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Zinc in PDB 6hff: Human Dihydroorotase Mutant F1563Y Apo Structure

Enzymatic activity of Human Dihydroorotase Mutant F1563Y Apo Structure

All present enzymatic activity of Human Dihydroorotase Mutant F1563Y Apo Structure:
2.1.3.2; 3.5.2.3; 6.3.5.5;

Protein crystallography data

The structure of Human Dihydroorotase Mutant F1563Y Apo Structure, PDB code: 6hff 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) 33.34 / 1.51
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 81.730, 159.200, 61.060, 90.00, 90.00, 90.00
R / Rfree (%) 12.6 / 15.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Dihydroorotase Mutant F1563Y Apo Structure (pdb code 6hff). 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 F1563Y Apo Structure, PDB code: 6hff:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6hff

Go back to Zinc Binding Sites List in 6hff
Zinc binding site 1 out of 4 in the Human Dihydroorotase Mutant F1563Y Apo Structure


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 F1563Y Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1901

b:18.6
occ:0.81
OQ1 A:KCX1556 1.9 22.4 1.0
O A:HOH2158 1.9 21.7 1.0
NE2 A:HIS1614 2.0 19.9 1.0
ND1 A:HIS1590 2.0 20.2 1.0
CX A:KCX1556 2.9 23.6 1.0
CE1 A:HIS1590 2.9 22.2 1.0
HB2 A:HIS1590 2.9 19.9 1.0
CE1 A:HIS1614 3.0 21.7 1.0
CD2 A:HIS1614 3.0 19.6 1.0
HE1 A:HIS1590 3.1 26.6 1.0
CG A:HIS1590 3.1 19.5 1.0
HE1 A:HIS1471 3.1 23.2 1.0
HE1 A:HIS1614 3.1 26.1 1.0
HD2 A:HIS1614 3.2 23.6 1.0
OQ2 A:KCX1556 3.2 23.6 1.0
HE1 A:TYR1558 3.3 28.9 0.4
ZN A:ZN1902 3.3 18.4 0.8
CB A:HIS1590 3.5 16.6 1.0
CE1 A:HIS1471 3.8 19.3 1.0
CE1 A:TYR1558 3.9 24.1 0.4
O A:HOH2259 4.0 62.9 1.0
NE2 A:HIS1471 4.0 18.1 1.0
NE2 A:HIS1590 4.0 22.2 1.0
HE1 A:TYR1558 4.1 22.7 0.6
ND1 A:HIS1614 4.1 21.1 1.0
NZ A:KCX1556 4.1 23.0 1.0
CG A:HIS1614 4.1 18.9 1.0
OD2 A:ASP1686 4.1 23.6 1.0
CD2 A:HIS1590 4.1 21.2 1.0
HB3 A:HIS1590 4.2 19.9 1.0
HA A:HIS1590 4.2 18.3 1.0
HE2 A:KCX1556 4.2 24.4 1.0
HD3 A:PRO1662 4.3 25.5 1.0
HB2 A:CYS1613 4.3 24.7 1.0
HB3 A:CYS1613 4.4 24.7 1.0
HD1 A:TYR1558 4.5 28.0 0.4
CA A:HIS1590 4.5 15.3 1.0
CD1 A:TYR1558 4.5 23.4 0.4
CE A:KCX1556 4.6 20.3 1.0
HE3 A:KCX1556 4.6 24.4 1.0
OH A:TYR1558 4.6 28.6 0.4
CZ A:TYR1558 4.6 26.5 0.4
O A:ARG1661 4.6 27.4 1.0
OD1 A:ASP1686 4.6 22.5 1.0
CG A:ASP1686 4.7 22.6 1.0
HD1 A:TYR1558 4.7 21.6 0.6
HZ A:KCX1556 4.7 27.6 1.0
CE1 A:TYR1558 4.7 18.9 0.6
CB A:CYS1613 4.8 20.6 1.0

Zinc binding site 2 out of 4 in 6hff

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Zinc binding site 2 out of 4 in the Human Dihydroorotase Mutant F1563Y Apo Structure


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 F1563Y Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1902

b:18.4
occ:0.82
NE2 A:HIS1471 2.0 18.1 1.0
NE2 A:HIS1473 2.0 19.8 1.0
O A:HOH2158 2.0 21.7 1.0
OQ2 A:KCX1556 2.2 23.6 1.0
OD1 A:ASP1686 2.3 22.5 1.0
CE1 A:HIS1473 2.9 21.0 1.0
CE1 A:HIS1471 2.9 19.3 1.0
CD2 A:HIS1471 3.0 18.2 1.0
CX A:KCX1556 3.0 23.6 1.0
HE1 A:HIS1473 3.1 25.1 1.0
CD2 A:HIS1473 3.1 20.0 1.0
HE1 A:HIS1471 3.1 23.2 1.0
CG A:ASP1686 3.2 22.6 1.0
HD2 A:HIS1471 3.2 21.8 1.0
ZN A:ZN1901 3.3 18.6 0.8
HD2 A:HIS1473 3.3 24.0 1.0
OQ1 A:KCX1556 3.4 22.4 1.0
HG3 A:MET1503 3.4 25.1 1.0
OD2 A:ASP1686 3.5 23.6 1.0
HD2 A:HIS1614 3.9 23.6 1.0
ND1 A:HIS1471 4.1 20.8 1.0
ND1 A:HIS1473 4.1 21.6 1.0
CG A:HIS1471 4.1 17.6 1.0
HH A:TYR1558 4.1 19.7 0.6
O A:HOH2259 4.2 62.9 1.0
NZ A:KCX1556 4.2 23.0 1.0
HA A:ASP1686 4.2 23.4 1.0
CG A:HIS1473 4.2 20.9 1.0
HE1 A:TYR1558 4.3 22.7 0.6
CG A:MET1503 4.4 21.0 1.0
NE2 A:HIS1614 4.4 19.9 1.0
CD2 A:HIS1614 4.4 19.6 1.0
CB A:ASP1686 4.4 20.9 1.0
HZ A:KCX1556 4.5 27.6 1.0
HE3 A:MET1503 4.6 28.2 1.0
HB2 A:ASP1686 4.7 25.1 1.0
O1 A:FMT1908 4.7 58.6 1.0
HE1 A:TYR1558 4.7 28.9 0.4
CA A:ASP1686 4.8 19.5 1.0
HG2 A:MET1503 4.8 25.1 1.0
HB2 A:ALA1688 4.9 26.2 1.0
OH A:TYR1558 4.9 16.4 0.6
HB2 A:MET1503 4.9 23.0 1.0

Zinc binding site 3 out of 4 in 6hff

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Zinc binding site 3 out of 4 in the Human Dihydroorotase Mutant F1563Y Apo Structure


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 F1563Y Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1903

b:19.3
occ:0.27
O A:HOH2137 2.1 23.6 1.0
ND1 A:HIS1471 2.1 20.8 1.0
OE1 A:GLU1637 2.2 22.9 1.0
SG A:CYS1613 2.4 22.4 1.0
HB3 A:CYS1613 2.7 24.7 1.0
CD A:GLU1637 2.8 21.4 1.0
OE2 A:GLU1637 2.9 21.5 1.0
HB2 A:HIS1471 2.9 20.0 1.0
CB A:CYS1613 3.0 20.6 1.0
CE1 A:HIS1471 3.0 19.3 1.0
CG A:HIS1471 3.1 17.6 1.0
HE3 A:MET1503 3.1 28.2 1.0
HE1 A:HIS1471 3.1 23.2 1.0
HA A:CYS1613 3.2 22.2 1.0
HG11 A:VAL1588 3.2 24.3 0.3
CB A:HIS1471 3.5 16.7 1.0
HE1 A:MET1503 3.6 28.2 1.0
CA A:CYS1613 3.7 18.5 1.0
CE A:MET1503 3.7 23.5 1.0
HG13 A:VAL1588 3.8 24.3 0.3
HB2 A:CYS1613 3.8 24.7 1.0
CG1 A:VAL1588 3.9 20.3 0.3
HE2 A:MET1503 3.9 28.2 1.0
H A:HIS1614 4.1 23.3 1.0
HD2 A:HIS1611 4.1 18.6 1.0
HB3 A:HIS1471 4.1 20.0 1.0
HG12 A:VAL1588 4.1 24.3 0.3
NE2 A:HIS1471 4.1 18.1 1.0
CD2 A:HIS1471 4.2 18.2 1.0
CG A:GLU1637 4.2 21.1 1.0
HG21 A:VAL1588 4.2 20.0 0.7
HB A:VAL1588 4.2 18.9 0.7
HG2 A:GLU1637 4.3 25.3 1.0
HG23 A:VAL1470 4.3 24.4 1.0
HA A:HIS1471 4.4 19.1 1.0
HG3 A:GLU1637 4.5 25.3 1.0
O A:VAL1470 4.5 18.1 1.0
CA A:HIS1471 4.6 15.9 1.0
N A:CYS1613 4.6 15.5 1.0
O A:HOH2171 4.6 32.9 1.0
N A:HIS1614 4.7 19.4 1.0
C A:CYS1613 4.7 19.0 1.0
CD2 A:HIS1611 4.7 15.5 1.0
HE2 A:KCX1556 4.8 24.4 1.0
NE2 A:HIS1611 4.8 17.3 1.0
H A:CYS1613 4.8 18.6 1.0
HG23 A:VAL1588 4.8 20.0 0.7
CG2 A:VAL1588 4.8 16.7 0.7
HG11 A:VAL1588 4.9 22.4 0.7
HB3 A:ALA1684 4.9 24.1 1.0
HG21 A:VAL1588 4.9 24.5 0.3
HD2 A:HIS1614 5.0 23.6 1.0
CB A:VAL1588 5.0 15.7 0.7

Zinc binding site 4 out of 4 in 6hff

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Zinc binding site 4 out of 4 in the Human Dihydroorotase Mutant F1563Y Apo Structure


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 F1563Y Apo Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1904

b:35.1
occ:1.00
O A:HOH2248 2.1 59.7 1.0
NE2 A:HIS1734 2.2 19.2 1.0
O A:HOH2260 2.2 37.4 1.0
HE1 A:HIS1734 2.8 24.5 1.0
CE1 A:HIS1734 2.8 20.4 1.0
CD2 A:HIS1734 3.4 17.1 1.0
HD2 A:HIS1734 3.7 20.6 1.0
ND1 A:HIS1734 4.1 17.1 1.0
HD2 A:HIS1733 4.2 21.9 1.0
CG A:HIS1734 4.3 15.6 1.0
O A:HOH2146 4.4 45.8 1.0
HG3 A:PRO1465 4.6 30.1 1.0
O A:HOH2089 4.7 42.6 1.0
HB3 A:LEU1729 4.9 22.5 1.0
HE22 A:GLN1730 4.9 21.7 1.0
CD2 A:HIS1733 4.9 18.3 1.0
HD13 A:LEU1729 5.0 28.3 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 11:56:48 2020

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