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Zinc in PDB 6gbk: Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions

Enzymatic activity of Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions

All present enzymatic activity of Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions:
3.1.8.1;

Protein crystallography data

The structure of Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions, PDB code: 6gbk was solved by O.Khersonsky, R.Lipsh, Z.Avizemer, M.Goldsmith, Y.Ashani, H.Leader, O.Dym, S.Rogotner, D.Trudeau, D.S.Tawfik, S.J.Fleishman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.47 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 156.749, 53.090, 89.230, 90.00, 106.81, 90.00
R / Rfree (%) 18.2 / 21.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions (pdb code 6gbk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions, PDB code: 6gbk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6gbk

Go back to Zinc Binding Sites List in 6gbk
Zinc binding site 1 out of 4 in the Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:13.4
occ:1.00
 O A:HOH575 2.0 14.2 1.0
O2 A:FMT401 2.0 14.7 1.0
NE2 A:HIS57 2.1 12.2 1.0
OD1 A:ASP301 2.1 13.2 1.0
NE2 A:HIS55 2.1 11.7 1.0
CG A:ASP301 3.0 14.0 1.0
CD2 A:HIS55 3.1 11.3 1.0
CE1 A:HIS57 3.1 12.8 1.0
CD2 A:HIS57 3.1 12.9 1.0
CE1 A:HIS55 3.1 11.4 1.0
C A:FMT401 3.2 14.6 1.0
OD2 A:ASP301 3.4 13.3 1.0
O1 A:FMT401 3.6 14.9 1.0
O A:HOH627 3.8 18.1 1.0
ZN A:ZN403 3.8 16.9 1.0
CE1 A:HIS230 4.0 15.1 1.0
NZ A:LYS169 4.1 14.9 1.0
CG2 A:VAL101 4.1 12.2 1.0
ND1 A:HIS57 4.2 12.0 1.0
CG A:HIS57 4.2 12.1 1.0
CG A:HIS55 4.2 11.4 1.0
ND1 A:HIS55 4.2 11.5 1.0
CB A:ASP301 4.3 13.0 1.0
NE2 A:HIS230 4.4 16.6 1.0
CA A:ASP301 4.9 13.1 1.0

Zinc binding site 2 out of 4 in 6gbk

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Zinc binding site 2 out of 4 in the Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:16.9
occ:1.00
 O1 A:FMT401 2.0 14.9 1.0
NE2 A:HIS230 2.1 16.6 1.0
O A:HOH627 2.1 18.1 1.0
ND1 A:HIS201 2.1 15.4 1.0
O A:HOH575 2.5 14.2 1.0
C A:FMT401 3.0 14.6 1.0
CE1 A:HIS201 3.0 15.1 1.0
CD2 A:HIS230 3.0 15.9 1.0
CE1 A:HIS230 3.1 15.1 1.0
CG A:HIS201 3.2 15.7 1.0
O2 A:FMT401 3.3 14.7 1.0
CB A:HIS201 3.5 16.1 1.0
ZN A:ZN402 3.8 13.4 1.0
NE1 A:TRP131 3.9 17.5 1.0
NZ A:LYS169 4.1 14.9 1.0
CG A:HIS230 4.2 15.5 1.0
ND1 A:HIS230 4.2 15.0 1.0
NE2 A:HIS201 4.2 14.8 1.0
CD2 A:HIS201 4.2 15.9 1.0
CE1 A:HIS55 4.3 11.4 1.0
CA A:HIS201 4.4 15.6 1.0
NE2 A:HIS55 4.4 11.7 1.0
C3 A:TRS404 4.5 49.4 1.0
CD1 A:TRP131 4.5 16.4 1.0
CE A:LYS169 4.6 14.1 1.0
OD2 A:ASP301 4.7 13.3 1.0
O3 A:TRS404 5.0 54.7 1.0

Zinc binding site 3 out of 4 in 6gbk

Go back to Zinc Binding Sites List in 6gbk
Zinc binding site 3 out of 4 in the Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:14.9
occ:1.00
 O B:HOH567 2.0 13.9 1.0
NE2 B:HIS57 2.0 15.1 1.0
O2 B:FMT401 2.0 16.3 1.0
NE2 B:HIS55 2.1 14.3 1.0
OD1 B:ASP301 2.1 17.3 1.0
CD2 B:HIS57 3.0 15.1 1.0
CG B:ASP301 3.0 15.1 1.0
CD2 B:HIS55 3.0 14.0 1.0
CE1 B:HIS57 3.0 15.2 1.0
CE1 B:HIS55 3.1 15.3 1.0
C B:FMT401 3.2 17.4 1.0
OD2 B:ASP301 3.3 17.6 1.0
O1 B:FMT401 3.5 16.7 1.0
ZN B:ZN403 3.8 18.1 1.0
O B:HOH612 3.9 17.3 1.0
NZ B:LYS169 4.1 15.8 1.0
CG2 B:VAL101 4.1 14.8 1.0
CE1 B:HIS230 4.1 20.1 1.0
ND1 B:HIS57 4.1 14.5 1.0
CG B:HIS57 4.1 15.3 1.0
CG B:HIS55 4.2 14.2 1.0
ND1 B:HIS55 4.2 14.1 1.0
CB B:ASP301 4.3 14.9 1.0
NE2 B:HIS230 4.3 19.4 1.0
CA B:ASP301 4.9 13.9 1.0

Zinc binding site 4 out of 4 in 6gbk

Go back to Zinc Binding Sites List in 6gbk
Zinc binding site 4 out of 4 in the Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:18.1
occ:1.00
 O1 B:FMT401 2.0 16.7 1.0
ND1 B:HIS201 2.0 17.0 1.0
O B:HOH612 2.0 17.3 1.0
NE2 B:HIS230 2.1 19.4 1.0
O B:HOH567 2.4 13.9 1.0
CE1 B:HIS201 2.9 17.9 1.0
C B:FMT401 2.9 17.4 1.0
CD2 B:HIS230 3.0 19.0 1.0
CG B:HIS201 3.1 16.9 1.0
CE1 B:HIS230 3.2 20.1 1.0
O2 B:FMT401 3.3 16.3 1.0
CB B:HIS201 3.5 16.6 1.0
ZN B:ZN402 3.8 14.9 1.0
NE1 B:TRP131 4.0 17.2 1.0
NZ B:LYS169 4.0 15.8 1.0
NE2 B:HIS201 4.1 17.2 1.0
CD2 B:HIS201 4.1 17.5 1.0
CG B:HIS230 4.2 19.6 1.0
ND1 B:HIS230 4.2 19.7 1.0
CE1 B:HIS55 4.2 15.3 1.0
CA B:HIS201 4.3 16.0 1.0
NE2 B:HIS55 4.3 14.3 1.0
CD1 B:TRP131 4.5 17.8 1.0
OD2 B:ASP301 4.6 17.6 1.0
CE B:LYS169 4.6 15.8 1.0

Reference:

O.Khersonsky, R.Lipsh, Z.Avizemer, Y.Ashani, M.Goldsmith, H.Leader, O.Dym, S.Rogotner, D.L.Trudeau, J.Prilusky, P.Amengual-Rigo, V.Guallar, D.S.Tawfik, S.J.Fleishman. Automated Design of Efficient and Functionally Diverse Enzyme Repertoires. Mol. Cell V. 72 178 2018.
ISSN: ISSN 1097-4164
PubMed: 30270109
DOI: 10.1016/J.MOLCEL.2018.08.033
Page generated: Mon Oct 28 21:43:53 2024

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