Atomistry » Zinc » PDB 6g2j-6gbx » 6gbk
Atomistry »
  Zinc »
    PDB 6g2j-6gbx »
      6gbk »

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

Go back to Zinc Binding Sites List in 6gbk
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy