Chlorine in PDB 6jb8: Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme

Enzymatic activity of Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme

All present enzymatic activity of Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme, PDB code: 6jb8 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)*	40.17 / 1.65
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	40.240, 49.480, 59.280, 90.00, 93.40, 90.00
*R / R_free (%)*	16.9 / 20.7

Other elements in 6jb8:

The structure of Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme (pdb code 6jb8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme, PDB code: 6jb8:

Chlorine binding site 1 out of 1 in 6jb8

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Chlorine Binding Sites List in 6jb8

Chlorine binding site 1 out of 1 in the Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme

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 in Complex with Hen Egg-White Lysozyme within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Cl205 b:48.5 occ:1.00	O	B:HOH432	2.9	42.3	1.0
	N	B:ILE88	3.6	27.6	1.0
	CE1	B:HIS15	3.7	28.6	1.0
	CG1	B:ILE88	3.7	26.2	1.0
	CB	B:ASP87	3.8	36.9	1.0
	CA	B:ASP87	3.8	33.4	1.0
	O	B:HOH313	4.1	34.0	1.0
	CB	B:ALA11	4.2	25.6	1.0
	C	B:ASP87	4.3	31.0	1.0
	NE2	B:HIS15	4.5	29.0	1.0
	CB	B:ILE88	4.5	26.6	1.0
	CZ	B:PHE3	4.5	26.2	1.0
	CD1	B:ILE88	4.5	25.7	1.0
	CA	B:ILE88	4.5	26.3	1.0
	CG2	B:ILE88	4.6	26.8	1.0
	ND1	B:HIS15	4.6	27.6	1.0
	OD2	B:ASP87	4.7	38.5	1.0
	CG	B:ASP87	4.8	39.2	1.0
	O	B:SER86	4.9	31.7	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 16:00:54 2025

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