Zinc in PDB 3m4b: A Zn-Mediated Tetrahedral Protein Lattice Cage

The structure of A Zn-Mediated Tetrahedral Protein Lattice Cage, PDB code: 3m4b was solved by F.A.Tezcan, T.W.Ni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.27 / 2.50
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	125.363, 125.363, 164.509, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 25.6

The structure of A Zn-Mediated Tetrahedral Protein Lattice Cage also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the A Zn-Mediated Tetrahedral Protein Lattice Cage (pdb code 3m4b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the A Zn-Mediated Tetrahedral Protein Lattice Cage, PDB code: 3m4b:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the A Zn-Mediated Tetrahedral Protein Lattice Cage


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Zn-Mediated Tetrahedral Protein Lattice Cage within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn107 b:35.7 occ:1.00 O A:HOH111 2.0 35.6 1.0 OD2 A:ASP39 2.0 35.6 1.0 O A:ALA1 2.1 35.5 1.0 N A:ALA1 2.1 34.9 1.0 CG A:ASP39 2.8 35.9 1.0 C A:ALA1 2.8 35.4 1.0 CA A:ALA1 2.9 35.0 1.0 OD1 A:ASP39 3.0 38.9 1.0 CB A:ALA1 3.6 34.3 1.0 N A:ASP2 4.1 36.1 1.0 CB A:ASP39 4.2 34.7 1.0 O A:HOH135 4.4 42.4 1.0 O A:HOH134 4.6 38.4 1.0 OD1 A:ASN6 4.6 32.8 1.0 CA A:ASP2 4.8 37.1 1.0 ND2 A:ASN6 4.8 36.1 1.0 O A:HOH132 4.9 45.7 1.0

Zinc binding site 2 out of 12 in the A Zn-Mediated Tetrahedral Protein Lattice Cage


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Zn-Mediated Tetrahedral Protein Lattice Cage within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn108 b:34.0 occ:1.00 OE2 A:GLU8 1.9 29.0 1.0 OD2 A:ASP12 2.1 29.8 1.0 CD A:GLU8 2.8 29.8 1.0 CG A:ASP12 2.8 29.2 1.0 OD1 A:ASP12 2.9 29.8 1.0 CG A:GLU8 3.1 28.7 1.0 OE1 A:GLU8 4.0 31.5 1.0 CB A:ASP12 4.3 28.1 1.0 CB A:GLU8 4.6 27.4 1.0 O A:GLU8 4.6 27.4 1.0

Zinc binding site 3 out of 12 in the A Zn-Mediated Tetrahedral Protein Lattice Cage


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A Zn-Mediated Tetrahedral Protein Lattice Cage within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn109 b:45.9 occ:1.00 NE2 A:HIS59 2.0 37.6 1.0 O A:HOH112 2.2 12.8 1.0 CE1 A:HIS59 2.7 35.9 1.0 CD2 A:HIS59 3.2 37.8 1.0 ND1 A:HIS59 4.0 35.7 1.0 CB A:ASP54 4.2 37.8 1.0 CG A:HIS59 4.2 36.7 1.0 CA A:ASP54 4.5 37.8 1.0 NH2 A:ARG62 4.6 42.8 1.0 O A:ASP54 4.9 36.6 1.0

Zinc binding site 4 out of 12 in the A Zn-Mediated Tetrahedral Protein Lattice Cage


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A Zn-Mediated Tetrahedral Protein Lattice Cage within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn110 b:46.0 occ:0.50 OE1 A:GLU57 1.9 34.6 1.0 O A:HOH131 2.3 13.0 1.0 CD A:GLU57 2.9 36.0 1.0 CG A:GLU57 3.3 36.0 1.0 CE A:LYS51 3.7 41.4 1.0 OE2 A:GLU57 4.0 37.1 1.0 CB A:GLU57 4.7 35.3 1.0 CD A:LYS51 4.7 41.5 1.0 NZ A:LYS51 4.8 42.2 1.0 CD2 A:LEU48 4.9 36.1 1.0

Zinc binding site 5 out of 12 in the A Zn-Mediated Tetrahedral Protein Lattice Cage


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of A Zn-Mediated Tetrahedral Protein Lattice Cage within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn107 b:39.8 occ:1.00 OD2 B:ASP39 2.1 35.1 1.0 N B:ALA1 2.2 34.9 1.0 O B:ALA1 2.2 34.8 1.0 O B:HOH120 2.3 30.7 1.0 OD1 B:ASP39 2.6 36.9 1.0 CG B:ASP39 2.6 33.7 1.0 CA B:ALA1 2.9 34.9 1.0 C B:ALA1 2.9 34.8 1.0 CB B:ALA1 3.3 34.5 1.0 CB B:ASP39 4.0 33.0 1.0 N B:ASP2 4.2 35.2 1.0 O B:HOH123 4.5 27.6 1.0 ND2 B:ASN6 4.5 35.6 1.0 CA B:ASP2 5.0 35.8 1.0 OD1 B:ASN6 5.0 34.0 1.0

Zinc binding site 6 out of 12 in the A Zn-Mediated Tetrahedral Protein Lattice Cage


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of A Zn-Mediated Tetrahedral Protein Lattice Cage within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn108 b:37.4 occ:1.00 OE2 B:GLU8 1.8 28.9 1.0 OE2 D:GLU8 1.9 31.3 1.0 OD2 B:ASP12 1.9 24.5 1.0 OD2 D:ASP12 2.1 30.4 1.0 OD1 D:ASP12 2.3 30.7 1.0 CG D:ASP12 2.3 29.8 1.0 CG B:ASP12 2.8 26.2 1.0 CD B:GLU8 2.8 30.2 1.0 CD D:GLU8 2.9 31.5 1.0 OD1 B:ASP12 2.9 27.8 1.0 CG D:GLU8 3.2 29.3 1.0 CG B:GLU8 3.3 29.2 1.0 CB D:ASP12 3.7 28.4 1.0 OE1 B:GLU8 3.9 30.6 1.0 OE1 D:GLU8 4.0 33.5 1.0 CB B:ASP12 4.2 26.8 1.0 O B:GLU8 4.4 26.6 1.0 O D:GLU8 4.6 28.6 1.0 CB D:GLU8 4.7 28.4 1.0 CB B:GLU8 4.7 28.5 1.0

Zinc binding site 7 out of 12 in the A Zn-Mediated Tetrahedral Protein Lattice Cage


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of A Zn-Mediated Tetrahedral Protein Lattice Cage within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn109 b:65.9 occ:1.00 NE2 B:HIS59 2.0 49.5 1.0 O B:HOH112 2.3 37.4 1.0 CE1 B:HIS59 2.9 48.3 1.0 CD2 B:HIS59 3.1 48.1 1.0 CB B:ASP54 3.7 52.7 1.0 CA B:ASP54 3.8 52.4 1.0 O B:ASP54 3.9 51.5 1.0 ND1 B:HIS59 4.0 48.3 1.0 CG B:HIS59 4.2 46.4 1.0 C B:ASP54 4.3 51.6 1.0 NH2 B:ARG62 4.7 45.0 1.0 O B:PRO53 4.8 52.3 1.0

Zinc binding site 8 out of 12 in the A Zn-Mediated Tetrahedral Protein Lattice Cage


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of A Zn-Mediated Tetrahedral Protein Lattice Cage within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn110 b:95.8 occ:1.00 OXT B:ACT151 2.1 54.7 1.0 C B:ACT151 3.2 55.1 1.0 O B:HOH125 3.5 47.8 1.0 O B:ACT151 4.0 56.5 1.0 CH3 B:ACT151 4.1 51.8 1.0 SG B:CYS67 4.7 40.1 1.0

Zinc binding site 9 out of 12 in the A Zn-Mediated Tetrahedral Protein Lattice Cage


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of A Zn-Mediated Tetrahedral Protein Lattice Cage within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn111 b:38.9 occ:1.00 NE2 B:HIS77 2.0 35.2 1.0 CE1 B:HIS77 2.9 34.9 1.0 CD2 B:HIS77 3.1 35.8 1.0 ND1 B:HIS77 4.1 36.5 1.0 CG B:HIS77 4.2 37.2 1.0 O B:HOH114 4.9 35.0 1.0

Zinc binding site 10 out of 12 in the A Zn-Mediated Tetrahedral Protein Lattice Cage


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of A Zn-Mediated Tetrahedral Protein Lattice Cage within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn107 b:47.5 occ:1.00 OXT C:ACT151 2.0 39.3 1.0 NE2 D:HIS59 2.0 38.9 1.0 NE2 C:HIS63 2.0 40.6 1.0 OD2 D:ASP54 2.1 41.1 1.0 O C:ACT151 2.4 40.1 1.0 C C:ACT151 2.5 39.8 1.0 CE1 D:HIS59 2.9 38.8 1.0 CE1 C:HIS63 3.0 41.3 1.0 CD2 C:HIS63 3.1 38.8 1.0 CD2 D:HIS59 3.1 38.0 1.0 CG D:ASP54 3.1 41.7 1.0 CA D:ASP54 3.7 40.2 1.0 CB D:ASP54 3.9 40.5 1.0 CH3 C:ACT151 3.9 37.5 1.0 OD1 D:ASP54 4.0 43.9 1.0 ND1 D:HIS59 4.0 39.2 1.0 ND1 C:HIS63 4.1 39.1 1.0 CG D:HIS59 4.2 38.2 1.0 CG C:HIS63 4.2 37.1 1.0 O D:ASP54 4.3 40.1 1.0 C D:ASP54 4.5 39.8 1.0 NH2 D:ARG62 4.6 40.9 1.0 O D:PRO53 4.7 40.8 1.0 N D:ASP54 4.8 40.4 1.0 CB C:CYS67 4.9 31.6 1.0 SG C:CYS67 4.9 34.3 1.0

T.W.Ni, F.A.Tezcan. Structural Characterization of A Microperoxidase Inside A Metal-Directed Protein Cage. Angew.Chem.Int.Ed.Engl. V. 49 7014 2010.
ISSN: ISSN 1433-7851
PubMed: 20721993
DOI: 10.1002/ANIE.201001487