Zinc in PDB 3pbj: Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein

The structure of Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein, PDB code: 3pbj was solved by M.L.Zastrow, A.F.A.Peacock, J.A.Stuckey, V.L.Pecoraro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.98 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	25.877, 38.649, 75.659, 90.00, 95.06, 90.00
R / Rfree (%)	20.5 / 26.4

The structure of Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein also contains other interesting chemical elements:

Mercury	(Hg)	2 atoms
Chlorine	(Cl)	3 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein (pdb code 3pbj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein, PDB code: 3pbj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn31 b:41.8 occ:1.00 NE2 C:HIS23 1.9 49.4 1.0 ND1 B:HIS23 1.9 50.9 1.0 NE2 A:HIS23 1.9 41.9 1.0 CL A:CL34 2.2 41.8 1.0 CE1 C:HIS23 2.7 50.3 1.0 CE1 B:HIS23 2.7 50.2 1.0 CD2 A:HIS23 2.9 41.6 1.0 CE1 A:HIS23 2.9 42.3 1.0 CD2 C:HIS23 3.1 49.6 1.0 CG B:HIS23 3.1 50.9 1.0 CB B:HIS23 3.7 49.1 1.0 ND1 C:HIS23 3.9 52.1 1.0 NE2 B:HIS23 3.9 51.6 1.0 CG A:HIS23 4.0 39.8 1.0 ND1 A:HIS23 4.0 42.2 1.0 CG C:HIS23 4.1 49.0 1.0 CD2 B:HIS23 4.1 52.7 1.0 CA B:HIS23 4.4 50.2 1.0 CD2 A:LEU19 4.5 32.0 1.0 O B:LEU19 4.6 48.5 1.0 O B:HOH36 4.6 43.0 1.0 N B:HIS23 4.8 50.2 1.0 CD2 B:LEU19 4.8 48.8 1.0

Zinc binding site 2 out of 7 in the Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn32 b:64.5 occ:0.75 OE2 A:GLU6 2.5 76.9 1.0 OE2 C:GLU1 2.6 64.3 0.6 OE1 C:GLU1 2.7 57.0 0.6 CD C:GLU1 2.8 71.8 0.6 O C:HOH34 2.9 61.7 1.0 O A:HOH37 3.0 41.3 1.0 OE1 A:GLU6 3.1 67.1 1.0 CD A:GLU6 3.1 75.2 1.0 O A:HOH52 3.7 45.0 1.0 CG C:GLU1 4.0 59.3 0.6 CB C:GLU1 4.5 47.5 1.0 CB A:TRP2 4.5 62.6 1.0 CE3 A:TRP2 4.5 61.4 1.0 CG A:GLU6 4.6 49.3 1.0 CG A:TRP2 4.8 63.1 1.0 CD2 A:TRP2 4.8 61.2 1.0

Zinc binding site 3 out of 7 in the Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn33 b:40.6 occ:0.58 OE1 A:GLU1 3.0 83.2 1.0 OE2 A:GLU1 3.6 92.4 1.0 CD A:GLU1 3.6 98.0 1.0

Zinc binding site 4 out of 7 in the Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn31 b:77.0 occ:1.00 NE2 D:HIS23 2.0 47.2 1.0 NE2 E:HIS23 2.0 74.5 1.0 NE2 F:HIS23 2.0 54.0 1.0 O F:HOH32 2.2 47.6 1.0 CD2 D:HIS23 2.4 46.7 1.0 CD2 E:HIS23 2.6 75.8 1.0 CD2 F:HIS23 2.9 53.7 1.0 CE1 F:HIS23 3.1 56.1 1.0 CE1 E:HIS23 3.2 75.2 1.0 CE1 D:HIS23 3.3 48.1 1.0 CG D:HIS23 3.7 45.9 1.0 CG E:HIS23 3.8 75.8 1.0 CG F:HIS23 4.1 52.9 1.0 ND1 D:HIS23 4.1 48.4 1.0 ND1 E:HIS23 4.1 77.6 1.0 ND1 F:HIS23 4.1 57.1 1.0 O E:LEU19 4.6 63.1 1.0 O D:LEU19 4.6 44.2 1.0 CD2 F:LEU19 4.7 39.9 1.0 O F:LEU19 4.8 42.2 1.0 CB E:LEU19 4.8 56.2 1.0 CB F:LEU19 4.8 35.9 1.0 CB D:HIS23 4.9 43.0 1.0 CB D:LEU19 4.9 36.9 1.0 CD2 E:LEU19 5.0 64.2 1.0 CD2 D:LEU19 5.0 45.9 1.0

Zinc binding site 5 out of 7 in the Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn32 b:55.0 occ:0.45 O F:HOH66 1.9 52.9 1.0 OE1 F:GLU1 1.9 60.9 1.0 OE2 D:GLU6 2.6 82.4 1.0 CD F:GLU1 2.8 80.3 1.0 OE2 F:GLU1 3.0 83.2 1.0 O D:HOH65 3.1 53.3 1.0 OE1 D:GLU6 3.2 79.9 1.0 CD D:GLU6 3.2 86.5 1.0 O F:HOH49 4.0 56.0 1.0 CG F:GLU1 4.2 64.3 1.0 CD1 F:LEU5 4.3 40.0 1.0 CZ2 D:TRP2 4.3 40.3 1.0 NE1 D:TRP2 4.3 42.7 1.0 CG F:LEU5 4.3 40.3 1.0 CD2 F:LEU5 4.4 39.8 1.0 CG D:GLU6 4.7 52.2 1.0 CE2 D:TRP2 4.7 42.4 1.0 CB F:GLU1 4.9 51.1 1.0

Zinc binding site 6 out of 7 in the Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn31 b:37.5 occ:0.96 OE1 E:GLU1 2.0 40.5 1.0 OE2 F:GLU6 2.1 36.6 1.0 O F:HOH37 2.4 40.8 1.0 OE1 F:GLU6 2.7 43.5 1.0 CD F:GLU6 2.7 45.1 1.0 CD E:GLU1 3.0 53.5 1.0 O E:HOH43 3.1 43.8 1.0 CL E:CL32 3.2 73.0 1.0 OE2 E:GLU1 3.3 45.4 1.0 O F:HOH35 4.0 30.1 1.0 CG F:GLU6 4.2 42.0 1.0 CG E:GLU1 4.3 41.1 1.0 CB F:TRP2 4.3 36.3 1.0 O F:TRP2 4.8 29.0 1.0 CB E:GLU1 4.8 34.5 1.0 C F:TRP2 5.0 33.6 1.0

Zinc binding site 7 out of 7 in the Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn31 b:24.6 occ:0.45 OE2 F:GLU3 1.9 49.4 1.0 CD F:GLU3 2.4 58.6 1.0 OE1 F:GLU3 2.5 57.2 1.0 CG F:GLU3 3.8 46.2 1.0 NZ F:LYS7 4.3 58.9 1.0 CE F:LYS7 4.7 36.2 1.0 CB F:GLU3 5.0 33.9 1.0

M.L.Zastrow, A.F.Peacock, J.A.Stuckey, V.L.Pecoraro. Hydrolytic Catalysis and Structural Stabilization in A Designed Metalloprotein. Nat Chem V. 4 118 2012.
ISSN: ESSN 1755-4349
PubMed: 22270627
DOI: 10.1038/NCHEM.1201