Atomistry » Zinc » PDB 6g4t-6gdc » 6gbj
Atomistry »
  Zinc »
    PDB 6g4t-6gdc »
      6gbj »

Zinc in PDB 6gbj: 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: 6gbj 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) 38.65 / 1.63
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.490, 69.490, 186.020, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 18.1

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

Zinc binding site 1 out of 2 in 6gbj

Go back to Zinc Binding Sites List in 6gbj
Zinc binding site 1 out of 2 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:13.0
occ:1.00
O A:HOH530 2.0 15.4 1.0
NE2 A:HIS57 2.0 11.4 1.0
NE2 A:HIS55 2.1 11.2 1.0
O2 A:FMT401 2.1 12.9 1.0
OD1 A:ASP301 2.2 13.0 1.0
CD2 A:HIS55 3.0 13.0 1.0
CG A:ASP301 3.0 11.9 1.0
CE1 A:HIS57 3.0 12.0 1.0
CD2 A:HIS57 3.1 11.6 1.0
CE1 A:HIS55 3.1 13.2 1.0
C A:FMT401 3.1 12.8 1.0
O1 A:EDO405 3.2 24.3 0.8
OD2 A:ASP301 3.3 12.4 1.0
O1 A:FMT401 3.5 12.4 1.0
ZN A:ZN403 3.6 13.1 1.0
O A:HOH526 3.8 21.0 1.0
O2 A:EDO404 4.0 23.9 1.0
CG2 A:VAL101 4.0 12.5 1.0
C1 A:EDO405 4.1 25.0 0.8
NZ A:LYS169 4.1 12.8 1.0
CE1 A:HIS230 4.1 12.4 1.0
ND1 A:HIS57 4.2 11.8 1.0
CG A:HIS55 4.2 11.5 1.0
O A:HOH502 4.2 12.9 1.0
CG A:HIS57 4.2 12.2 1.0
ND1 A:HIS55 4.2 11.0 1.0
CB A:ASP301 4.3 12.1 1.0
NE2 A:HIS230 4.4 11.1 1.0
CA A:ASP301 4.9 12.9 1.0

Zinc binding site 2 out of 2 in 6gbj

Go back to Zinc Binding Sites List in 6gbj
Zinc binding site 2 out of 2 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:13.1
occ:1.00
O1 A:FMT401 2.0 12.4 1.0
NE2 A:HIS230 2.1 11.1 1.0
O A:HOH502 2.1 12.9 1.0
ND1 A:HIS201 2.1 13.1 1.0
O A:HOH530 2.2 15.4 1.0
C A:FMT401 3.0 12.8 1.0
CE1 A:HIS201 3.0 13.1 1.0
CE1 A:HIS230 3.0 12.4 1.0
CD2 A:HIS230 3.1 13.1 1.0
CG A:HIS201 3.2 12.3 1.0
O2 A:FMT401 3.3 12.9 1.0
ZN A:ZN402 3.6 13.0 1.0
CB A:HIS201 3.6 12.2 1.0
O1 A:EDO405 3.7 24.3 0.8
NH2 A:ARG254 3.7 13.6 1.0
NE1 A:TRP131 4.0 13.9 1.0
O A:HOH526 4.0 21.0 1.0
ND1 A:HIS230 4.2 11.8 1.0
NZ A:LYS169 4.2 12.8 1.0
OD2 A:ASP301 4.2 12.4 1.0
CE1 A:HIS55 4.2 13.2 1.0
CG A:HIS230 4.2 12.1 1.0
NE2 A:HIS201 4.2 12.9 1.0
NE2 A:HIS55 4.2 11.2 1.0
CD2 A:HIS201 4.3 14.3 1.0
O2 A:EDO407 4.3 20.1 1.0
CA A:HIS201 4.4 12.1 1.0
CZ A:ARG254 4.4 14.0 1.0
CD1 A:TRP131 4.6 12.8 1.0
CE A:LYS169 4.6 11.9 1.0
NE A:ARG254 4.8 13.3 1.0
CG A:ASP301 5.0 11.9 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: Wed Dec 16 11:51:32 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy