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Chlorine in PDB 6jb5: Crystal Structure of Nanobody D3-L11 Mutant Y102A in Complex with Hen Egg-White Lysozyme (Form II)

Enzymatic activity of Crystal Structure of Nanobody D3-L11 Mutant Y102A in Complex with Hen Egg-White Lysozyme (Form II)

All present enzymatic activity of Crystal Structure of Nanobody D3-L11 Mutant Y102A in Complex with Hen Egg-White Lysozyme (Form II):
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Nanobody D3-L11 Mutant Y102A in Complex with Hen Egg-White Lysozyme (Form II), PDB code: 6jb5 was solved by J.M.M.Caaveiro, H.Tamura, H.Akiba, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.44 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.010, 49.440, 57.940, 90.00, 93.79, 90.00
R / Rfree (%) 13.2 / 16.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Nanobody D3-L11 Mutant Y102A in Complex with Hen Egg-White Lysozyme (Form II) (pdb code 6jb5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Nanobody D3-L11 Mutant Y102A in Complex with Hen Egg-White Lysozyme (Form II), PDB code: 6jb5:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6jb5

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Chlorine binding site 1 out of 4 in the Crystal Structure of Nanobody D3-L11 Mutant Y102A in Complex with Hen Egg-White Lysozyme (Form II)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Nanobody D3-L11 Mutant Y102A in Complex with Hen Egg-White Lysozyme (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:20.9
occ:1.00
 OE1 A:GLN3 3.3 29.3 1.0
O A:HOH309 3.5 37.2 1.0
CD A:GLN3 4.2 31.7 1.0
NE2 A:GLN3 4.3 38.5 1.0

Chlorine binding site 2 out of 4 in 6jb5

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Chlorine binding site 2 out of 4 in the Crystal Structure of Nanobody D3-L11 Mutant Y102A in Complex with Hen Egg-White Lysozyme (Form II)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Nanobody D3-L11 Mutant Y102A in Complex with Hen Egg-White Lysozyme (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:28.2
occ:1.00
 OG1 A:THR95 2.7 12.8 1.0
O A:HOH336 2.8 28.8 1.0
O A:ILE93 3.1 12.9 1.0
CB A:THR95 3.4 11.7 1.0
CA A:ARG38 3.5 11.0 1.0
N A:GLN39 3.6 12.1 1.0
C A:ARG38 3.6 11.2 1.0
NE A:ARG45 3.7 26.1 1.0
N A:THR95 3.7 10.3 1.0
CB A:GLN39 3.9 16.6 1.0
O A:PHE37 3.9 10.3 1.0
N A:ARG38 3.9 10.6 1.0
C A:ILE93 3.9 12.7 1.0
C A:PHE37 4.0 10.1 1.0
CA A:THR95 4.2 10.9 1.0
CG A:ARG45 4.2 22.7 1.0
NH2 A:ARG45 4.2 35.6 1.0
CG2 A:ILE93 4.2 16.4 1.0
C A:TYR94 4.3 12.7 1.0
O A:ARG38 4.3 12.6 1.0
O A:HOH344 4.3 24.0 1.0
CA A:GLN39 4.3 14.6 1.0
CZ A:ARG45 4.4 28.6 1.0
CA A:TYR94 4.4 10.8 1.0
CD A:ARG45 4.4 24.8 1.0
CB A:PHE37 4.5 10.7 1.0
CB A:ILE93 4.5 15.7 1.0
N A:TYR94 4.5 12.8 1.0
CG2 A:THR95 4.7 12.1 1.0
CB A:ARG38 4.9 11.4 1.0
CA A:PHE37 4.9 10.1 1.0
CA A:ILE93 4.9 12.7 1.0
OE1 A:GLN39 4.9 28.6 1.0
CB A:ARG45 5.0 21.1 1.0
O A:HOH430 5.0 33.6 0.6

Chlorine binding site 3 out of 4 in 6jb5

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Chlorine binding site 3 out of 4 in the Crystal Structure of Nanobody D3-L11 Mutant Y102A in Complex with Hen Egg-White Lysozyme (Form II)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Nanobody D3-L11 Mutant Y102A in Complex with Hen Egg-White Lysozyme (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:20.7
occ:1.00
 O B:HOH439 2.9 36.5 1.0
OG B:SER24 3.0 12.7 1.0
N B:GLY26 3.1 9.5 1.0
CB B:SER24 3.4 12.1 1.0
CA B:GLY26 3.5 9.3 1.0
CA B:GLN121 3.5 18.6 0.5
CA B:GLN121 3.6 18.9 0.5
CB B:GLN121 3.8 20.6 0.5
N B:GLN121 3.9 17.8 1.0
CG B:GLN121 3.9 22.8 0.5
N B:LEU25 4.0 10.3 1.0
CB B:GLN121 4.0 21.5 0.5
CD1 B:ILE124 4.1 19.8 1.0
C B:SER24 4.1 11.2 1.0
C B:LEU25 4.2 10.1 1.0
C B:VAL120 4.3 15.2 1.0
CG2 B:VAL120 4.3 15.4 1.0
O B:VAL120 4.3 13.7 1.0
CG1 B:ILE124 4.3 18.9 1.0
CG B:GLN121 4.4 24.4 0.5
CA B:SER24 4.4 11.0 1.0
O B:SER24 4.5 10.9 1.0
CA B:LEU25 4.5 10.6 1.0
C B:GLY26 4.6 8.4 1.0
O B:HOH362 4.6 29.4 1.0
N B:ASN27 4.7 8.7 1.0
C B:GLN121 4.8 17.9 1.0
CB B:LEU25 4.9 10.2 1.0
CB B:VAL120 5.0 15.0 1.0
O B:GLN121 5.0 19.0 1.0

Chlorine binding site 4 out of 4 in 6jb5

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Chlorine binding site 4 out of 4 in the Crystal Structure of Nanobody D3-L11 Mutant Y102A in Complex with Hen Egg-White Lysozyme (Form II)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Nanobody D3-L11 Mutant Y102A in Complex with Hen Egg-White Lysozyme (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl204

b:23.9
occ:0.60
 O B:HOH369 2.2 13.7 0.4
OH B:TYR23 2.9 12.5 1.0
O B:HOH446 3.4 27.2 0.6
ND2 B:ASN106 3.8 10.6 1.0
CH2 B:TRP111 3.8 10.5 1.0
CZ B:TYR23 3.9 11.7 1.0
CE1 B:TYR23 4.0 10.4 1.0
CE B:LYS116 4.2 15.6 1.0
O B:HOH369 4.5 14.4 0.6
CZ3 B:TRP111 4.6 9.5 1.0
CZ2 B:TRP111 4.7 9.8 1.0
NZ B:LYS116 4.7 15.8 1.0
CG B:ASN106 4.7 9.6 1.0
OD1 B:ASN106 4.9 11.6 1.0
CD B:LYS116 4.9 13.4 1.0

Reference:

H.Akiba, H.Tamura, M.Kiyoshi, S.Yanaka, K.Sugase, J.M.M.Caaveiro, K.Tsumoto. Structural and Thermodynamic Basis For the Recognition of the Substrate-Binding Cleft on Hen Egg Lysozyme By A Single-Domain Antibody. Sci Rep V. 9 15481 2019.
ISSN: ESSN 2045-2322
PubMed: 31664051
DOI: 10.1038/S41598-019-50722-Y
Page generated: Sat Jul 12 16:00:45 2025

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