Atomistry » Zinc » PDB 5jmy-5k0w » 5jqj
Atomistry »
  Zinc »
    PDB 5jmy-5k0w »
      5jqj »

Zinc in PDB 5jqj: Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-1

Enzymatic activity of Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-1

All present enzymatic activity of Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-1:
3.5.2.6;

Protein crystallography data

The structure of Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-1, PDB code: 5jqj was solved by N.-S.Hong, C.J.Jackson, P.D.Carr, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.45 / 1.67
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 37.795, 137.724, 77.455, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 18.7

Other elements in 5jqj:

The structure of Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-1 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-1 (pdb code 5jqj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-1, PDB code: 5jqj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5jqj

Go back to Zinc Binding Sites List in 5jqj
Zinc binding site 1 out of 2 in the Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:20.3
occ:1.00
O A:HOH536 1.9 22.7 1.0
ND1 A:HIS122 2.0 20.1 1.0
NE2 A:HIS189 2.1 18.2 1.0
NE2 A:HIS120 2.1 15.0 1.0
CE1 A:HIS122 3.0 19.3 1.0
CE1 A:HIS120 3.0 18.6 1.0
CD2 A:HIS189 3.0 16.9 1.0
CG A:HIS122 3.0 17.8 1.0
CD2 A:HIS120 3.1 17.4 1.0
CE1 A:HIS189 3.1 20.2 1.0
CB A:HIS122 3.4 16.8 1.0
ZN A:ZN302 3.6 20.0 1.0
O A:HOH433 3.7 47.5 1.0
OD1 A:ASP124 3.9 18.4 1.0
SG A:CYS208 3.9 16.0 1.0
NE2 A:HIS122 4.1 19.5 1.0
CB A:CYS208 4.1 16.0 1.0
ND1 A:HIS120 4.1 17.1 1.0
CD2 A:HIS122 4.1 19.4 1.0
ND1 A:HIS189 4.2 19.3 1.0
CG A:HIS189 4.2 17.4 1.0
CG A:HIS120 4.2 14.3 1.0
C3 A:MES304 4.2 56.5 1.0
N4 A:MES304 4.3 53.4 1.0
C2 A:MES304 4.4 54.8 1.0
CG2 A:THR190 4.5 16.2 1.0
OD2 A:ASP124 4.5 20.6 1.0
CG A:ASP124 4.6 18.1 1.0
CA A:HIS122 4.9 15.9 1.0

Zinc binding site 2 out of 2 in 5jqj

Go back to Zinc Binding Sites List in 5jqj
Zinc binding site 2 out of 2 in the Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Directed Evolutionary Changes in Mbl Super Family - Ndm-1 Round 10 Crystal-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:20.0
occ:1.00
OD2 A:ASP124 2.0 20.6 1.0
O A:HOH433 2.0 47.5 1.0
NE2 A:HIS250 2.1 17.4 1.0
O A:HOH536 2.2 22.7 1.0
SG A:CYS208 2.2 16.0 1.0
CE1 A:HIS250 3.0 19.2 1.0
CG A:ASP124 3.0 18.1 1.0
CD2 A:HIS250 3.1 17.2 1.0
CB A:CYS208 3.3 16.0 1.0
OD1 A:ASP124 3.4 18.4 1.0
ZN A:ZN301 3.6 20.3 1.0
N4 A:MES304 3.9 53.4 1.0
ND1 A:HIS250 4.2 18.1 1.0
CG A:HIS250 4.2 16.3 1.0
NE2 A:HIS189 4.3 18.2 1.0
CB A:SER249 4.3 16.1 1.0
CB A:ASP124 4.3 16.9 1.0
C8 A:MES304 4.4 46.5 1.0
C5 A:MES304 4.4 53.3 1.0
CE1 A:HIS189 4.5 20.2 1.0
C7 A:MES304 4.5 48.7 1.0
CA A:CYS208 4.5 14.7 1.0
O1S A:MES304 4.5 40.4 1.0
C6 A:MES304 4.5 52.2 1.0
OG A:SER249 4.6 18.8 1.0
CE1 A:HIS120 4.6 18.6 1.0
NE2 A:HIS120 4.6 15.0 1.0
CE A:LYS125 4.8 21.4 1.0
O A:HOH499 4.9 17.9 1.0
C3 A:MES304 5.0 56.5 1.0
CD A:LYS125 5.0 21.2 1.0

Reference:

F.Baier, N.-S.Hong, G.Yang, P.D.Carr, C.Jackson, N.Tokuriki. Enzyme Evolvability Is Contingent on the Initial Sequence Background To Be Published.
Page generated: Wed Dec 16 06:25:43 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy