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Chlorine in PDB 4i0c: The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme

Enzymatic activity of The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme

All present enzymatic activity of The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme:
3.2.1.17;

Protein crystallography data

The structure of The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme, PDB code: 4i0c was solved by E.De Genst, P.H.Chan, E.Pardon, J.R.Kumita, J.Christodoulou, L.Menzer, D.Y.Chirgadze, C.V.Robinson, S.Muyldermans, A.Matagne, L.Wyns, C.M.Dobson, M.Dumoulin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.91 / 1.95
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.321, 96.321, 156.750, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme (pdb code 4i0c). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme, PDB code: 4i0c:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 4i0c

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Chlorine binding site 1 out of 7 in the The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:23.5
occ:1.00
 N A:GLY72 3.0 32.9 1.0
O A:HOH383 3.3 37.5 1.0
CA A:PRO71 3.8 26.5 1.0
CA A:GLY72 3.9 32.4 1.0
C A:PRO71 3.9 34.9 1.0
N A:ALA73 4.5 28.3 1.0
CB A:PRO71 4.5 28.3 1.0
O A:THR70 4.6 22.4 1.0
C A:GLY72 4.7 32.1 1.0

Chlorine binding site 2 out of 7 in 4i0c

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Chlorine binding site 2 out of 7 in the The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:38.1
occ:0.50
 O A:HOH320 3.3 22.6 1.0
NH2 A:ARG101 3.7 17.4 1.0
NH1 A:ARG98 3.9 15.3 0.3
O A:HOH368 3.9 30.6 1.0
CD A:ARG98 4.0 15.5 0.3
CB A:ARG98 4.3 15.0 0.3
CB A:ARG98 4.4 14.7 0.7
CD A:ARG98 4.6 14.4 0.7
CG A:ARG98 4.7 17.9 0.7
CG A:ARG98 4.7 16.6 0.3
O A:ALA94 4.8 17.0 1.0
CZ A:ARG101 4.8 21.9 1.0
CZ A:ARG98 4.9 16.6 0.3
NE A:ARG98 4.9 19.3 0.3
NH1 A:ARG101 5.0 18.1 1.0

Chlorine binding site 3 out of 7 in 4i0c

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Chlorine binding site 3 out of 7 in the The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:25.2
occ:1.00
 N A:ARG21 3.0 12.7 1.0
O D:HOH218 3.0 20.9 1.0
O D:HOH238 3.1 33.2 1.0
NH2 A:ARG21 3.2 16.3 1.0
CD1 A:TYR20 3.8 13.3 1.0
CA A:TYR20 3.8 12.8 1.0
CA A:ARG21 3.8 15.8 1.0
CD A:ARG21 3.9 25.7 1.0
CG2 D:THR30 3.9 16.5 1.0
C A:TYR20 3.9 19.1 1.0
CE1 A:TYR20 4.2 16.6 1.0
CA D:GLY99 4.2 28.7 1.0
O A:GLY19 4.2 18.1 1.0
CZ A:ARG21 4.2 25.6 1.0
CG A:TYR20 4.3 16.6 1.0
O D:THR98 4.3 27.0 1.0
CG A:ARG21 4.4 20.5 1.0
NE A:ARG21 4.5 23.3 1.0
C D:GLY99 4.5 24.4 1.0
N D:ALA100 4.5 19.7 1.0
CB A:TYR20 4.6 15.4 1.0
CB A:ARG21 4.7 18.7 1.0
O D:HOH244 4.8 33.0 1.0
N A:TYR20 4.8 15.4 1.0
CZ A:TYR20 4.9 14.1 1.0
C A:GLY19 4.9 16.4 1.0
CD2 A:TYR20 5.0 15.2 1.0

Chlorine binding site 4 out of 7 in 4i0c

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Chlorine binding site 4 out of 7 in the The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:22.7
occ:1.00
 O B:HOH370 3.0 29.2 1.0
NZ B:LYS33 3.4 15.6 1.0
CB B:ARG5 3.8 24.9 1.0
CE2 B:TYR38 3.8 13.2 1.0
O B:HOH333 4.1 22.8 1.0
CD B:ARG5 4.3 22.9 1.0
CD2 B:TYR38 4.4 15.5 1.0
CE B:LYS33 4.5 14.4 1.0
CG B:ARG5 4.5 20.8 1.0
N B:ARG5 4.6 20.6 1.0
CA B:ARG5 4.6 22.0 1.0
CZ B:TYR38 4.8 15.0 1.0
OH B:TYR38 4.8 17.9 1.0
NE B:ARG5 4.9 22.1 1.0
O B:HOH350 5.0 27.5 1.0

Chlorine binding site 5 out of 7 in 4i0c

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Chlorine binding site 5 out of 7 in the The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:41.2
occ:0.50
 O B:HOH317 3.3 20.5 1.0
NH1 B:ARG98 3.7 16.0 0.4
NH2 B:ARG101 3.7 21.4 1.0
CB B:ARG98 4.3 15.1 0.6
CB B:ARG98 4.4 15.4 0.4
CD B:ARG98 4.6 23.3 0.4
CD B:ARG98 4.6 23.6 0.6
O B:ALA94 4.7 16.8 1.0
CG B:ARG98 4.7 18.9 0.4
CG B:ARG98 4.7 18.9 0.6
CZ B:ARG101 4.9 21.2 1.0
CZ B:ARG98 4.9 20.5 0.4
O B:CYS77 5.0 19.6 1.0

Chlorine binding site 6 out of 7 in 4i0c

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Chlorine binding site 6 out of 7 in the The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:19.8
occ:1.00
 N C:SER102 3.2 19.0 1.0
NZ C:LYS97 3.3 20.5 1.0
OG C:SER105 3.4 38.5 1.0
CB C:SER105 3.6 25.0 1.0
CA C:PHE101 3.7 13.7 1.0
CB C:ALA112 3.8 20.5 1.0
CA C:ALA112 3.8 22.2 1.0
O C:ALA100 3.9 18.3 1.0
O C:ALA112 3.9 24.5 1.0
CB C:SER102 3.9 20.5 1.0
O C:HOH350 3.9 34.4 1.0
C C:PHE101 4.0 20.1 1.0
OG C:SER102 4.0 23.2 1.0
CA C:SER102 4.1 19.4 1.0
CE C:LYS97 4.3 18.6 1.0
CD1 C:PHE101 4.3 20.7 1.0
C C:ALA112 4.4 21.3 1.0
CB C:PHE101 4.6 17.1 1.0
C C:ALA100 4.7 20.6 1.0
N C:PHE101 4.7 16.4 1.0
CG C:PHE101 4.8 20.2 1.0
O C:SER102 4.9 21.9 1.0

Chlorine binding site 7 out of 7 in 4i0c

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Chlorine binding site 7 out of 7 in the The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of The Structure of the Camelid Antibody CABHUL5 in Complex with Human Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl202

b:23.8
occ:1.00
 OG1 C:THR123 3.0 19.3 1.0
O C:HOH356 3.2 33.6 1.0
CB C:THR123 3.7 16.6 1.0
C C:GLY10 3.8 20.2 1.0
NE2 C:GLN121 3.8 16.0 1.0
N C:SER11 3.8 18.3 1.0
CA C:GLY10 4.0 19.7 1.0
CG C:GLN121 4.1 16.9 1.0
O C:GLY10 4.2 19.7 1.0
CB C:SER11 4.2 29.3 1.0
CD C:GLN121 4.2 19.4 1.0
CA C:SER11 4.3 22.3 1.0
N C:THR123 4.4 16.8 1.0
CA C:THR123 4.7 14.1 1.0
O C:GLN121 4.7 17.4 1.0
O C:HOH344 4.7 30.6 1.0
CG2 C:THR123 4.8 18.1 1.0
CB C:GLN121 4.9 23.6 1.0
O C:HOH376 5.0 16.9 1.0
N C:GLY10 5.0 23.9 1.0

Reference:

E.De Genst, P.H.Chan, E.Pardon, S.T.Hsu, J.R.Kumita, J.Christodoulou, L.Menzer, D.Y.Chirgadze, C.V.Robinson, S.Muyldermans, A.Matagne, L.Wyns, C.M.Dobson, M.Dumoulin. A Nanobody Binding to Non-Amyloidogenic Regions of the Protein Human Lysozyme Enhances Partial Unfolding But Inhibits Amyloid Fibril Formation. J.Phys.Chem.B V. 117 13245 2013.
ISSN: ISSN 1089-5647
PubMed: 23919586
DOI: 10.1021/JP403425Z
Page generated: Sun Jul 21 16:16:56 2024

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