Atomistry » Zinc » PDB 4bua-4c09 » 4by3
Atomistry »
  Zinc »
    PDB 4bua-4c09 »
      4by3 »

Zinc in PDB 4by3: Crystal Structure of the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From E. Coli.

Enzymatic activity of Crystal Structure of the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From E. Coli.

All present enzymatic activity of Crystal Structure of the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From E. Coli.:
3.4.2.3;

Protein crystallography data

The structure of Crystal Structure of the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From E. Coli., PDB code: 4by3 was solved by S.Ramon-Maiques, N.Lallous, A.Grande-Garcia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.856 / 1.73
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 82.120, 159.320, 61.510, 90.00, 90.00, 90.00
R / Rfree (%) 12.57 / 13.62

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From E. Coli. (pdb code 4by3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From E. Coli., PDB code: 4by3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4by3

Go back to Zinc Binding Sites List in 4by3
Zinc binding site 1 out of 4 in the Crystal Structure of the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From E. Coli.


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 the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From E. Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1000

b:16.5
occ:0.83
 NE2 A:HIS1471 2.0 16.7 1.0
NE2 A:HIS1473 2.0 18.2 1.0
O A:HOH2061 2.1 20.6 1.0
OQ2 A:KCX1556 2.2 19.9 1.0
OD1 A:ASP1686 2.2 20.3 1.0
CE1 A:HIS1473 2.9 21.9 1.0
CE1 A:HIS1471 3.0 15.9 1.0
CD2 A:HIS1471 3.0 17.4 1.0
CX A:KCX1556 3.0 20.0 1.0
HE1 A:HIS1473 3.1 26.3 1.0
CD2 A:HIS1473 3.1 20.9 1.0
CG A:ASP1686 3.1 19.9 1.0
HE1 A:HIS1471 3.2 19.1 1.0
HD2 A:HIS1471 3.2 20.9 1.0
OQ1 A:KCX1556 3.3 19.5 1.0
ZN A:ZN1001 3.3 18.4 0.9
HD2 A:HIS1473 3.4 25.1 1.0
HG3 A:MET1503 3.4 22.3 1.0
OD2 A:ASP1686 3.5 22.5 1.0
HD2 A:HIS1614 3.9 20.6 1.0
O A:HOH2062 4.0 44.8 1.0
ND1 A:HIS1471 4.1 17.9 1.0
ND1 A:HIS1473 4.1 21.0 1.0
CG A:HIS1471 4.1 17.6 1.0
HA A:ASP1686 4.2 20.0 1.0
HH A:TYR1558 4.2 18.3 0.6
HZ A:KCX1556 4.2 23.8 1.0
NZ A:KCX1556 4.2 19.8 1.0
CG A:HIS1473 4.2 19.2 1.0
H A:FMT2825 4.3 53.5 1.0
HE1 A:TYR1558 4.3 23.0 0.6
CG A:MET1503 4.4 18.6 1.0
NE2 A:HIS1614 4.4 17.8 1.0
CB A:ASP1686 4.4 18.6 1.0
CD2 A:HIS1614 4.5 17.2 1.0
HE1 A:MET1503 4.7 26.5 1.0
HB2 A:ASP1686 4.7 22.3 1.0
CA A:ASP1686 4.8 16.6 1.0
HG2 A:MET1503 4.8 22.3 1.0
OH A:TYR1558 4.8 15.2 0.6
HD1 A:HIS1473 4.9 25.2 1.0
HB3 A:ALA1688 4.9 21.8 1.0
HB2 A:MET1503 4.9 23.3 1.0
HE2 A:TYR1558 5.0 26.4 0.4

Zinc binding site 2 out of 4 in 4by3

Go back to Zinc Binding Sites List in 4by3
Zinc binding site 2 out of 4 in the Crystal Structure of the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From E. Coli.


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 the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From E. Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:18.4
occ:0.92
 OQ1 A:KCX1556 1.9 19.5 1.0
O A:HOH2061 2.0 20.6 1.0
NE2 A:HIS1614 2.0 17.8 1.0
ND1 A:HIS1590 2.0 20.4 1.0
CX A:KCX1556 2.9 20.0 1.0
CE1 A:HIS1590 2.9 22.2 1.0
CE1 A:HIS1614 3.0 19.1 1.0
HB2 A:HIS1590 3.0 18.4 1.0
HE1 A:HIS1590 3.0 26.7 1.0
CD2 A:HIS1614 3.1 17.2 1.0
CG A:HIS1590 3.1 18.1 1.0
HE1 A:HIS1614 3.1 22.9 1.0
HE1 A:HIS1471 3.2 19.1 1.0
OQ2 A:KCX1556 3.2 19.9 1.0
HD2 A:HIS1614 3.3 20.6 1.0
ZN A:ZN1000 3.3 16.5 0.8
CB A:HIS1590 3.5 15.3 1.0
O A:HOH2062 3.6 44.8 1.0
HE2 A:TYR1558 3.8 26.4 0.4
CE1 A:HIS1471 3.9 15.9 1.0
NE2 A:HIS1590 4.0 23.1 1.0
HE1 A:TYR1558 4.0 23.0 0.6
NE2 A:HIS1471 4.1 16.7 1.0
ND1 A:HIS1614 4.1 18.6 1.0
CD2 A:HIS1590 4.1 20.4 1.0
HA A:HIS1590 4.2 16.5 1.0
OD2 A:ASP1686 4.2 22.5 1.0
NZ A:KCX1556 4.2 19.8 1.0
CG A:HIS1614 4.2 16.8 1.0
CE2 A:TYR1558 4.2 22.0 0.4
HE3 A:KCX1556 4.2 22.3 1.0
HB3 A:HIS1590 4.2 18.4 1.0
HD3 A:PRO1662 4.4 27.0 1.0
HB2 A:CYS1613 4.4 19.6 1.0
HB3 A:CYS1613 4.4 19.6 1.0
CA A:HIS1590 4.5 13.8 1.0
HE2 A:KCX1556 4.5 22.3 1.0
CE A:KCX1556 4.5 18.6 1.0
O A:ARG1661 4.6 27.2 1.0
OD1 A:ASP1686 4.6 20.3 1.0
CG A:ASP1686 4.7 19.9 1.0
HZ A:KCX1556 4.7 23.8 1.0
CE1 A:TYR1558 4.7 19.2 0.6
OH A:TYR1558 4.7 22.8 0.4
CZ A:TYR1558 4.7 23.1 0.4
HD1 A:TYR1558 4.7 23.6 0.6
HE2 A:HIS1590 4.8 27.7 1.0
CD2 A:TYR1558 4.9 21.1 0.4
CB A:CYS1613 4.9 16.4 1.0
HD1 A:HIS1614 4.9 22.4 1.0
HD2 A:TYR1558 4.9 25.3 0.4
HD2 A:HIS1590 5.0 24.4 1.0

Zinc binding site 3 out of 4 in 4by3

Go back to Zinc Binding Sites List in 4by3
Zinc binding site 3 out of 4 in the Crystal Structure of the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From E. Coli.


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 the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From E. Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:20.0
occ:0.83
 OE2 A:GLU1637 2.0 19.8 1.0
ND1 A:HIS1471 2.1 17.9 1.0
O A:HOH2063 2.1 18.4 1.0
SG A:CYS1613 2.3 20.0 1.0
HB3 A:CYS1613 2.8 19.6 1.0
CD A:GLU1637 2.8 19.2 1.0
HB2 A:HIS1471 2.8 17.8 1.0
CE1 A:HIS1471 3.0 15.9 1.0
CB A:CYS1613 3.0 16.4 1.0
OE1 A:GLU1637 3.1 22.0 1.0
CG A:HIS1471 3.1 17.6 1.0
HE1 A:HIS1471 3.1 19.1 1.0
HE1 A:MET1503 3.2 26.5 1.0
HA A:CYS1613 3.3 19.1 1.0
CB A:HIS1471 3.5 14.8 1.0
CA A:CYS1613 3.7 15.9 1.0
HE2 A:MET1503 3.7 26.5 1.0
CE A:MET1503 3.9 22.1 1.0
HB2 A:CYS1613 3.9 19.6 1.0
HB3 A:HIS1471 4.0 17.8 1.0
H A:HIS1614 4.1 19.3 1.0
HE3 A:MET1503 4.1 26.5 1.0
NE2 A:HIS1471 4.1 16.7 1.0
CG A:GLU1637 4.2 18.7 1.0
CD2 A:HIS1471 4.2 17.4 1.0
HD2 A:HIS1611 4.2 19.6 1.0
HG21 A:VAL1470 4.3 22.2 1.0
HG2 A:GLU1637 4.3 22.4 1.0
HG22 A:VAL1588 4.3 24.6 1.0
HB A:VAL1588 4.3 23.0 1.0
HE2 A:HIS1611 4.4 23.0 1.0
O A:VAL1470 4.4 18.3 1.0
HG3 A:GLU1637 4.4 22.4 1.0
HA A:HIS1471 4.4 15.7 1.0
O A:HOH2197 4.5 33.2 1.0
CA A:HIS1471 4.6 13.1 1.0
N A:CYS1613 4.7 13.9 1.0
N A:HIS1614 4.7 16.1 1.0
HE3 A:KCX1556 4.7 22.3 1.0
C A:CYS1613 4.8 17.4 1.0
CD2 A:HIS1611 4.8 16.3 1.0
H A:CYS1613 4.9 16.6 1.0
HB1 A:ALA1684 4.9 20.4 1.0
HG21 A:VAL1588 4.9 24.6 1.0
HG12 A:VAL1588 4.9 22.7 1.0
NE2 A:HIS1611 4.9 19.2 1.0
CG2 A:VAL1588 4.9 20.5 1.0
HD2 A:HIS1614 5.0 20.6 1.0

Zinc binding site 4 out of 4 in 4by3

Go back to Zinc Binding Sites List in 4by3
Zinc binding site 4 out of 4 in the Crystal Structure of the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From E. Coli.


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 the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From E. Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:25.7
occ:0.78
 NE2 A:HIS1734 2.1 20.4 1.0
O A:HOH2065 2.2 20.5 1.0
O A:HOH2064 2.2 27.3 1.0
CE1 A:HIS1734 2.9 21.6 1.0
HE1 A:HIS1734 2.9 25.9 1.0
CD2 A:HIS1734 3.2 18.2 1.0
HD2 A:HIS1734 3.5 21.8 1.0
ND1 A:HIS1734 4.1 18.8 1.0
HD2 A:HIS1733 4.1 19.3 1.0
CG A:HIS1734 4.3 16.7 1.0
O A:HOH2381 4.4 46.0 1.0
O A:HOH2301 4.5 46.4 1.0
HG3 A:PRO1465 4.5 29.6 1.0
HB3 A:LEU1729 4.6 23.2 1.0
HD11 A:LEU1729 4.7 28.7 1.0
HD1 A:HIS1734 4.8 22.6 1.0
CD2 A:HIS1733 4.9 16.1 1.0
O A:HOH2310 4.9 32.7 1.0
O A:HOH2308 5.0 35.5 1.0
HE22 A:GLN1730 5.0 21.2 1.0

Reference:

A.Grande-Garcia, N.Lallous, C.Diaz-Tejada, S.Ramon-Maiques. Structure, Functional Characterization, and Evolution of the Dihydroorotase Domain of Human Cad. Structure V. 22 185 2014.
ISSN: ISSN 0969-2126
PubMed: 24332717
DOI: 10.1016/J.STR.2013.10.016
Page generated: Wed Dec 16 05:06:33 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