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Zinc in PDB 8pbt: Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate

Enzymatic activity of Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate

All present enzymatic activity of Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate:
2.1.3.2; 3.5.2.3; 6.3.5.5;

Protein crystallography data

The structure of Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate, PDB code: 8pbt was solved by F.Del Cano-Ochoa, S.Ramon-Maiques, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.36 / 1.43
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 82.067, 158.72, 61.115, 90, 90, 90
R / Rfree (%) 14.8 / 17.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate (pdb code 8pbt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate, PDB code: 8pbt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 8pbt

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Zinc binding site 1 out of 7 in the Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1903

b:22.8
occ:0.90
 NE2 A:HIS1481 1.9 28.3 1.0
OE1 A:GLU1694 2.0 29.2 1.0
ND1 A:HIS1690 2.0 21.1 1.0
O1 A:FMT1917 2.2 42.1 1.0
C A:FMT1917 2.5 42.6 1.0
CD A:GLU1694 2.7 27.8 1.0
OE2 A:GLU1694 2.8 28.8 1.0
CE1 A:HIS1690 2.9 20.8 1.0
CE1 A:HIS1481 2.9 29.5 1.0
O2 A:FMT1917 2.9 43.8 1.0
CD2 A:HIS1481 2.9 29.0 1.0
HE1 A:HIS1690 2.9 25.0 1.0
H A:FMT1917 3.1 51.2 1.0
HD2 A:HIS1481 3.1 34.8 1.0
HE1 A:HIS1481 3.1 35.4 1.0
CG A:HIS1690 3.2 21.9 1.0
HG3 A:PRO1701 3.2 28.9 1.0
HB3 A:HIS1690 3.3 26.4 1.0
HA A:HIS1690 3.5 25.1 1.0
CB A:HIS1690 3.7 22.0 1.0
CG A:PRO1701 3.9 24.1 1.0
HG2 A:PRO1701 3.9 28.9 1.0
ND1 A:HIS1481 4.0 29.7 1.0
CG A:HIS1481 4.0 29.1 1.0
NE2 A:HIS1690 4.0 21.5 1.0
CA A:HIS1690 4.1 20.9 1.0
CG A:GLU1694 4.1 26.0 1.0
HB2 A:PRO1701 4.2 28.9 1.0
CD2 A:HIS1690 4.2 21.2 1.0
O A:PRO1689 4.3 22.2 1.0
HB3 A:GLU1694 4.3 31.3 1.0
O A:HOH2193 4.4 43.2 1.0
HB3 A:PRO1701 4.4 28.9 1.0
CB A:PRO1701 4.4 24.1 1.0
HG2 A:GLU1694 4.5 31.2 1.0
HB2 A:HIS1690 4.6 26.4 1.0
HB2 A:GLU1694 4.6 31.3 1.0
CB A:GLU1694 4.6 26.1 1.0
HG3 A:GLU1694 4.8 31.2 1.0
H A:THR1691 4.8 28.6 1.0
HD1 A:HIS1481 4.8 35.7 1.0
HE2 A:HIS1690 4.8 25.8 1.0
HE A:ARG1475 4.9 26.1 1.0
HH21 A:ARG1475 4.9 25.2 1.0
N A:HIS1690 5.0 20.9 1.0

Zinc binding site 2 out of 7 in 8pbt

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Zinc binding site 2 out of 7 in the Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1904

b:17.7
occ:0.96
 OQ1 A:KCX1556 1.9 16.6 1.0
O A:HOH2104 2.0 18.0 1.0
NE2 A:HIS1614 2.0 15.9 1.0
ND1 A:HIS1590 2.1 18.2 1.0
O4 A:DOR1902 2.9 23.6 1.0
CE1 A:HIS1590 2.9 18.0 1.0
CX A:KCX1556 2.9 17.3 1.0
CE1 A:HIS1614 3.0 16.5 1.0
HE1 A:HIS1590 3.0 21.6 1.0
HB2 A:HIS1590 3.0 18.3 1.0
CD2 A:HIS1614 3.1 15.8 1.0
CG A:HIS1590 3.1 16.7 1.0
HE1 A:HIS1614 3.2 19.8 1.0
HE1 A:HIS1471 3.2 21.1 1.0
HD2 A:HIS1614 3.3 18.9 1.0
OQ2 A:KCX1556 3.3 17.3 1.0
ZN A:ZN1907 3.4 17.8 1.0
C4 A:DOR1902 3.6 22.7 1.0
CB A:HIS1590 3.6 15.3 1.0
HE1 A:TYR1558 3.8 22.1 1.0
H51 A:DOR1902 3.9 28.6 1.0
CE1 A:HIS1471 3.9 17.6 1.0
NE2 A:HIS1590 4.0 18.1 1.0
NE2 A:HIS1471 4.1 16.6 1.0
ND1 A:HIS1614 4.1 16.9 1.0
NZ A:KCX1556 4.1 17.2 1.0
HN3 A:DOR1902 4.2 27.0 1.0
CD2 A:HIS1590 4.2 18.2 1.0
OD2 A:ASP1686 4.2 18.6 1.0
CG A:HIS1614 4.2 15.7 1.0
N3 A:DOR1902 4.3 22.5 1.0
HD3 A:PRO1662 4.3 22.8 1.0
HB3 A:HIS1590 4.3 18.3 1.0
HA A:HIS1590 4.3 17.2 1.0
C5 A:DOR1902 4.3 23.8 1.0
HE2 A:KCX1556 4.4 22.0 1.0
O A:ARG1661 4.4 20.5 1.0
HB2 A:CYS1613 4.5 22.9 1.0
CE1 A:TYR1558 4.5 18.4 1.0
HE3 A:KCX1556 4.6 22.0 1.0
HD1 A:TYR1558 4.6 22.1 1.0
CA A:HIS1590 4.6 14.4 1.0
CE A:KCX1556 4.6 18.3 1.0
OD1 A:ASP1686 4.7 18.6 1.0
HB3 A:CYS1613 4.7 22.9 1.0
CG A:ASP1686 4.7 17.8 1.0
HE2 A:HIS1590 4.8 21.7 1.0
HZ A:KCX1556 4.8 20.6 1.0
HD1 A:HIS1614 4.9 20.2 1.0
H52 A:DOR1902 4.9 28.6 1.0
CD1 A:TYR1558 4.9 18.4 1.0
O A:HOH2090 5.0 39.7 1.0

Zinc binding site 3 out of 7 in 8pbt

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Zinc binding site 3 out of 7 in the Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1905

b:27.5
occ:0.14
 O A:HOH2124 2.1 22.0 1.0
ND1 A:HIS1471 2.1 17.8 1.0
OE2 A:GLU1637 2.2 20.1 1.0
SG A:CYS1613 2.5 21.6 1.0
HB3 A:CYS1613 2.5 22.9 1.0
OE1 A:GLU1637 2.8 19.4 1.0
CD A:GLU1637 2.8 19.7 1.0
HB2 A:HIS1471 2.8 18.0 1.0
CB A:CYS1613 2.9 19.1 1.0
CE1 A:HIS1471 3.0 17.6 1.0
CG A:HIS1471 3.0 16.4 1.0
HE3 A:MET1503 3.0 22.3 1.0
HA A:CYS1613 3.2 20.9 1.0
HE1 A:HIS1471 3.2 21.1 1.0
CB A:HIS1471 3.4 15.0 1.0
HE1 A:MET1503 3.5 22.3 1.0
CE A:MET1503 3.6 18.6 1.0
CA A:CYS1613 3.6 17.4 1.0
HE2 A:MET1503 3.8 22.3 1.0
HB2 A:CYS1613 3.8 22.9 1.0
H A:HIS1614 4.0 20.8 1.0
HB3 A:HIS1471 4.0 18.0 1.0
NE2 A:HIS1471 4.0 16.6 1.0
CD2 A:HIS1471 4.1 16.8 1.0
HD2 A:HIS1611 4.1 19.0 1.0
HG23 A:VAL1470 4.2 20.4 1.0
CG A:GLU1637 4.2 18.3 1.0
HE2 A:HIS1611 4.3 20.0 1.0
HG2 A:GLU1637 4.3 21.9 1.0
HB A:VAL1588 4.4 22.2 1.0
HA A:HIS1471 4.5 17.6 1.0
O A:VAL1470 4.5 15.6 1.0
CA A:HIS1471 4.5 14.7 1.0
HG3 A:GLU1637 4.6 21.9 1.0
N A:HIS1614 4.6 17.3 1.0
N A:CYS1613 4.6 15.2 1.0
C A:CYS1613 4.7 17.7 1.0
O A:HOH2143 4.7 24.8 1.0
HE2 A:KCX1556 4.7 22.0 1.0
CD2 A:HIS1611 4.8 15.8 1.0
HG21 A:VAL1588 4.8 26.3 1.0
NE2 A:HIS1611 4.8 16.6 1.0
H A:CYS1613 4.8 18.2 1.0
HB3 A:ALA1684 4.8 23.3 1.0
HD2 A:HIS1471 4.9 20.2 1.0
HG11 A:VAL1588 4.9 22.9 1.0

Zinc binding site 4 out of 7 in 8pbt

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Zinc binding site 4 out of 7 in the Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1906

b:18.4
occ:0.91
 O1 A:FMT1915 1.9 21.4 1.0
O2 A:FMT1914 2.0 26.5 1.0
ND1 A:HIS1741 2.0 22.7 1.0
O1 A:FMT1914 2.6 29.9 1.0
C A:FMT1914 2.6 28.0 1.0
C A:FMT1915 2.8 23.9 1.0
CE1 A:HIS1741 3.0 23.1 1.0
HA A:HIS1741 3.0 19.2 1.0
CG A:HIS1741 3.1 20.5 1.0
O2 A:FMT1915 3.1 24.9 1.0
HB3 A:HIS1741 3.1 21.2 1.0
HE1 A:HIS1741 3.2 27.8 1.0
CB A:HIS1741 3.4 17.7 1.0
CA A:HIS1741 3.7 16.0 1.0
H A:FMT1914 3.7 33.6 1.0
H A:FMT1915 3.8 28.6 1.0
NE2 A:HIS1741 4.1 22.7 1.0
CD2 A:HIS1741 4.2 21.8 1.0
HD3 A:PRO1818 4.3 31.3 1.0
HD2 A:PRO1818 4.3 31.3 1.0
HA A:ARG1738 4.3 16.5 1.0
HB2 A:HIS1741 4.3 21.2 1.0
HG2 A:PRO1818 4.4 33.1 1.0
O A:HOH2172 4.5 28.8 1.0
C A:HIS1741 4.6 16.6 1.0
H A:HIS1741 4.6 19.4 1.0
CD A:PRO1818 4.6 26.1 1.0
O A:ARG1737 4.6 16.7 1.0
N A:HIS1741 4.7 16.1 1.0
O A:HOH2283 4.8 35.5 1.0
HE2 A:HIS1741 4.9 27.2 1.0
CG A:PRO1818 4.9 27.6 1.0
O A:HOH2066 5.0 25.1 1.0

Zinc binding site 5 out of 7 in 8pbt

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Zinc binding site 5 out of 7 in the Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1907

b:17.8
occ:1.00
 O A:HOH2104 1.9 18.0 1.0
NE2 A:HIS1473 2.0 15.6 1.0
NE2 A:HIS1471 2.0 16.6 1.0
OD1 A:ASP1686 2.1 18.6 1.0
OQ2 A:KCX1556 2.2 17.3 1.0
CE1 A:HIS1473 2.9 16.2 1.0
CE1 A:HIS1471 3.0 17.6 1.0
CD2 A:HIS1471 3.0 16.8 1.0
CG A:ASP1686 3.0 17.8 1.0
H51 A:DOR1902 3.1 28.6 1.0
CD2 A:HIS1473 3.1 15.3 1.0
HE1 A:HIS1473 3.1 19.5 1.0
CX A:KCX1556 3.1 17.3 1.0
HD2 A:HIS1471 3.2 20.2 1.0
HE1 A:HIS1471 3.2 21.1 1.0
HD2 A:HIS1473 3.3 18.4 1.0
ZN A:ZN1904 3.4 17.7 1.0
HG3 A:MET1503 3.4 21.4 1.0
OD2 A:ASP1686 3.4 18.6 1.0
OQ1 A:KCX1556 3.5 16.6 1.0
H6 A:DOR1902 3.5 26.6 1.0
HD2 A:HIS1614 3.8 18.9 1.0
C5 A:DOR1902 3.9 23.8 1.0
HH A:TYR1558 4.0 23.9 1.0
ND1 A:HIS1473 4.1 17.0 1.0
ND1 A:HIS1471 4.1 17.8 1.0
HA A:ASP1686 4.1 20.0 1.0
CG A:HIS1471 4.1 16.4 1.0
CG A:HIS1473 4.2 16.5 1.0
NZ A:KCX1556 4.2 17.2 1.0
C4 A:DOR1902 4.2 22.7 1.0
CB A:ASP1686 4.3 17.1 1.0
C6 A:DOR1902 4.3 22.2 1.0
CG A:MET1503 4.4 17.9 1.0
HE1 A:TYR1558 4.4 22.1 1.0
HZ A:KCX1556 4.4 20.6 1.0
NE2 A:HIS1614 4.4 15.9 1.0
CD2 A:HIS1614 4.4 15.8 1.0
O4 A:DOR1902 4.4 23.6 1.0
HB2 A:ASP1686 4.5 20.6 1.0
HE3 A:MET1503 4.6 22.3 1.0
H52 A:DOR1902 4.7 28.6 1.0
CA A:ASP1686 4.7 16.7 1.0
HG2 A:MET1503 4.8 21.4 1.0
OH A:TYR1558 4.8 19.9 1.0
HB2 A:MET1503 4.8 19.4 1.0
HD1 A:HIS1473 4.8 20.4 1.0
HB2 A:ALA1688 4.9 22.1 1.0
N3 A:DOR1902 4.9 22.5 1.0
HB3 A:MET1503 4.9 19.4 1.0

Zinc binding site 6 out of 7 in 8pbt

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Zinc binding site 6 out of 7 in the Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1908

b:32.9
occ:0.53
 OD2 A:ASP1753 1.9 31.8 1.0
O A:HOH2253 2.1 46.4 1.0
O A:HOH2247 2.4 42.8 1.0
HE1 A:HIS1756 2.4 59.6 1.0
ND1 A:HIS1756 2.7 48.9 1.0
CE1 A:HIS1756 2.8 49.7 1.0
CG A:ASP1753 2.8 30.8 1.0
OD1 A:ASP1753 3.1 30.8 1.0
HH11 A:ARG1784 3.5 36.3 1.0
HH12 A:ARG1784 3.6 36.3 1.0
NH1 A:ARG1784 3.8 30.2 1.0
CG A:HIS1756 4.0 47.6 1.0
NE2 A:HIS1756 4.1 49.7 1.0
CB A:ASP1753 4.2 28.8 1.0
HB2 A:ASP1753 4.3 34.5 1.0
HB2 A:HIS1756 4.5 53.6 1.0
HB3 A:ASP1753 4.5 34.5 1.0
HE2 A:HIS1756 4.6 59.6 1.0
CD2 A:HIS1756 4.7 48.7 1.0
HD3 A:ARG1784 4.7 33.2 1.0
CB A:GLU1755 4.7 38.5 1.0
HD21 A:LEU1461 4.8 44.2 1.0
H A:GLU1755 4.9 43.2 1.0
CB A:HIS1756 4.9 44.6 1.0
CZ A:ARG1784 5.0 30.2 1.0

Zinc binding site 7 out of 7 in 8pbt

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Zinc binding site 7 out of 7 in the Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Mutant K1482M of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Dihydroorotate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1909

b:53.2
occ:1.00
 O A:ALA1816 2.2 19.9 1.0
O2 A:FMT1915 2.2 24.9 1.0
O A:HOH2097 2.2 33.3 1.0
O A:HOH2172 2.3 28.8 1.0
O A:GLN1814 2.5 23.8 1.0
C A:FMT1915 3.2 23.9 1.0
HD3 A:PRO1818 3.2 31.3 1.0
C A:GLN1814 3.3 23.7 1.0
C A:ALA1816 3.4 20.4 1.0
H A:FMT1915 3.4 28.6 1.0
H A:ALA1816 3.6 25.1 1.0
N A:ALA1816 3.6 20.9 1.0
HA A:GLN1814 3.8 31.4 1.0
HG3 A:PRO1818 3.8 33.1 1.0
HA2 A:GLY1815 3.8 24.7 1.0
O A:HOH2190 3.9 40.0 1.0
C A:GLY1815 3.9 20.6 1.0
N A:GLY1815 4.0 22.8 1.0
HA A:VAL1817 4.1 26.6 1.0
CA A:ALA1816 4.1 21.8 1.0
O A:HOH2282 4.1 42.0 1.0
CA A:GLY1815 4.1 20.6 1.0
CD A:PRO1818 4.1 26.1 1.0
CA A:GLN1814 4.2 26.2 0.6
CA A:GLN1814 4.2 25.2 0.4
HB3 A:ALA1816 4.2 28.8 1.0
HB3 A:HIS1741 4.3 21.2 1.0
O1 A:FMT1915 4.3 21.4 1.0
O2 A:FMT1914 4.4 26.5 1.0
N A:VAL1817 4.4 21.1 1.0
CG A:PRO1818 4.4 27.6 1.0
O A:PRO1813 4.6 29.8 1.0
CA A:VAL1817 4.6 22.2 1.0
O A:GLY1815 4.6 21.1 1.0
H A:GLY1815 4.7 27.4 1.0
CB A:ALA1816 4.7 24.0 1.0
N A:PRO1818 4.8 23.8 1.0
HD2 A:PRO1818 4.8 31.3 1.0
HB3 A:GLN1814 4.8 34.8 0.6
HG2 A:PRO1818 4.9 33.1 1.0
HB2 A:GLN1814 4.9 30.9 0.4
HA A:ALA1816 4.9 26.2 1.0
O A:HIS1741 4.9 18.5 1.0
C A:VAL1817 5.0 22.6 1.0

Reference:

F.Del Cano-Ochoa, B.G.Ng, A.Rubio-Del-Campo, S.Mahajan, M.P.Wilson, M.Vilar, D.Rymen, P.Sanchez-Pintos, J.Kenny, M.Ley Martos, T.Campos, S.B.Wortmann, H.H.Freeze, S.Ramon-Maiques. Beyond Genetics: Deciphering the Impact of Missense Variants in Cad Deficiency. J Inherit Metab Dis 2023.
ISSN: ISSN 1573-2665
PubMed: 37540500
DOI: 10.1002/JIMD.12667
Page generated: Thu Oct 31 09:24:27 2024

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