Zinc in PDB 2ymk: Crystal Structure of the Hexameric Anti-Microbial Peptide Channel Dermcidin

The structure of Crystal Structure of the Hexameric Anti-Microbial Peptide Channel Dermcidin, PDB code: 2ymk was solved by K.Zeth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.79 / 2.49
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	76.354, 50.724, 45.738, 90.00, 117.74, 90.00
R / Rfree (%)	20.466 / 27.384

The binding sites of Zinc atom in the Crystal Structure of the Hexameric Anti-Microbial Peptide Channel Dermcidin (pdb code 2ymk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Hexameric Anti-Microbial Peptide Channel Dermcidin, PDB code: 2ymk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the Hexameric Anti-Microbial Peptide Channel Dermcidin


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 the Hexameric Anti-Microbial Peptide Channel Dermcidin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1049 b:73.4 occ:1.00 OD2 A:ASP42 1.9 51.7 1.0 NE2 A:HIS38 2.4 54.1 1.0 CG A:ASP42 2.8 51.0 1.0 CD2 A:HIS38 3.0 50.3 1.0 OD1 A:ASP42 3.1 53.8 1.0 CE1 A:HIS38 3.5 54.3 1.0 CB A:ASP42 4.2 49.6 1.0 CG A:HIS38 4.2 45.7 1.0 ND1 A:HIS38 4.5 51.5 1.0 OD1 A:ASP39 4.5 49.0 1.0 CE B:LYS41 4.8 63.8 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the Hexameric Anti-Microbial Peptide Channel Dermcidin


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 the Hexameric Anti-Microbial Peptide Channel Dermcidin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1050 b:0.5 occ:1.00 OD2 A:ASP28 2.3 50.8 1.0 O A:HOH2003 2.3 60.8 1.0 O A:HOH2010 3.1 56.2 1.0 OD1 A:ASP24 3.2 57.0 1.0 CG A:ASP28 3.3 45.0 1.0 OD1 A:ASP28 3.8 46.8 1.0 CG A:ASP24 4.2 52.1 1.0 O A:ASP24 4.3 43.9 1.0 OD2 A:ASP24 4.4 59.0 1.0 CB A:ASP28 4.5 40.2 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the Hexameric Anti-Microbial Peptide Channel Dermcidin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Hexameric Anti-Microbial Peptide Channel Dermcidin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1049 b:70.3 occ:1.00 OD2 B:ASP42 2.3 58.8 1.0 NE2 B:HIS38 2.4 64.7 1.0 OD1 B:ASP42 2.8 58.3 1.0 CG B:ASP42 2.9 56.9 1.0 CD2 B:HIS38 2.9 59.9 1.0 CE1 B:HIS38 3.3 63.8 1.0 CG B:HIS38 4.0 54.0 1.0 O B:HOH2006 4.0 18.9 1.0 ND1 B:HIS38 4.1 58.8 1.0 CB B:ASP42 4.4 54.2 1.0 O B:HOH2005 4.5 28.0 1.0 O B:HIS38 4.7 44.6 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the Hexameric Anti-Microbial Peptide Channel Dermcidin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Hexameric Anti-Microbial Peptide Channel Dermcidin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1050 b:0.7 occ:1.00 O B:HOH2002 2.5 13.5 1.0 OD2 B:ASP28 2.6 50.0 1.0 O B:HOH2009 2.7 16.2 1.0 OD2 B:ASP24 2.7 57.4 1.0 OD1 B:ASP24 3.4 60.1 1.0 CG B:ASP24 3.5 53.3 1.0 CG B:ASP28 3.7 47.1 1.0 OD1 B:ASP28 4.2 51.3 1.0 CB B:ASP28 5.0 42.5 1.0 CB B:ASP24 5.0 48.2 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the Hexameric Anti-Microbial Peptide Channel Dermcidin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Hexameric Anti-Microbial Peptide Channel Dermcidin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1049 b:73.0 occ:1.00 OD2 C:ASP42 2.0 57.2 1.0 NE2 C:HIS38 2.2 58.7 1.0 OD1 C:ASP42 2.5 56.4 1.0 CG C:ASP42 2.6 56.0 1.0 CD2 C:HIS38 3.0 55.4 1.0 CE1 C:HIS38 3.1 58.4 1.0 CG C:HIS38 4.0 49.7 1.0 ND1 C:HIS38 4.1 55.2 1.0 CB C:ASP42 4.2 55.1 1.0 OD1 C:ASP39 4.6 55.0 1.0 O C:HIS38 4.9 42.2 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the Hexameric Anti-Microbial Peptide Channel Dermcidin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Hexameric Anti-Microbial Peptide Channel Dermcidin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1050 b:0.0 occ:1.00 O C:HOH2005 2.4 34.2 1.0 OD2 C:ASP28 2.6 51.7 1.0 O C:HOH2004 3.3 20.0 1.0 OD2 C:ASP24 3.3 58.6 1.0 OD1 C:ASP24 3.7 57.0 1.0 CG C:ASP28 3.9 47.9 1.0 CG C:ASP24 3.9 51.8 1.0 OD1 C:ASP28 4.6 49.7 1.0 CB C:ASP28 4.9 43.1 1.0

C.Song, C.Weichbrodt, E.S.Salnikov, M.Dynowski, B.O.Forsberg, B.Bechinger, C.Steinem, B.L.De Groot, U.Zachariae, K.Zeth. Crystal Structure and Functional Mechanism of A Human Antimicrobial Membrane Channel. Proc.Natl.Acad.Sci.Usa V. 110 4586 2013.
ISSN: ISSN 0027-8424
PubMed: 23426625
DOI: 10.1073/PNAS.1214739110