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Zinc in PDB 1j79: Molecular Structure of Dihydroorotase: A Paradigm For Catalysis Through the Use of A Binuclear Metal Center

Enzymatic activity of Molecular Structure of Dihydroorotase: A Paradigm For Catalysis Through the Use of A Binuclear Metal Center

All present enzymatic activity of Molecular Structure of Dihydroorotase: A Paradigm For Catalysis Through the Use of A Binuclear Metal Center:
3.5.2.3;

Protein crystallography data

The structure of Molecular Structure of Dihydroorotase: A Paradigm For Catalysis Through the Use of A Binuclear Metal Center, PDB code: 1j79 was solved by J.B.Thoden, G.N.Phillips Jr., T.M.Neal, F.M.Raushel, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.600, 78.800, 180.300, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 25.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Molecular Structure of Dihydroorotase: A Paradigm For Catalysis Through the Use of A Binuclear Metal Center (pdb code 1j79). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Molecular Structure of Dihydroorotase: A Paradigm For Catalysis Through the Use of A Binuclear Metal Center, PDB code: 1j79:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1j79

Go back to Zinc Binding Sites List in 1j79
Zinc binding site 1 out of 4 in the Molecular Structure of Dihydroorotase: A Paradigm For Catalysis Through the Use of A Binuclear Metal Center


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Molecular Structure of Dihydroorotase: A Paradigm For Catalysis Through the Use of A Binuclear Metal Center within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:22.0
occ:1.00
 O A:HOH1407 2.1 16.6 1.0
NE2 A:HIS18 2.1 15.4 1.0
NE2 A:HIS16 2.1 14.8 1.0
OQ2 A:KCX102 2.2 20.2 1.0
OD1 A:ASP250 2.3 18.7 1.0
CX A:KCX102 3.0 30.9 1.0
CE1 A:HIS18 3.0 16.2 1.0
CD2 A:HIS16 3.1 13.8 1.0
CE1 A:HIS16 3.1 18.6 1.0
CD2 A:HIS18 3.1 14.5 1.0
CG A:ASP250 3.1 17.4 1.0
OQ1 A:KCX102 3.3 20.7 1.0
ZN A:ZN401 3.5 29.0 1.0
OD2 A:ASP250 3.5 21.2 1.0
NZ A:KCX102 4.1 17.8 1.0
C4 A:ORO410 4.2 0.0 1.0
O4 A:ORO410 4.2 39.8 1.0
ND1 A:HIS18 4.2 15.1 1.0
C5 A:ORO410 4.2 30.4 1.0
ND1 A:HIS16 4.3 17.9 1.0
CG A:HIS18 4.3 13.4 1.0
CG A:HIS16 4.3 13.6 1.0
CD2 A:HIS177 4.3 19.4 1.0
NE2 A:HIS177 4.4 15.4 1.0
CB A:ASP250 4.4 13.5 1.0
C6 A:ORO410 4.5 29.0 1.0
CG A:MET42 4.5 10.7 1.0
OH A:TYR104 4.6 17.5 1.0
N3 A:ORO410 4.6 26.8 1.0
CA A:ASP250 4.8 11.5 1.0
CB A:MET42 5.0 13.2 1.0

Zinc binding site 2 out of 4 in 1j79

Go back to Zinc Binding Sites List in 1j79
Zinc binding site 2 out of 4 in the Molecular Structure of Dihydroorotase: A Paradigm For Catalysis Through the Use of A Binuclear Metal Center


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Molecular Structure of Dihydroorotase: A Paradigm For Catalysis Through the Use of A Binuclear Metal Center within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:29.0
occ:1.00
 OQ1 A:KCX102 2.0 20.7 1.0
NE2 A:HIS177 2.1 15.4 1.0
ND1 A:HIS139 2.2 22.9 1.0
O A:HOH1407 2.4 16.6 1.0
CE1 A:HIS139 2.9 22.7 1.0
O4 A:ORO410 2.9 39.8 1.0
CX A:KCX102 3.0 30.9 1.0
CE1 A:HIS177 3.0 17.0 1.0
CD2 A:HIS177 3.2 19.4 1.0
CG A:HIS139 3.2 25.3 1.0
OQ2 A:KCX102 3.4 20.2 1.0
ZN A:ZN400 3.5 22.0 1.0
CB A:HIS139 3.7 21.7 1.0
C4 A:ORO410 3.8 0.0 1.0
CE1 A:HIS16 4.0 18.6 1.0
NE2 A:HIS139 4.0 21.6 1.0
ND1 A:HIS177 4.2 19.4 1.0
NE2 A:HIS16 4.2 14.8 1.0
CD2 A:HIS139 4.2 26.6 1.0
CG A:HIS177 4.3 18.9 1.0
N3 A:ORO410 4.3 26.8 1.0
OD2 A:ASP250 4.3 21.2 1.0
NZ A:KCX102 4.3 17.8 1.0
CE2 A:TYR104 4.4 23.5 1.0
CE A:KCX102 4.5 27.0 1.0
CA A:HIS139 4.6 15.9 1.0
O A:LEU222 4.6 20.8 1.0
C5 A:ORO410 4.7 30.4 1.0
OD1 A:ASP250 4.9 18.7 1.0
CD A:PRO223 4.9 18.8 1.0
CG A:ASP250 4.9 17.4 1.0

Zinc binding site 3 out of 4 in 1j79

Go back to Zinc Binding Sites List in 1j79
Zinc binding site 3 out of 4 in the Molecular Structure of Dihydroorotase: A Paradigm For Catalysis Through the Use of A Binuclear Metal Center


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Molecular Structure of Dihydroorotase: A Paradigm For Catalysis Through the Use of A Binuclear Metal Center within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn400

b:30.1
occ:1.00
 NE2 B:HIS18 2.0 23.0 1.0
NE2 B:HIS16 2.2 20.3 1.0
OD1 B:ASP250 2.2 19.7 1.0
O4 B:NCD411 2.3 40.3 1.0
OQ2 B:KCX102 2.4 24.1 1.0
CD2 B:HIS16 3.0 18.8 1.0
CD2 B:HIS18 3.0 22.9 1.0
CE1 B:HIS18 3.0 23.4 1.0
CG B:ASP250 3.1 25.5 1.0
CX B:KCX102 3.1 30.9 1.0
C4 B:NCD411 3.1 40.9 1.0
CE1 B:HIS16 3.2 20.7 1.0
OQ1 B:KCX102 3.3 27.3 1.0
OD2 B:ASP250 3.5 19.5 1.0
ZN B:ZN401 3.7 36.0 1.0
O5 B:NCD411 3.9 40.1 1.0
C5 B:NCD411 4.0 25.2 1.0
CG B:HIS18 4.2 23.1 1.0
CG B:HIS16 4.2 18.6 1.0
ND1 B:HIS18 4.2 24.7 1.0
CB B:ASP250 4.3 18.3 1.0
ND1 B:HIS16 4.3 23.9 1.0
C6 B:NCD411 4.3 30.4 1.0
CG B:MET42 4.3 21.1 1.0
CD2 B:HIS177 4.4 18.1 1.0
NZ B:KCX102 4.4 52.1 1.0
NE2 B:HIS177 4.5 22.8 1.0
OH B:TYR104 4.6 24.2 1.0
N3 B:NCD411 4.6 26.4 1.0
CA B:ASP250 4.7 16.7 1.0

Zinc binding site 4 out of 4 in 1j79

Go back to Zinc Binding Sites List in 1j79
Zinc binding site 4 out of 4 in the Molecular Structure of Dihydroorotase: A Paradigm For Catalysis Through the Use of A Binuclear Metal Center


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Molecular Structure of Dihydroorotase: A Paradigm For Catalysis Through the Use of A Binuclear Metal Center within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:36.0
occ:1.00
 NE2 B:HIS177 2.1 22.8 1.0
OQ1 B:KCX102 2.2 27.3 1.0
O5 B:NCD411 2.2 40.1 1.0
ND1 B:HIS139 2.3 35.1 1.0
O4 B:NCD411 2.9 40.3 1.0
C4 B:NCD411 2.9 40.9 1.0
CE1 B:HIS177 3.0 19.3 1.0
CD2 B:HIS177 3.1 18.1 1.0
CE1 B:HIS139 3.2 33.1 1.0
CX B:KCX102 3.2 30.9 1.0
CG B:HIS139 3.3 30.3 1.0
OQ2 B:KCX102 3.7 24.1 1.0
CB B:HIS139 3.7 24.7 1.0
ZN B:ZN400 3.7 30.1 1.0
ND1 B:HIS177 4.2 24.1 1.0
CG B:HIS177 4.3 20.5 1.0
CE1 B:HIS16 4.3 20.7 1.0
NE2 B:HIS139 4.3 28.8 1.0
C5 B:NCD411 4.4 25.2 1.0
NE2 B:HIS16 4.4 20.3 1.0
CD2 B:HIS139 4.4 32.4 1.0
CE2 B:TYR104 4.4 40.9 1.0
NZ B:KCX102 4.5 52.1 1.0
N3 B:NCD411 4.5 26.4 1.0
OD2 B:ASP250 4.5 19.5 1.0
CE B:KCX102 4.5 27.2 1.0
CA B:HIS139 4.5 25.6 1.0
O B:LEU222 4.6 27.2 1.0
CD2 B:TYR104 4.9 36.9 1.0

Reference:

J.B.Thoden, G.N.Phillips Jr., T.M.Neal, F.M.Raushel, H.M.Holden. Molecular Structure of Dihydroorotase: A Paradigm For Catalysis Through the Use of A Binuclear Metal Center. Biochemistry V. 40 6989 2001.
ISSN: ISSN 0006-2960
PubMed: 11401542
DOI: 10.1021/BI010682I
Page generated: Sun Oct 13 03:24:06 2024

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