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Zinc in PDB 3sfw: Crystal Structure of Dihydropyrimidinase From Brevibacillus Agri NCHU1002

Enzymatic activity of Crystal Structure of Dihydropyrimidinase From Brevibacillus Agri NCHU1002

All present enzymatic activity of Crystal Structure of Dihydropyrimidinase From Brevibacillus Agri NCHU1002:
3.5.2.2;

Protein crystallography data

The structure of Crystal Structure of Dihydropyrimidinase From Brevibacillus Agri NCHU1002, PDB code: 3sfw was solved by W.C.Wang, H.M.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.73
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 65.807, 109.112, 140.984, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 19

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Dihydropyrimidinase From Brevibacillus Agri NCHU1002 (pdb code 3sfw). 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 Dihydropyrimidinase From Brevibacillus Agri NCHU1002, PDB code: 3sfw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3sfw

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Zinc binding site 1 out of 4 in the Crystal Structure of Dihydropyrimidinase From Brevibacillus Agri NCHU1002


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 Dihydropyrimidinase From Brevibacillus Agri NCHU1002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:15.9
occ:1.00
OQ1 A:KCX150 2.1 8.8 1.0
O A:HOH732 2.1 15.5 1.0
NE2 A:HIS239 2.2 10.0 1.0
ND1 A:HIS183 2.2 11.9 1.0
O A:HOH866 2.2 18.5 1.0
CE1 A:HIS183 3.0 14.5 1.0
CX A:KCX150 3.0 12.2 1.0
CD2 A:HIS239 3.1 9.7 1.0
CE1 A:HIS239 3.2 10.1 1.0
OQ2 A:KCX150 3.3 10.2 1.0
CG A:HIS183 3.3 10.8 1.0
ZN A:ZN502 3.4 14.9 1.0
CB A:HIS183 3.8 9.6 1.0
OH A:TYR155 4.1 19.2 1.0
NE2 A:HIS183 4.2 10.3 1.0
O A:SER288 4.2 13.4 1.0
NZ A:KCX150 4.2 10.1 1.0
CG A:HIS239 4.3 9.3 1.0
ND1 A:HIS239 4.3 10.4 1.0
CE2 A:PHE152 4.4 11.9 1.0
OD2 A:ASP315 4.4 10.6 1.0
CD2 A:HIS183 4.4 12.2 1.0
CG2 A:VAL238 4.5 9.1 1.0
CE2 A:TYR155 4.5 16.3 1.0
NE2 A:HIS58 4.5 9.3 1.0
CE1 A:HIS58 4.6 10.7 1.0
OD1 A:ASP315 4.7 11.4 1.0
CA A:HIS183 4.8 9.2 1.0
CD2 A:PHE152 4.8 10.7 1.0
CE A:KCX150 4.8 8.2 1.0
CG A:ASP315 4.8 11.8 1.0
CZ A:TYR155 4.8 17.8 1.0

Zinc binding site 2 out of 4 in 3sfw

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Zinc binding site 2 out of 4 in the Crystal Structure of Dihydropyrimidinase From Brevibacillus Agri NCHU1002


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 Dihydropyrimidinase From Brevibacillus Agri NCHU1002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:14.9
occ:1.00
OQ2 A:KCX150 2.0 10.2 1.0
NE2 A:HIS60 2.1 10.7 1.0
OD1 A:ASP315 2.1 11.4 1.0
NE2 A:HIS58 2.1 9.3 1.0
CE1 A:HIS60 3.0 10.9 1.0
CG A:ASP315 3.0 11.8 1.0
CX A:KCX150 3.1 12.2 1.0
CD2 A:HIS58 3.1 10.8 1.0
CD2 A:HIS60 3.1 10.1 1.0
CE1 A:HIS58 3.1 10.7 1.0
ZN A:ZN501 3.4 15.9 1.0
OQ1 A:KCX150 3.4 8.8 1.0
O A:HOH732 3.5 15.5 1.0
OD2 A:ASP315 3.6 10.6 1.0
ND1 A:HIS60 4.1 9.6 1.0
CB A:ASP315 4.2 11.0 1.0
NZ A:KCX150 4.2 10.1 1.0
O A:HOH866 4.2 18.5 1.0
CG A:HIS60 4.2 7.7 1.0
ND1 A:HIS58 4.2 10.0 1.0
CG A:HIS58 4.2 7.9 1.0
O A:HOH717 4.4 26.2 1.0
CD2 A:HIS239 4.4 9.7 1.0
CA A:ASP315 4.6 11.0 1.0
CE1 A:PHE92 4.6 11.2 1.0
NE2 A:HIS239 4.6 10.0 1.0
CD1 A:PHE92 4.7 10.4 1.0

Zinc binding site 3 out of 4 in 3sfw

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Zinc binding site 3 out of 4 in the Crystal Structure of Dihydropyrimidinase From Brevibacillus Agri NCHU1002


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 Dihydropyrimidinase From Brevibacillus Agri NCHU1002 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:18.3
occ:1.00
OQ1 B:KCX150 2.1 10.1 1.0
O B:HOH500 2.1 18.1 1.0
ND1 B:HIS183 2.2 15.0 1.0
O B:HOH586 2.2 19.9 1.0
NE2 B:HIS239 2.2 11.5 1.0
CE1 B:HIS183 3.0 13.6 1.0
CX B:KCX150 3.0 14.0 1.0
CD2 B:HIS239 3.1 12.7 1.0
CE1 B:HIS239 3.2 12.6 1.0
OQ2 B:KCX150 3.3 12.8 1.0
CG B:HIS183 3.3 11.3 1.0
ZN B:ZN504 3.4 18.8 1.0
CB B:HIS183 3.7 13.5 1.0
OH B:TYR155 4.2 23.5 1.0
NE2 B:HIS183 4.2 13.6 1.0
O B:SER288 4.2 13.3 1.0
NZ B:KCX150 4.2 13.2 1.0
CG B:HIS239 4.3 11.6 1.0
ND1 B:HIS239 4.3 11.6 1.0
CE2 B:PHE152 4.3 15.0 1.0
CD2 B:HIS183 4.4 13.8 1.0
OD2 B:ASP315 4.4 13.8 1.0
CG2 B:VAL238 4.4 12.9 1.0
CE2 B:TYR155 4.5 20.3 1.0
NE2 B:HIS58 4.6 13.9 1.0
CE1 B:HIS58 4.6 12.8 1.0
OD1 B:ASP315 4.6 12.4 1.0
CA B:HIS183 4.7 11.1 1.0
CD2 B:PHE152 4.7 13.6 1.0
CE B:KCX150 4.8 11.7 1.0
CG B:ASP315 4.8 11.6 1.0
CZ B:TYR155 4.9 20.6 1.0

Zinc binding site 4 out of 4 in 3sfw

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Zinc binding site 4 out of 4 in the Crystal Structure of Dihydropyrimidinase From Brevibacillus Agri NCHU1002


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 Dihydropyrimidinase From Brevibacillus Agri NCHU1002 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:18.8
occ:1.00
OQ2 B:KCX150 2.0 12.8 1.0
OD1 B:ASP315 2.1 12.4 1.0
NE2 B:HIS60 2.1 10.3 1.0
NE2 B:HIS58 2.2 13.9 1.0
CX B:KCX150 3.0 14.0 1.0
CE1 B:HIS60 3.0 13.7 1.0
CG B:ASP315 3.1 11.6 1.0
CD2 B:HIS60 3.1 14.9 1.0
CD2 B:HIS58 3.2 11.6 1.0
CE1 B:HIS58 3.2 12.8 1.0
O B:HOH500 3.4 18.1 1.0
ZN B:ZN503 3.4 18.3 1.0
OQ1 B:KCX150 3.4 10.1 1.0
OD2 B:ASP315 3.6 13.8 1.0
NZ B:KCX150 4.1 13.2 1.0
ND1 B:HIS60 4.1 13.1 1.0
CB B:ASP315 4.2 13.1 1.0
O B:HOH586 4.2 19.9 1.0
CG B:HIS60 4.2 12.2 1.0
ND1 B:HIS58 4.3 12.8 1.0
CG B:HIS58 4.3 12.7 1.0
O B:HOH595 4.4 22.0 1.0
CD2 B:HIS239 4.5 12.7 1.0
CA B:ASP315 4.5 12.6 1.0
NE2 B:HIS239 4.6 11.5 1.0
CE1 B:PHE92 4.7 16.0 1.0
CD1 B:PHE92 4.8 16.1 1.0

Reference:

W.C.Wang, H.M.Wu. Crystal Structure of Dihydropyrimidinase From Brevibacillus Agri NCHU1002 To Be Published.
Page generated: Wed Dec 16 04:50:07 2020

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