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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

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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 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

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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: Sat Oct 26 20:09:06 2024

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