Zinc in PDB 3ljm: Structure of De Novo Designed Apo Peptide Coil Ser L9C

The structure of Structure of De Novo Designed Apo Peptide Coil Ser L9C, PDB code: 3ljm was solved by S.Chakraborty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.03 / 1.36
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.940, 29.856, 44.361, 90.00, 119.15, 90.00
R / Rfree (%)	18.2 / 21.5

The structure of Structure of De Novo Designed Apo Peptide Coil Ser L9C also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the Structure of De Novo Designed Apo Peptide Coil Ser L9C (pdb code 3ljm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Structure of De Novo Designed Apo Peptide Coil Ser L9C, PDB code: 3ljm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Structure of De Novo Designed Apo Peptide Coil Ser L9C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of De Novo Designed Apo Peptide Coil Ser L9C within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn31 b:9.0 occ:0.90 NE2 A:HIS28 2.0 8.5 1.0 CE1 A:HIS28 3.0 9.7 1.0 CD2 A:HIS28 3.1 10.4 1.0 ND1 A:HIS28 4.1 10.8 1.0 CG A:HIS28 4.2 11.1 1.0 OE2 A:GLU27 4.4 17.6 0.4 O A:HOH44 4.8 20.9 1.0 OE2 A:GLU24 4.8 8.7 1.0 OE2 A:GLU27 4.9 9.3 0.4 CD A:GLU27 5.0 10.3 0.5

Zinc binding site 2 out of 5 in the Structure of De Novo Designed Apo Peptide Coil Ser L9C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of De Novo Designed Apo Peptide Coil Ser L9C within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn32 b:18.7 occ:0.30 OE1 A:GLU6 2.3 32.5 1.0 O A:HOH55 2.3 30.0 1.0 O A:HOH43 2.3 30.0 1.0 OE2 A:GLU6 2.6 32.9 1.0 CD A:GLU6 2.7 26.6 1.0 NE1 A:TRP2 3.5 27.2 0.6 CD1 A:TRP2 3.8 28.4 1.0 CG A:GLU6 4.1 20.2 1.0 CE2 A:TRP2 4.8 28.3 1.0

Zinc binding site 3 out of 5 in the Structure of De Novo Designed Apo Peptide Coil Ser L9C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of De Novo Designed Apo Peptide Coil Ser L9C within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn31 b:8.8 occ:1.00 OE2 B:GLU24 2.0 9.2 1.0 NE2 B:HIS28 2.0 8.3 1.0 O B:HOH37 2.0 14.1 1.0 CD B:GLU24 2.9 8.2 1.0 CD2 B:HIS28 2.9 8.3 1.0 CE1 B:HIS28 3.0 9.5 1.0 OE1 B:GLU24 3.1 9.0 1.0 OE1 B:GLU27 3.5 12.3 0.9 CD B:GLU27 4.1 11.0 1.0 CG B:HIS28 4.1 9.7 1.0 ND1 B:HIS28 4.1 10.6 1.0 CG B:GLU24 4.3 8.7 1.0 OE2 B:GLU27 4.6 14.8 1.0 CA B:GLU24 4.7 6.8 1.0 CB B:GLU24 4.7 8.5 1.0 O B:HOH40 4.9 10.4 0.8 CG B:GLU27 4.9 11.6 1.0

Zinc binding site 4 out of 5 in the Structure of De Novo Designed Apo Peptide Coil Ser L9C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of De Novo Designed Apo Peptide Coil Ser L9C within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn32 b:54.4 occ:0.80 OE2 B:GLU1 2.0 19.3 0.5 OE2 C:GLU6 2.1 25.4 0.6 CD B:GLU1 2.7 22.6 0.8 CD C:GLU6 2.7 19.8 0.6 OE1 B:GLU1 2.7 22.2 0.8 O C:HOH36 2.9 44.8 1.0 OE1 C:GLU6 2.9 25.4 0.6 O B:HOH41 3.5 33.0 1.0 CG C:GLU6 4.0 18.4 1.0 CG B:GLU1 4.1 15.8 0.4 NE1 C:TRP2 4.3 18.8 1.0 CD1 C:TRP2 4.9 16.4 0.8

Zinc binding site 5 out of 5 in the Structure of De Novo Designed Apo Peptide Coil Ser L9C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of De Novo Designed Apo Peptide Coil Ser L9C within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn33 b:8.2 occ:0.30 ND1 B:HIS28 2.1 10.6 1.0 CE1 B:HIS28 2.9 9.5 1.0 CG B:HIS28 3.3 9.7 1.0 CB B:HIS28 3.8 10.8 1.0 NE2 B:HIS28 4.1 8.3 1.0 CA B:HIS28 4.2 9.2 1.0 CD2 B:HIS28 4.3 8.3 1.0 O B:GLU27 4.8 10.9 1.0

S.Chakraborty, D.S.Touw, A.F.Peacock, J.Stuckey, V.L.Pecoraro. Structural Comparisons of Apo- and Metalated Three-Stranded Coiled Coils Clarify Metal Binding Determinants in Thiolate Containing Designed Peptides. J.Am.Chem.Soc. V. 132 13240 2010.
ISSN: ISSN 0002-7863
PubMed: 20825181
DOI: 10.1021/JA101812C