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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

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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

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