Atomistry » Zinc » PDB 4c11-4c6m » 4c6c
Atomistry »
  Zinc »
    PDB 4c11-4c6m »
      4c6c »

Zinc in PDB 4c6c: Crystal Structure of the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From HEK293 Cells.

Enzymatic activity of Crystal Structure of the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From HEK293 Cells.

All present enzymatic activity of Crystal Structure of the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From HEK293 Cells.:
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 HEK293 Cells., PDB code: 4c6c 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) 41.055 / 1.45
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 82.110, 158.800, 60.760, 90.00, 90.00, 90.00
R / Rfree (%) 12.25 / 14.78

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 HEK293 Cells. (pdb code 4c6c). 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 HEK293 Cells., PDB code: 4c6c:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4c6c

Go back to Zinc Binding Sites List in 4c6c
Zinc binding site 1 out of 4 in the Crystal Structure of the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From HEK293 Cells.


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 HEK293 Cells. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2822

b:11.0
occ:0.89
 O A:HOH2066 2.0 12.8 1.0
NE2 A:HIS1471 2.0 11.5 1.0
NE2 A:HIS1473 2.1 12.0 1.0
OQ2 A:KCX1556 2.1 14.0 1.0
OD1 A:ASP1686 2.2 12.3 1.0
CD2 A:HIS1471 3.0 10.4 1.0
CE1 A:HIS1473 3.0 13.1 1.0
CX A:KCX1556 3.0 12.7 1.0
CE1 A:HIS1471 3.0 13.1 1.0
CD2 A:HIS1473 3.1 11.7 1.0
CG A:ASP1686 3.1 13.0 1.0
HD2 A:HIS1471 3.1 12.5 1.0
HE1 A:HIS1473 3.2 15.7 1.0
HE1 A:HIS1471 3.3 15.7 1.0
HD2 A:HIS1473 3.3 14.0 1.0
ZN A:ZN2823 3.3 10.9 0.9
OQ1 A:KCX1556 3.4 12.2 1.0
HG3 A:MET1503 3.4 16.5 1.0
OD2 A:ASP1686 3.5 13.9 1.0
HD2 A:HIS1614 3.9 13.0 1.0
ND1 A:HIS1473 4.1 12.1 1.0
ND1 A:HIS1471 4.1 13.0 1.0
CG A:HIS1471 4.1 11.2 1.0
O A:HOH2135 4.1 27.6 1.0
HA A:ASP1686 4.1 13.6 1.0
HH A:TYR1558 4.2 14.6 0.6
NZ A:KCX1556 4.2 13.2 1.0
CG A:HIS1473 4.2 12.0 1.0
H A:FMT2829 4.3 46.6 1.0
HE1 A:TYR1558 4.3 17.1 0.6
CB A:ASP1686 4.4 12.5 1.0
CG A:MET1503 4.4 13.8 1.0
NE2 A:HIS1614 4.4 11.1 1.0
CD2 A:HIS1614 4.5 10.8 1.0
HZ A:KCX1556 4.5 15.8 1.0
HE1 A:MET1503 4.5 17.4 1.0
HB2 A:ASP1686 4.6 15.0 1.0
CA A:ASP1686 4.8 11.4 1.0
HE2 A:TYR1558 4.8 17.2 0.4
HB3 A:ALA1688 4.8 16.8 1.0
HG2 A:MET1503 4.8 16.5 1.0
OH A:TYR1558 4.8 12.2 0.6
HD1 A:HIS1473 4.9 14.6 1.0
HB2 A:MET1503 4.9 14.1 1.0

Zinc binding site 2 out of 4 in 4c6c

Go back to Zinc Binding Sites List in 4c6c
Zinc binding site 2 out of 4 in the Crystal Structure of the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From HEK293 Cells.


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 HEK293 Cells. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2823

b:10.9
occ:0.86
 OQ1 A:KCX1556 1.9 12.2 1.0
O A:HOH2066 2.0 12.8 1.0
NE2 A:HIS1614 2.0 11.1 1.0
ND1 A:HIS1590 2.1 12.1 1.0
CX A:KCX1556 2.9 12.7 1.0
CE1 A:HIS1590 2.9 12.2 1.0
HB2 A:HIS1590 2.9 13.2 1.0
CE1 A:HIS1614 3.0 11.2 1.0
CD2 A:HIS1614 3.1 10.8 1.0
HE1 A:HIS1590 3.1 14.6 1.0
CG A:HIS1590 3.1 11.6 1.0
HE1 A:HIS1614 3.1 13.4 1.0
HE1 A:HIS1471 3.2 15.7 1.0
OQ2 A:KCX1556 3.2 14.0 1.0
HD2 A:HIS1614 3.3 13.0 1.0
ZN A:ZN2822 3.3 11.0 0.9
HE2 A:TYR1558 3.4 17.2 0.4
CB A:HIS1590 3.5 11.0 1.0
O A:HOH2135 3.7 27.6 1.0
CE1 A:HIS1471 3.8 13.1 1.0
NE2 A:HIS1471 4.0 11.5 1.0
CE2 A:TYR1558 4.0 14.4 0.4
HE1 A:TYR1558 4.0 17.1 0.6
NE2 A:HIS1590 4.0 13.4 1.0
OD2 A:ASP1686 4.1 13.9 1.0
ND1 A:HIS1614 4.1 11.4 1.0
CD2 A:HIS1590 4.1 12.9 1.0
NZ A:KCX1556 4.2 13.2 1.0
HA A:HIS1590 4.2 13.0 1.0
CG A:HIS1614 4.2 11.0 1.0
HB3 A:HIS1590 4.2 13.2 1.0
HD3 A:PRO1662 4.2 16.5 1.0
HE3 A:KCX1556 4.3 15.3 1.0
HB3 A:CYS1613 4.4 14.1 1.0
CA A:HIS1590 4.5 10.8 1.0
HB2 A:CYS1613 4.5 14.1 1.0
HD2 A:TYR1558 4.5 17.1 0.4
O A:ARG1661 4.6 16.8 1.0
OD1 A:ASP1686 4.6 12.3 1.0
CE A:KCX1556 4.6 12.8 1.0
CD2 A:TYR1558 4.6 14.2 0.4
CG A:ASP1686 4.6 13.0 1.0
HE2 A:KCX1556 4.6 15.3 1.0
CZ A:TYR1558 4.7 15.5 0.4
CE1 A:TYR1558 4.7 14.2 0.6
HZ A:KCX1556 4.7 15.8 1.0
OH A:TYR1558 4.7 17.1 0.4
HD1 A:TYR1558 4.7 18.1 0.6
HE2 A:HIS1590 4.8 16.1 1.0
HD1 A:HIS1614 4.9 13.7 1.0
CB A:CYS1613 4.9 11.7 1.0
HH A:TYR1558 4.9 20.6 0.4

Zinc binding site 3 out of 4 in 4c6c

Go back to Zinc Binding Sites List in 4c6c
Zinc binding site 3 out of 4 in the Crystal Structure of the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From HEK293 Cells.


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 HEK293 Cells. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2824

b:14.1
occ:0.61
 ND1 A:HIS1471 2.0 13.0 1.0
O A:HOH2065 2.0 13.3 1.0
OE2 A:GLU1637 2.1 14.2 1.0
SG A:CYS1613 2.3 13.1 1.0
HB3 A:CYS1613 2.7 14.1 1.0
HB2 A:HIS1471 2.8 13.5 1.0
CD A:GLU1637 2.9 13.2 1.0
CE1 A:HIS1471 2.9 13.1 1.0
CB A:CYS1613 3.0 11.7 1.0
OE1 A:GLU1637 3.0 13.8 1.0
CG A:HIS1471 3.0 11.2 1.0
HE1 A:HIS1471 3.1 15.7 1.0
HA A:CYS1613 3.2 12.9 1.0
HE1 A:MET1503 3.2 17.4 1.0
CB A:HIS1471 3.4 11.2 1.0
CA A:CYS1613 3.6 10.7 1.0
HE2 A:MET1503 3.7 17.4 1.0
CE A:MET1503 3.8 14.5 1.0
HB2 A:CYS1613 3.9 14.1 1.0
HE3 A:MET1503 3.9 17.4 1.0
H A:HIS1614 4.0 12.9 1.0
HB3 A:HIS1471 4.0 13.5 1.0
NE2 A:HIS1471 4.1 11.5 1.0
CD2 A:HIS1471 4.1 10.4 1.0
HD2 A:HIS1611 4.2 14.2 1.0
HG22 A:VAL1588 4.2 16.3 1.0
HB A:VAL1588 4.2 15.3 1.0
CG A:GLU1637 4.2 12.6 1.0
HG21 A:VAL1470 4.3 14.9 1.0
HE2 A:HIS1611 4.4 15.3 1.0
HG2 A:GLU1637 4.4 15.1 1.0
O A:VAL1470 4.4 12.0 1.0
HA A:HIS1471 4.4 12.2 1.0
HG3 A:GLU1637 4.5 15.1 1.0
CA A:HIS1471 4.6 10.2 1.0
O A:HOH2177 4.6 18.9 1.0
N A:HIS1614 4.6 10.7 1.0
N A:CYS1613 4.6 9.9 1.0
C A:CYS1613 4.7 10.6 1.0
HG21 A:VAL1588 4.8 16.3 1.0
H A:CYS1613 4.8 11.9 1.0
CG2 A:VAL1588 4.8 13.6 1.0
CD2 A:HIS1611 4.8 11.8 1.0
HE3 A:KCX1556 4.8 15.3 1.0
HB1 A:ALA1684 4.8 16.6 1.0
HG12 A:VAL1588 4.9 14.9 1.0
NE2 A:HIS1611 4.9 12.7 1.0
CB A:VAL1588 4.9 12.8 1.0
HD2 A:HIS1614 5.0 13.0 1.0
HD2 A:HIS1471 5.0 12.5 1.0

Zinc binding site 4 out of 4 in 4c6c

Go back to Zinc Binding Sites List in 4c6c
Zinc binding site 4 out of 4 in the Crystal Structure of the Dihydroorotase Domain of Human Cad in Apo-Form Obtained Recombinantly From HEK293 Cells.


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 HEK293 Cells. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2825

b:18.1
occ:0.68
 O A:HOH2290 2.0 21.3 1.0
O A:HOH2289 2.0 22.9 1.0
NE2 A:HIS1734 2.1 16.1 1.0
CE1 A:HIS1734 2.8 15.7 1.0
HE1 A:HIS1734 2.8 18.8 1.0
CD2 A:HIS1734 3.3 14.2 1.0
HD2 A:HIS1734 3.6 17.1 1.0
ND1 A:HIS1734 4.0 13.6 1.0
HD2 A:HIS1733 4.1 16.8 1.0
CG A:HIS1734 4.3 12.6 1.0
O A:HOH2001 4.4 31.4 1.0
HG3 A:PRO1465 4.6 23.0 1.0
O A:HOH2280 4.6 26.1 1.0
O A:HOH2288 4.7 31.8 1.0
HD1 A:HIS1734 4.8 16.4 1.0
O A:HOH2292 4.9 26.8 1.0
CD2 A:HIS1733 4.9 14.0 1.0
HB3 A:LEU1729 4.9 18.5 1.0
HE22 A:GLN1730 5.0 15.6 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: Sat Oct 26 20:30:48 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