14.6 1.0
CZ2 X:TRP112 4.5 12.6 1.0
CG X:GLN117 4.6 13.6 1.0
OD1 X:ASN118 4.7 20.6 1.0
CZ3 X:TRP112 4.8 13.6 1.0

Reference:

A.Kar, J.Mannuthodikayil, S.Singh, A.Biswas, P.Dubey, A.Das, K.Mandal. Efficient Chemical Protein Synthesis Using Fmoc-Masked N-Terminal Cysteine in Peptide Thioester Segments. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 32333711
DOI: 10.1002/ANIE.202000491
Page generated: Sun Jul 28 02:49:50 2024

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