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Zinc in PDB 3jze: 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2

Enzymatic activity of 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2

All present enzymatic activity of 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2:
3.5.2.3;

Protein crystallography data

The structure of 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2, PDB code: 3jze was solved by G.Minasov, A.Halavaty, L.Shuvalova, I.Dubrovska, J.Winsor, L.Papazisi, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.83 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.437, 79.486, 180.610, 90.00, 90.35, 90.00
R / Rfree (%) 16.3 / 20.3

Other elements in 3jze:

The structure of 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2 (pdb code 3jze). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2, PDB code: 3jze:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3jze

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Zinc binding site 1 out of 8 in the 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:27.5
occ:0.75
OQ2 A:KCX103 2.0 27.0 1.0
O A:HOH419 2.0 17.6 1.0
NE2 A:HIS19 2.1 20.2 1.0
NE2 A:HIS17 2.1 22.6 1.0
OD1 A:ASP251 2.2 25.6 1.0
CX A:KCX103 3.0 28.2 1.0
CE1 A:HIS19 3.0 19.2 1.0
CD2 A:HIS17 3.1 20.8 1.0
CG A:ASP251 3.1 22.5 1.0
CE1 A:HIS17 3.1 22.8 1.0
CD2 A:HIS19 3.2 16.7 1.0
ZN A:ZN402 3.4 30.2 0.7
OQ1 A:KCX103 3.5 23.2 1.0
OD2 A:ASP251 3.6 25.6 1.0
NZ A:KCX103 4.0 20.0 1.0
ND1 A:HIS19 4.2 17.1 1.0
ND1 A:HIS17 4.2 21.5 1.0
CG A:HIS17 4.2 17.8 1.0
CB A:ASP251 4.2 20.5 1.0
CD2 A:HIS178 4.2 18.2 1.0
CG A:MET43 4.3 20.4 1.0
CG A:HIS19 4.3 14.2 1.0
NE2 A:HIS178 4.3 19.7 1.0
O A:HOH490 4.3 32.6 1.0
CH3 A:ACY423 4.3 38.5 1.0
CA A:ASP251 4.6 19.6 1.0
OH A:TYR105 4.6 20.1 1.0

Zinc binding site 2 out of 8 in 3jze

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Zinc binding site 2 out of 8 in the 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:30.2
occ:0.70
OQ1 A:KCX103 2.0 23.2 1.0
O A:HOH419 2.0 17.6 1.0
NE2 A:HIS178 2.1 19.7 1.0
ND1 A:HIS140 2.2 21.7 1.0
CX A:KCX103 2.8 28.2 1.0
CE1 A:HIS140 2.9 23.8 1.0
CE1 A:HIS178 3.0 20.4 1.0
OQ2 A:KCX103 3.1 27.0 1.0
CD2 A:HIS178 3.2 18.2 1.0
O A:HOH490 3.2 32.6 1.0
CG A:HIS140 3.3 21.1 1.0
ZN A:ZN401 3.4 27.5 0.8
CB A:HIS140 3.8 19.1 1.0
CE1 A:HIS17 4.0 22.8 1.0
NZ A:KCX103 4.1 20.0 1.0
NE2 A:HIS140 4.1 20.5 1.0
NE2 A:HIS17 4.2 22.6 1.0
ND1 A:HIS178 4.2 18.8 1.0
CG A:HIS178 4.3 16.0 1.0
CD2 A:HIS140 4.3 24.1 1.0
O A:LEU223 4.4 25.3 1.0
CE1 A:TYR105 4.5 16.6 1.0
OD2 A:ASP251 4.5 25.6 1.0
CA A:HIS140 4.5 19.1 1.0
CG2 A:THR110 4.6 29.7 1.0
CE A:KCX103 4.6 20.3 1.0
OD1 A:ASP251 4.7 25.6 1.0
CG A:ASP251 4.9 22.5 1.0

Zinc binding site 3 out of 8 in 3jze

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Zinc binding site 3 out of 8 in the 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:23.1
occ:0.75
OQ2 B:KCX103 2.0 24.5 1.0
O B:HOH1334 2.0 17.2 1.0
NE2 B:HIS17 2.1 25.9 1.0
NE2 B:HIS19 2.1 20.2 1.0
OD1 B:ASP251 2.2 26.6 1.0
CX B:KCX103 2.9 25.4 1.0
CE1 B:HIS17 3.1 23.9 1.0
CE1 B:HIS19 3.1 24.9 1.0
CD2 B:HIS19 3.1 22.0 1.0
CD2 B:HIS17 3.1 20.4 1.0
CG B:ASP251 3.1 23.9 1.0
O B:HOH371 3.2 28.6 0.5
OQ1 B:KCX103 3.2 19.4 1.0
ZN B:ZN404 3.5 26.7 0.7
OD2 B:ASP251 3.6 25.0 1.0
OXT B:ACY428 3.9 28.8 0.7
NZ B:KCX103 4.0 17.2 1.0
ND1 B:HIS17 4.2 21.1 1.0
CG B:MET43 4.2 17.6 1.0
ND1 B:HIS19 4.2 16.9 1.0
CG B:HIS17 4.2 19.3 1.0
CD2 B:HIS178 4.2 19.5 1.0
CG B:HIS19 4.3 18.7 1.0
CB B:ASP251 4.3 19.7 1.0
NE2 B:HIS178 4.3 17.7 1.0
O B:HOH435 4.4 23.5 1.0
C B:ACY428 4.5 31.5 0.7
OH B:TYR105 4.7 20.9 1.0
CA B:ASP251 4.7 19.8 1.0
O B:ACY428 4.8 32.5 0.7
CB B:MET43 4.9 15.5 1.0

Zinc binding site 4 out of 8 in 3jze

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Zinc binding site 4 out of 8 in the 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:26.7
occ:0.70
OQ1 B:KCX103 2.0 19.4 1.0
O B:HOH1334 2.1 17.2 1.0
NE2 B:HIS178 2.2 17.7 1.0
ND1 B:HIS140 2.2 19.8 1.0
OXT B:ACY428 2.2 28.8 0.7
O B:HOH435 2.4 23.5 1.0
CE1 B:HIS140 2.9 17.2 1.0
CX B:KCX103 3.0 25.4 1.0
CE1 B:HIS178 3.1 19.5 1.0
CD2 B:HIS178 3.1 19.5 1.0
C B:ACY428 3.2 31.5 0.7
OQ2 B:KCX103 3.3 24.5 1.0
CG B:HIS140 3.3 16.4 1.0
ZN B:ZN403 3.5 23.1 0.8
O B:ACY428 3.6 32.5 0.7
CB B:HIS140 3.9 15.9 1.0
NE2 B:HIS140 4.1 16.9 1.0
NZ B:KCX103 4.2 17.2 1.0
ND1 B:HIS178 4.2 19.0 1.0
CE1 B:HIS17 4.3 23.9 1.0
CG B:HIS178 4.3 15.1 1.0
CD2 B:HIS140 4.3 17.4 1.0
OD2 B:ASP251 4.4 25.0 1.0
NE2 B:HIS17 4.4 25.9 1.0
O B:LEU223 4.4 24.7 1.0
O B:HOH371 4.5 28.6 0.5
CE1 B:TYR105 4.5 20.9 1.0
CH3 B:ACY428 4.5 32.5 0.7
O B:HOH658 4.7 40.9 1.0
CE B:KCX103 4.7 21.0 1.0
OD1 B:ASP251 4.8 26.6 1.0
CA B:HIS140 4.8 15.2 1.0
CG B:ASP251 4.9 23.9 1.0

Zinc binding site 5 out of 8 in 3jze

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Zinc binding site 5 out of 8 in the 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn405

b:24.6
occ:0.75
OQ2 C:KCX103 2.0 23.0 1.0
O C:HOH1333 2.1 23.5 1.0
NE2 C:HIS19 2.1 21.8 1.0
NE2 C:HIS17 2.1 17.3 1.0
OD1 C:ASP251 2.2 21.4 1.0
CX C:KCX103 3.0 29.1 1.0
CE1 C:HIS19 3.0 22.5 1.0
CD2 C:HIS17 3.0 21.3 1.0
CG C:ASP251 3.2 24.0 1.0
CD2 C:HIS19 3.2 19.4 1.0
CE1 C:HIS17 3.2 22.5 1.0
ZN C:ZN406 3.4 30.0 0.7
OQ1 C:KCX103 3.5 28.2 1.0
OD2 C:ASP251 3.6 25.9 1.0
NZ C:KCX103 4.0 24.5 1.0
ND1 C:HIS19 4.2 17.8 1.0
CG C:HIS17 4.2 19.4 1.0
ND1 C:HIS17 4.3 20.8 1.0
CG C:HIS19 4.3 16.3 1.0
CG C:MET43 4.3 22.8 1.0
CD2 C:HIS178 4.3 24.2 1.0
CB C:ASP251 4.3 19.3 1.0
CH3 C:ACY424 4.4 38.6 1.0
NE2 C:HIS178 4.4 28.7 1.0
O C:HOH511 4.5 39.3 1.0
OH C:TYR105 4.6 18.3 1.0
CA C:ASP251 4.7 20.2 1.0

Zinc binding site 6 out of 8 in 3jze

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Zinc binding site 6 out of 8 in the 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn406

b:30.0
occ:0.65
O C:HOH1333 1.9 23.5 1.0
OQ1 C:KCX103 2.0 28.2 1.0
NE2 C:HIS178 2.1 28.7 1.0
ND1 C:HIS140 2.2 24.8 1.0
CX C:KCX103 2.9 29.1 1.0
CE1 C:HIS140 3.0 28.3 1.0
CD2 C:HIS178 3.1 24.2 1.0
CE1 C:HIS178 3.1 24.8 1.0
OQ2 C:KCX103 3.1 23.0 1.0
CG C:HIS140 3.3 23.7 1.0
O C:HOH511 3.4 39.3 1.0
ZN C:ZN405 3.4 24.6 0.8
CB C:HIS140 3.7 22.4 1.0
CE1 C:HIS17 4.0 22.5 1.0
NE2 C:HIS17 4.1 17.3 1.0
NZ C:KCX103 4.1 24.5 1.0
NE2 C:HIS140 4.2 24.1 1.0
ND1 C:HIS178 4.2 23.3 1.0
CG C:HIS178 4.2 20.8 1.0
CD2 C:HIS140 4.3 26.6 1.0
CE1 C:TYR105 4.4 16.6 1.0
OD2 C:ASP251 4.4 25.9 1.0
CA C:HIS140 4.5 21.6 1.0
O C:LEU223 4.5 23.7 1.0
CG2 C:THR110 4.6 32.6 1.0
CE C:KCX103 4.6 23.2 1.0
OD1 C:ASP251 4.7 21.4 1.0
CG C:ASP251 4.8 24.0 1.0
CD1 C:TYR105 5.0 18.9 1.0

Zinc binding site 7 out of 8 in 3jze

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Zinc binding site 7 out of 8 in the 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn407

b:23.6
occ:0.80
O D:HOH925 1.9 18.6 1.0
OQ2 D:KCX103 2.0 26.3 1.0
NE2 D:HIS17 2.1 20.0 1.0
NE2 D:HIS19 2.2 21.3 1.0
OD1 D:ASP251 2.2 22.8 1.0
CX D:KCX103 2.9 24.9 1.0
CE1 D:HIS17 3.1 20.7 1.0
CD2 D:HIS19 3.1 21.5 1.0
CD2 D:HIS17 3.1 14.5 1.0
CE1 D:HIS19 3.1 17.6 1.0
CG D:ASP251 3.2 21.4 1.0
OQ1 D:KCX103 3.3 25.7 1.0
ZN D:ZN408 3.4 27.5 0.7
OD2 D:ASP251 3.7 27.5 1.0
NZ D:KCX103 4.0 22.5 1.0
O D:ACY427 4.1 31.1 0.7
ND1 D:HIS17 4.2 19.0 1.0
CD2 D:HIS178 4.2 18.5 1.0
CG D:MET43 4.2 18.9 1.0
CG D:HIS17 4.2 16.9 1.0
ND1 D:HIS19 4.2 16.5 1.0
CG D:HIS19 4.3 18.6 1.0
NE2 D:HIS178 4.3 20.3 1.0
CB D:ASP251 4.4 16.8 1.0
C D:ACY427 4.4 32.1 0.7
O D:HOH435 4.5 32.7 1.0
OH D:TYR105 4.6 19.1 1.0
CA D:ASP251 4.7 15.3 1.0
CH3 D:ACY427 4.7 33.2 0.7
OXT D:ACY427 4.9 33.5 0.7
CB D:MET43 5.0 17.9 1.0

Zinc binding site 8 out of 8 in 3jze

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Zinc binding site 8 out of 8 in the 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn408

b:27.5
occ:0.65
O D:HOH925 1.9 18.6 1.0
OQ1 D:KCX103 2.0 25.7 1.0
NE2 D:HIS178 2.2 20.3 1.0
ND1 D:HIS140 2.2 16.6 1.0
O D:ACY427 2.2 31.1 0.7
O D:HOH435 2.3 32.7 1.0
CE1 D:HIS140 2.9 16.9 1.0
CX D:KCX103 3.0 24.9 1.0
CE1 D:HIS178 3.1 15.8 1.0
CD2 D:HIS178 3.1 18.5 1.0
C D:ACY427 3.2 32.1 0.7
CG D:HIS140 3.3 18.9 1.0
OQ2 D:KCX103 3.4 26.3 1.0
ZN D:ZN407 3.4 23.6 0.8
OXT D:ACY427 3.6 33.5 0.7
CB D:HIS140 3.9 16.6 1.0
NE2 D:HIS140 4.1 15.5 1.0
NZ D:KCX103 4.2 22.5 1.0
ND1 D:HIS178 4.2 17.8 1.0
CE1 D:HIS17 4.2 20.7 1.0
CG D:HIS178 4.3 11.6 1.0
CD2 D:HIS140 4.3 17.3 1.0
CH3 D:ACY427 4.4 33.2 0.7
CE1 D:TYR105 4.4 18.4 1.0
NE2 D:HIS17 4.4 20.0 1.0
OD2 D:ASP251 4.5 27.5 1.0
O D:LEU223 4.6 22.8 1.0
OD1 D:ASP251 4.6 22.8 1.0
CE D:KCX103 4.7 22.3 1.0
O D:HOH671 4.8 39.8 1.0
CA D:HIS140 4.8 15.8 1.0
CG D:ASP251 4.9 21.4 1.0
CD1 D:TYR105 4.9 19.5 1.0

Reference:

G.Minasov, A.Halavaty, L.Shuvalova, I.Dubrovska, J.Winsor, L.Papazisi, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (Pyrc) From Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. LT2. To Be Published.
Page generated: Wed Dec 16 04:29:15 2020

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