Zinc in PDB 7m6u: Crystal Structure of A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2

All present enzymatic activity of Crystal Structure of A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2:
3.4.17.11;

The structure of Crystal Structure of A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2, PDB code: 7m6u was solved by B.J.Yachnin, S.D.Khare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.27 / 2.59
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.54, 106.36, 121.93, 90, 107.48, 90
R / Rfree (%)	22.2 / 27.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2 (pdb code 7m6u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 20 binding sites of Zinc where determined in the Crystal Structure of A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2, PDB code: 7m6u:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 20 in the Crystal Structure of A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2


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 A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn500 b:33.1 occ:1.00 OD2 A:ASP50 1.8 34.0 1.0 OE2 A:GLU85 1.8 39.7 1.0 NE2 A:HIS294 1.9 39.1 1.0 O A:HOH640 2.0 37.6 1.0 OE1 A:GLU85 2.3 38.4 1.0 CD A:GLU85 2.3 41.1 1.0 CG A:ASP50 2.8 34.6 1.0 CE1 A:HIS294 2.9 35.6 1.0 CD2 A:HIS294 3.0 40.9 1.0 ZN A:ZN501 3.1 33.2 1.0 OD1 A:ASP50 3.2 32.5 1.0 CG A:GLU85 3.8 40.0 1.0 O A:HOH612 3.9 30.4 1.0 ND1 A:HIS294 4.0 34.9 1.0 OE1 A:GLU84 4.0 37.6 1.0 CG A:HIS294 4.1 35.1 1.0 CB A:ASP50 4.2 31.9 1.0 NE2 A:HIS21 4.2 36.9 1.0 CE1 A:HIS21 4.3 36.4 1.0 CG1 A:VAL25 4.5 30.5 1.0 OE1 A:GLU109 4.7 31.6 1.0 CB A:GLU85 4.9 38.6 1.0

Zinc binding site 2 out of 20 in the Crystal Structure of A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2


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 A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:33.2 occ:1.00 OD1 A:ASP50 1.9 32.5 1.0 OE1 A:GLU109 1.9 31.6 1.0 NE2 A:HIS21 1.9 36.9 1.0 O A:HOH640 2.1 37.6 1.0 CD A:GLU109 2.5 31.8 1.0 OE2 A:GLU109 2.5 28.3 1.0 CG A:ASP50 2.8 34.6 1.0 CE1 A:HIS21 2.9 36.4 1.0 CD2 A:HIS21 3.0 35.2 1.0 ZN A:ZN500 3.1 33.1 1.0 OD2 A:ASP50 3.1 34.0 1.0 OE1 A:GLU84 3.4 37.6 1.0 OE2 A:GLU85 3.8 39.7 1.0 CG A:GLU109 4.0 31.5 1.0 ND1 A:HIS21 4.0 34.8 1.0 CD A:GLU84 4.1 36.6 1.0 CG A:HIS21 4.1 35.8 1.0 CB A:ASP51 4.2 38.0 1.0 CB A:ASP50 4.2 31.9 1.0 CD A:GLU85 4.2 41.1 1.0 OE1 A:GLU85 4.4 38.4 1.0 OE2 A:GLU84 4.5 37.3 1.0 CA A:ASP50 4.6 34.4 1.0 CB A:GLU109 4.8 32.1 1.0 C A:ASP50 4.8 35.4 1.0 CG A:ASP51 4.8 41.2 1.0 NE2 A:HIS294 4.8 39.1 1.0 CD A:PRO110 4.9 37.8 1.0 CG A:GLU84 5.0 36.1 1.0 N A:ASP51 5.0 35.1 1.0

Zinc binding site 3 out of 20 in the Crystal Structure of A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2


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 A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:44.0 occ:1.00 OE2 A:GLU375 2.0 47.9 1.0 O A:HOH644 2.1 5.4 1.0 CD A:GLU375 2.7 49.8 1.0 OE1 A:GLU375 2.9 53.3 1.0 NE A:ARG387 3.6 42.1 1.0 O A:HOH622 3.7 40.7 1.0 CG A:GLU375 4.2 43.2 1.0 NH2 A:ARG387 4.3 40.4 1.0 CD A:ARG387 4.4 43.2 1.0 NZ A:LYS379 4.4 35.7 1.0 CZ A:ARG387 4.4 40.6 1.0 CE A:LYS379 5.0 34.1 1.0

Zinc binding site 4 out of 20 in the Crystal Structure of A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2


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 A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:50.0 occ:1.00 ND1 A:HIS138 1.9 43.6 1.0 O A:HOH647 2.4 34.9 1.0 CE1 A:HIS138 2.8 46.1 1.0 CG A:HIS138 2.9 46.2 1.0 CB A:HIS138 3.4 45.2 1.0 ND2 A:ASN184 3.7 60.9 1.0 NE2 A:HIS138 4.0 43.7 1.0 CD2 A:HIS138 4.0 46.8 1.0 CA A:HIS138 4.5 46.9 1.0 N A:GLY140 4.8 49.0 1.0 CG A:ASN184 5.0 52.1 1.0

Zinc binding site 5 out of 20 in the Crystal Structure of A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2


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 A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:85.3 occ:1.00 OD2 A:ASP363 2.6 70.9 1.0 OD1 A:ASP363 3.1 60.3 1.0 CG A:ASP363 3.2 54.6 1.0 O A:HOH653 3.3 34.2 1.0 O A:GLU358 4.2 44.6 1.0 CB A:GLU358 4.4 40.9 1.0 N A:GLY366 4.4 47.5 1.0 CA A:GLY366 4.4 43.5 1.0 OE1 A:GLU358 4.5 47.6 1.0 CB A:ASP363 4.7 48.1 1.0

Zinc binding site 6 out of 20 in the Crystal Structure of A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2


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 A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:121.8 occ:1.00 O A:HOH651 2.4 71.9 1.0 OE1 A:GLU263 2.7 88.7 1.0 OE2 A:GLU263 3.2 83.2 1.0 CD A:GLU263 3.3 77.1 1.0 OE2 B:GLU39 3.3 87.6 1.0 OE1 B:GLU39 3.6 66.5 1.0 CD B:GLU39 3.8 79.4 1.0 NH1 B:ARG37 4.8 63.4 1.0 CG A:GLU263 4.8 64.7 1.0

Zinc binding site 7 out of 20 in the Crystal Structure of A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:129.2 occ:1.00 OE2 A:GLU377 3.5 50.0 1.0 OE1 A:GLU377 3.5 57.4 1.0 CD A:GLU377 3.9 53.9 1.0 ND2 A:ASN380 4.1 36.4 1.0 NZ A:LYS353 4.6 56.8 1.0

Zinc binding site 8 out of 20 in the Crystal Structure of A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:38.1 occ:1.00 OD2 B:ASP50 1.9 36.4 1.0 OE2 B:GLU85 1.9 35.0 1.0 NE2 B:HIS294 1.9 51.3 1.0 OE1 B:GLU85 2.3 36.0 1.0 CD B:GLU85 2.3 37.8 1.0 O B:HOH615 2.4 31.5 1.0 CE1 B:HIS294 2.8 58.5 1.0 CG B:ASP50 2.9 36.4 1.0 CD2 B:HIS294 3.0 53.1 1.0 ZN B:ZN501 3.1 38.3 1.0 OD1 B:ASP50 3.2 34.8 1.0 CG B:GLU85 3.8 42.0 1.0 OE1 B:GLU84 3.9 44.0 1.0 ND1 B:HIS294 4.0 55.0 1.0 CG B:HIS294 4.1 54.1 1.0 NE2 B:HIS21 4.2 42.4 1.0 CB B:ASP50 4.2 37.3 1.0 CE1 B:HIS21 4.3 36.2 1.0 CG1 B:VAL25 4.5 41.4 1.0 OE1 B:GLU109 4.7 37.5 1.0 CB B:GLU85 4.9 42.6 1.0 CD B:GLU84 4.9 40.9 1.0 OE2 B:GLU109 5.0 35.3 1.0

Zinc binding site 9 out of 20 in the Crystal Structure of A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:38.3 occ:1.00 OE1 B:GLU109 1.8 37.5 1.0 OD1 B:ASP50 1.9 34.8 1.0 NE2 B:HIS21 2.0 42.4 1.0 O B:HOH615 2.1 31.5 1.0 OE2 B:GLU109 2.4 35.3 1.0 CD B:GLU109 2.4 37.4 1.0 CG B:ASP50 2.8 36.4 1.0 CD2 B:HIS21 3.0 43.9 1.0 CE1 B:HIS21 3.1 36.2 1.0 ZN B:ZN500 3.1 38.1 1.0 OD2 B:ASP50 3.1 36.4 1.0 OE1 B:GLU84 3.4 44.0 1.0 OE2 B:GLU85 3.9 35.0 1.0 CG B:GLU109 3.9 37.7 1.0 CD B:GLU84 4.0 40.9 1.0 ND1 B:HIS21 4.1 32.7 1.0 CG B:HIS21 4.2 39.3 1.0 CB B:ASP50 4.2 37.3 1.0 CB B:ASP51 4.2 43.1 1.0 CD B:GLU85 4.3 37.8 1.0 OE2 B:GLU84 4.4 43.6 1.0 OE1 B:GLU85 4.5 36.0 1.0 CA B:ASP50 4.6 41.7 1.0 CB B:GLU109 4.7 36.6 1.0 NE2 B:HIS294 4.8 51.3 1.0 CD B:PRO110 4.8 42.8 1.0 CG B:ASP51 4.8 46.3 1.0 C B:ASP50 4.8 40.2 1.0 CG B:GLU84 5.0 41.2 1.0

Zinc binding site 10 out of 20 in the Crystal Structure of A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of A Circular Permutation and Computationally Designed Pro-Enzyme of Carboxypeptidase G2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:57.8 occ:1.00 ND1 B:HIS138 1.8 60.0 1.0 O B:HOH629 2.2 27.7 1.0 CE1 B:HIS138 2.8 60.6 1.0 CG B:HIS138 2.8 57.2 1.0 CB B:HIS138 3.2 55.6 1.0 ND2 B:ASN184 3.8 57.7 1.0 NE2 B:HIS138 3.9 58.3 1.0 CD2 B:HIS138 3.9 58.8 1.0 CA B:HIS138 4.4 56.8 1.0 N B:GLY140 4.7 67.8 1.0

B.J.Yachnin, L.R.Azouz, R.E.White, C.A.S.A.Minetti, D.P.Remeta, V.M.Tan, J.M.Drake, S.D.Khare. Massively Parallel, Computationally-Guided Design of A Pro-Enzyme Biorxiv 2021.
DOI: 10.1101/2021.03.25.437042