Zinc in PDB 5b0h: Crystal Structure of Human Leukocyte Cell-Derived Chemotaxin 2

The structure of Crystal Structure of Human Leukocyte Cell-Derived Chemotaxin 2, PDB code: 5b0h was solved by H.Zheng, T.Miyakawa, Y.Sawano, M.Tanokura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.07 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.415, 63.514, 63.976, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 22.3

The binding sites of Zinc atom in the Crystal Structure of Human Leukocyte Cell-Derived Chemotaxin 2 (pdb code 5b0h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human Leukocyte Cell-Derived Chemotaxin 2, PDB code: 5b0h:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human Leukocyte Cell-Derived Chemotaxin 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Leukocyte Cell-Derived Chemotaxin 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:12.3 occ:1.00 OD1 A:ASP39 1.9 9.6 1.0 ND1 A:HIS120 2.0 11.8 1.0 NE2 A:HIS35 2.1 11.6 1.0 O A:HOH350 2.6 19.0 1.0 CG A:ASP39 2.8 10.1 1.0 CE1 A:HIS120 2.9 12.6 1.0 OD2 A:ASP39 3.0 10.9 1.0 CE1 A:HIS35 3.0 12.2 1.0 CD2 A:HIS35 3.1 11.4 1.0 CG A:HIS120 3.1 11.1 1.0 CB A:HIS120 3.5 11.3 1.0 NE2 A:HIS120 4.0 10.5 1.0 NH2 A:ARG30 4.0 14.7 1.0 CD2 A:HIS120 4.1 11.3 1.0 ND1 A:HIS35 4.1 11.8 1.0 CB A:ASP39 4.2 10.5 1.0 NE2 A:HIS118 4.2 8.7 1.0 CG A:HIS35 4.2 11.7 1.0 O A:HOH351 4.3 20.4 1.0 CA A:HIS120 4.3 10.7 1.0 CD2 A:HIS118 4.5 8.4 1.0 N A:ASP39 4.6 11.9 1.0 CA A:ASP39 4.6 11.1 1.0 C A:VAL38 4.7 12.1 1.0 O A:HOH376 4.8 30.7 1.0 OH A:TYR86 4.9 11.4 1.0 O A:VAL38 4.9 13.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human Leukocyte Cell-Derived Chemotaxin 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Leukocyte Cell-Derived Chemotaxin 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:11.3 occ:1.00 OD1 B:ASP39 2.0 9.5 1.0 NE2 B:HIS35 2.0 12.4 1.0 ND1 B:HIS120 2.1 11.0 1.0 O B:HOH351 2.8 18.8 1.0 CG B:ASP39 2.8 9.9 1.0 OD2 B:ASP39 2.9 10.3 1.0 CE1 B:HIS35 3.0 12.8 1.0 CE1 B:HIS120 3.0 11.2 1.0 CD2 B:HIS35 3.0 13.4 1.0 CG B:HIS120 3.1 10.2 1.0 CB B:HIS120 3.5 9.9 1.0 NH2 B:ARG30 3.9 15.3 1.0 ND1 B:HIS35 4.1 13.0 1.0 NE2 B:HIS120 4.1 10.0 1.0 CG B:HIS35 4.1 13.4 1.0 CB B:ASP39 4.2 10.8 1.0 CD2 B:HIS120 4.2 11.2 1.0 NE2 B:HIS118 4.2 8.3 1.0 CA B:HIS120 4.3 10.0 1.0 O B:HOH372 4.5 25.0 1.0 N B:ASP39 4.6 10.9 1.0 CD2 B:HIS118 4.6 7.9 1.0 C B:VAL38 4.6 12.1 1.0 CA B:ASP39 4.6 10.4 1.0 O B:VAL38 4.7 11.6 1.0 CZ B:ARG30 4.9 15.2 1.0

H.Zheng, T.Miyakawa, Y.Sawano, A.Asano, A.Okumura, S.Yamagoe, M.Tanokura. Crystal Structure of Human Leukocyte Cell-Derived Chemotaxin 2 (LECT2) Reveals A Mechanistic Basis of Functional Evolution in A Mammalian Protein with An M23 Metalloendopeptidase Fold J.Biol.Chem. V. 291 17133 2016.
ISSN: ESSN 1083-351X
PubMed: 27334921
DOI: 10.1074/JBC.M116.720375