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Zinc in PDB 6hfh: Human Dihydroorotase Mutant F1563A Co-Crystallized with Carbamoyl Aspartate at pH 7.0

Enzymatic activity of Human Dihydroorotase Mutant F1563A Co-Crystallized with Carbamoyl Aspartate at pH 7.0

All present enzymatic activity of Human Dihydroorotase Mutant F1563A Co-Crystallized with Carbamoyl Aspartate at pH 7.0:
2.1.3.2; 3.5.2.3; 6.3.5.5;

Protein crystallography data

The structure of Human Dihydroorotase Mutant F1563A Co-Crystallized with Carbamoyl Aspartate at pH 7.0, PDB code: 6hfh was solved by S.Ramon-Maiques, A.Grande Garcia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.01 / 1.45
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 82.026, 159.073, 61.591, 90.00, 90.00, 90.00
R / Rfree (%) 11.8 / 14.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Dihydroorotase Mutant F1563A Co-Crystallized with Carbamoyl Aspartate at pH 7.0 (pdb code 6hfh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human Dihydroorotase Mutant F1563A Co-Crystallized with Carbamoyl Aspartate at pH 7.0, PDB code: 6hfh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6hfh

Go back to Zinc Binding Sites List in 6hfh
Zinc binding site 1 out of 4 in the Human Dihydroorotase Mutant F1563A Co-Crystallized with Carbamoyl Aspartate at pH 7.0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Dihydroorotase Mutant F1563A Co-Crystallized with Carbamoyl Aspartate at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1901

b:12.8
occ:0.88
OQ1 A:KCX1556 1.9 13.1 1.0
O A:HOH2205 1.9 13.8 1.0
NE2 A:HIS1614 2.1 13.1 1.0
ND1 A:HIS1590 2.1 12.8 1.0
CX A:KCX1556 2.9 13.8 1.0
CE1 A:HIS1590 2.9 12.6 1.0
O4 A:DOR1908 3.0 18.2 0.8
HB2 A:HIS1590 3.0 12.9 1.0
CE1 A:HIS1614 3.0 13.7 1.0
HE1 A:HIS1590 3.0 15.2 1.0
CD2 A:HIS1614 3.1 12.8 1.0
CG A:HIS1590 3.1 11.6 1.0
HE1 A:HIS1614 3.2 16.5 1.0
HD2 A:HIS1614 3.3 15.4 1.0
OQ2 A:KCX1556 3.3 14.1 1.0
HE1 A:HIS1471 3.3 15.1 1.0
ZN A:ZN1902 3.4 13.2 1.0
CB A:HIS1590 3.6 10.8 1.0
C4 A:DOR1908 3.6 16.1 0.8
H52 A:DOR1908 3.8 20.4 0.8
HE1 A:TYR1558 3.9 18.2 1.0
CE1 A:HIS1471 3.9 12.6 1.0
NE2 A:HIS1590 4.1 13.6 1.0
NE2 A:HIS1471 4.1 10.8 1.0
ND1 A:HIS1614 4.1 12.7 1.0
NZ A:KCX1556 4.2 13.9 1.0
CD2 A:HIS1590 4.2 13.0 1.0
OD2 A:ASP1686 4.2 15.1 1.0
CG A:HIS1614 4.2 12.1 1.0
HD3 A:PRO1662 4.2 15.8 1.0
HB3 A:HIS1590 4.2 12.9 1.0
N3 A:DOR1908 4.3 17.8 0.8
HN3 A:DOR1908 4.3 21.4 0.8
C5 A:DOR1908 4.3 17.0 0.8
HA A:HIS1590 4.3 13.2 1.0
HE2 A:KCX1556 4.3 14.5 1.0
O A:ARG1661 4.5 16.6 1.0
CE1 A:TYR1558 4.5 15.1 1.0
HB3 A:CYS1613 4.6 15.9 1.0
CA A:HIS1590 4.6 11.0 1.0
HB2 A:CYS1613 4.6 15.9 1.0
CE A:KCX1556 4.6 12.1 1.0
HE3 A:KCX1556 4.6 14.5 1.0
HD1 A:TYR1558 4.6 17.8 1.0
OD1 A:ASP1686 4.7 13.1 1.0
CG A:ASP1686 4.7 13.6 1.0
HE2 A:HIS1590 4.8 16.3 1.0
HZ A:KCX1556 4.9 16.7 1.0
HD1 A:HIS1614 4.9 15.3 1.0
H51 A:DOR1908 4.9 20.4 0.8
CD1 A:TYR1558 5.0 14.8 1.0

Zinc binding site 2 out of 4 in 6hfh

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Zinc binding site 2 out of 4 in the Human Dihydroorotase Mutant F1563A Co-Crystallized with Carbamoyl Aspartate at pH 7.0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Dihydroorotase Mutant F1563A Co-Crystallized with Carbamoyl Aspartate at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1902

b:13.2
occ:0.96
O A:HOH2205 2.0 13.8 1.0
NE2 A:HIS1471 2.0 10.8 1.0
NE2 A:HIS1473 2.0 11.3 1.0
OQ2 A:KCX1556 2.2 14.1 1.0
OD1 A:ASP1686 2.2 13.1 1.0
CE1 A:HIS1473 3.0 13.5 1.0
CD2 A:HIS1471 3.0 11.5 1.0
CE1 A:HIS1471 3.0 12.6 1.0
CX A:KCX1556 3.0 13.8 1.0
H52 A:DOR1908 3.0 20.4 0.8
CD2 A:HIS1473 3.1 12.4 1.0
HE1 A:HIS1473 3.1 16.2 1.0
CG A:ASP1686 3.1 13.6 1.0
HD2 A:HIS1471 3.2 13.8 1.0
HE1 A:HIS1471 3.2 15.1 1.0
HD2 A:HIS1473 3.3 14.9 1.0
ZN A:ZN1901 3.4 12.8 0.9
OQ1 A:KCX1556 3.4 13.1 1.0
HG3 A:MET1503 3.4 16.1 1.0
OD2 A:ASP1686 3.5 15.1 1.0
H6 A:DOR1908 3.5 18.4 0.8
HD2 A:HIS1614 3.8 15.4 1.0
C5 A:DOR1908 3.9 17.0 0.8
HH A:TYR1558 4.0 18.2 1.0
ND1 A:HIS1473 4.1 13.3 1.0
ND1 A:HIS1471 4.1 13.1 1.0
CG A:HIS1471 4.1 11.6 1.0
HA A:ASP1686 4.1 12.9 1.0
CG A:HIS1473 4.2 12.0 1.0
NZ A:KCX1556 4.2 13.9 1.0
C6 A:DOR1908 4.3 15.3 0.8
C4 A:DOR1908 4.3 16.1 0.8
HE1 A:TYR1558 4.3 18.2 1.0
HZ A:KCX1556 4.4 16.7 1.0
CB A:ASP1686 4.4 12.7 1.0
CG A:MET1503 4.4 13.4 1.0
CD2 A:HIS1614 4.4 12.8 1.0
NE2 A:HIS1614 4.4 13.1 1.0
O4 A:DOR1908 4.5 18.2 0.8
HB2 A:ASP1686 4.5 15.3 1.0
HE3 A:MET1503 4.6 18.7 1.0
H51 A:DOR1908 4.7 20.4 0.8
OH A:TYR1558 4.7 15.1 1.0
CA A:ASP1686 4.8 10.7 1.0
HB2 A:ALA1688 4.8 16.0 1.0
HG2 A:MET1503 4.8 16.1 1.0
HD1 A:HIS1473 4.9 16.0 1.0
HB2 A:MET1503 4.9 15.0 1.0
HB3 A:MET1503 5.0 15.0 1.0
N3 A:DOR1908 5.0 17.8 0.8

Zinc binding site 3 out of 4 in 6hfh

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Zinc binding site 3 out of 4 in the Human Dihydroorotase Mutant F1563A Co-Crystallized with Carbamoyl Aspartate at pH 7.0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Dihydroorotase Mutant F1563A Co-Crystallized with Carbamoyl Aspartate at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1903

b:13.9
occ:0.45
ND1 A:HIS1471 2.1 13.1 1.0
O A:HOH2161 2.1 14.3 1.0
OE1 A:GLU1637 2.1 14.6 1.0
SG A:CYS1613 2.3 14.2 1.0
HB3 A:CYS1613 2.8 15.9 1.0
CD A:GLU1637 2.8 12.6 1.0
HB2 A:HIS1471 2.9 12.6 1.0
CE1 A:HIS1471 3.0 12.6 1.0
OE2 A:GLU1637 3.0 14.1 1.0
CB A:CYS1613 3.0 13.2 1.0
CG A:HIS1471 3.1 11.6 1.0
HE3 A:MET1503 3.1 18.7 1.0
HE1 A:HIS1471 3.1 15.1 1.0
HA A:CYS1613 3.2 14.8 1.0
CB A:HIS1471 3.5 10.5 1.0
HE1 A:MET1503 3.5 18.7 1.0
CE A:MET1503 3.7 15.6 1.0
CA A:CYS1613 3.7 12.3 1.0
HE2 A:MET1503 3.8 18.7 1.0
HB2 A:CYS1613 3.9 15.9 1.0
HB3 A:HIS1471 4.0 12.6 1.0
H A:HIS1614 4.0 14.6 1.0
NE2 A:HIS1471 4.1 10.8 1.0
CD2 A:HIS1471 4.1 11.5 1.0
HD2 A:HIS1611 4.2 12.9 1.0
CG A:GLU1637 4.2 12.1 1.0
HB A:VAL1588 4.2 15.2 1.0
HG21 A:VAL1588 4.2 18.7 1.0
HG23 A:VAL1470 4.3 15.0 1.0
HG2 A:GLU1637 4.3 14.5 1.0
HE2 A:HIS1611 4.4 14.7 1.0
O A:VAL1470 4.5 12.0 1.0
HA A:HIS1471 4.5 11.8 1.0
HG3 A:GLU1637 4.5 14.5 1.0
CA A:HIS1471 4.6 9.8 1.0
N A:HIS1614 4.6 12.2 1.0
N A:CYS1613 4.6 10.6 1.0
O A:HOH2257 4.7 19.7 1.0
C A:CYS1613 4.7 12.3 1.0
HE2 A:KCX1556 4.8 14.5 1.0
CD2 A:HIS1611 4.8 10.8 1.0
HG23 A:VAL1588 4.8 18.7 1.0
H A:CYS1613 4.8 12.7 1.0
CG2 A:VAL1588 4.9 15.6 1.0
HB3 A:ALA1684 4.9 16.7 1.0
NE2 A:HIS1611 4.9 12.3 1.0
HG11 A:VAL1588 4.9 15.4 1.0
CB A:VAL1588 5.0 12.7 1.0
HD2 A:KCX1556 5.0 15.7 1.0

Zinc binding site 4 out of 4 in 6hfh

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Zinc binding site 4 out of 4 in the Human Dihydroorotase Mutant F1563A Co-Crystallized with Carbamoyl Aspartate at pH 7.0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Dihydroorotase Mutant F1563A Co-Crystallized with Carbamoyl Aspartate at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1904

b:22.0
occ:1.00
O A:HOH2306 2.0 22.2 1.0
NE2 A:HIS1734 2.1 14.4 1.0
O A:HOH2304 2.2 13.3 1.0
CE1 A:HIS1734 2.8 15.0 1.0
HE1 A:HIS1734 2.8 18.0 1.0
CD2 A:HIS1734 3.3 13.2 1.0
HD2 A:HIS1734 3.6 15.8 1.0
ND1 A:HIS1734 4.0 12.0 1.0
HD2 A:HIS1733 4.1 15.1 1.0
CG A:HIS1734 4.3 11.6 1.0
O A:HOH2336 4.4 31.3 1.0
HG3 A:PRO1465 4.5 21.2 1.0
HB3 A:LEU1729 4.6 17.0 1.0
HD13 A:LEU1729 4.7 22.1 1.0
O A:HOH2078 4.7 34.7 1.0
HD1 A:HIS1734 4.7 14.4 1.0
CD2 A:HIS1733 4.8 12.6 1.0
HE22 A:GLN1730 5.0 15.1 1.0

Reference:

F.Del Cano-Ochoa, A.Grande-Garcia, M.Reverte-Lopez, M.D'abramo, S.Ramon-Maiques. Characterization of the Catalytic Flexible Loop in the Dihydroorotase Domain of the Human Multi-Enzymatic Protein Cad. J. Biol. Chem. V. 293 18903 2018.
ISSN: ESSN 1083-351X
PubMed: 30315107
DOI: 10.1074/JBC.RA118.005494
Page generated: Wed Dec 16 11:56:51 2020

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