Zinc in PDB 5vgm: Crystal Structure of Dihydroorotase Pyrc From Vibrio Cholerae in Complex with Zinc at 1.95 A Resolution.

Enzymatic activity of Crystal Structure of Dihydroorotase Pyrc From Vibrio Cholerae in Complex with Zinc at 1.95 A Resolution.

All present enzymatic activity of Crystal Structure of Dihydroorotase Pyrc From Vibrio Cholerae in Complex with Zinc at 1.95 A Resolution.:
3.5.2.3;

Protein crystallography data

The structure of Crystal Structure of Dihydroorotase Pyrc From Vibrio Cholerae in Complex with Zinc at 1.95 A Resolution., PDB code: 5vgm was solved by J.Lipowska, I.G.Shabalin, C.D.Miks, J.Winsor, D.R.Cooper, L.Shuvalova, K.Kwon, K.Lewinski, W.F.Anderson, W.Minor, Center For Structuralgenomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.507, 57.257, 87.524, 90.00, 105.09, 90.00
R / Rfree (%) 16.8 / 20.3

Other elements in 5vgm:

The structure of Crystal Structure of Dihydroorotase Pyrc From Vibrio Cholerae in Complex with Zinc at 1.95 A Resolution. also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Dihydroorotase Pyrc From Vibrio Cholerae in Complex with Zinc at 1.95 A Resolution. (pdb code 5vgm). 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 Dihydroorotase Pyrc From Vibrio Cholerae in Complex with Zinc at 1.95 A Resolution., PDB code: 5vgm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5vgm

Go back to Zinc Binding Sites List in 5vgm
Zinc binding site 1 out of 4 in the Crystal Structure of Dihydroorotase Pyrc From Vibrio Cholerae in Complex with Zinc at 1.95 A Resolution.


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 Dihydroorotase Pyrc From Vibrio Cholerae in Complex with Zinc at 1.95 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:59.6
occ:1.00
 OQ2 A:KCX98 1.9 70.4 1.0
O A:HOH536 2.0 79.9 1.0
NE2 A:HIS173 2.1 40.8 1.0
ND1 A:HIS135 2.1 53.6 1.0
CX A:KCX98 3.0 61.5 1.0
CE1 A:HIS135 3.0 55.2 1.0
CD2 A:HIS173 3.1 38.5 1.0
CE1 A:HIS173 3.1 42.2 1.0
CG A:HIS135 3.2 53.1 1.0
OQ1 A:KCX98 3.2 61.2 1.0
ZN A:ZN402 3.2 54.0 1.0
CB A:HIS135 3.6 49.9 1.0
CE1 A:HIS13 4.0 47.5 1.0
NZ A:KCX98 4.1 65.6 1.0
NE2 A:HIS135 4.2 56.3 1.0
NE2 A:HIS13 4.2 41.1 1.0
ND1 A:HIS173 4.2 40.9 1.0
CG A:HIS173 4.2 40.4 1.0
CD2 A:HIS135 4.3 54.2 1.0
CE1 A:TYR100 4.4 60.1 1.0
CA A:HIS135 4.4 53.0 1.0
O A:LEU218 4.5 49.0 1.0
CE A:KCX98 4.5 62.6 1.0
OD1 A:ASP246 4.5 42.2 1.0
OD2 A:ASP246 4.6 41.6 1.0
CG A:ASP246 4.8 36.7 1.0

Zinc binding site 2 out of 4 in 5vgm

Go back to Zinc Binding Sites List in 5vgm
Zinc binding site 2 out of 4 in the Crystal Structure of Dihydroorotase Pyrc From Vibrio Cholerae in Complex with Zinc at 1.95 A Resolution.


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 Dihydroorotase Pyrc From Vibrio Cholerae in Complex with Zinc at 1.95 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:54.0
occ:1.00
 O A:HOH536 2.0 79.9 1.0
OQ1 A:KCX98 2.1 61.2 1.0
OD1 A:ASP246 2.1 42.2 1.0
NE2 A:HIS15 2.1 50.1 1.0
NE2 A:HIS13 2.1 41.1 1.0
CX A:KCX98 3.0 61.5 1.0
CE1 A:HIS15 3.0 52.5 1.0
CE1 A:HIS13 3.1 47.5 1.0
CG A:ASP246 3.1 36.7 1.0
CD2 A:HIS15 3.2 48.4 1.0
CD2 A:HIS13 3.2 43.8 1.0
ZN A:ZN401 3.2 59.6 1.0
OQ2 A:KCX98 3.3 70.4 1.0
OD2 A:ASP246 3.6 41.6 1.0
CD2 A:HIS173 4.1 38.5 1.0
NZ A:KCX98 4.2 65.6 1.0
ND1 A:HIS15 4.2 51.0 1.0
ND1 A:HIS13 4.2 50.5 1.0
NE2 A:HIS173 4.2 40.8 1.0
CG A:HIS15 4.3 45.0 1.0
CG A:HIS13 4.3 44.8 1.0
CB A:ASP246 4.3 40.3 1.0
CG A:MET39 4.4 47.9 1.0
OH A:TYR100 4.7 61.5 1.0
CA A:ASP246 4.8 39.5 1.0
CB A:MET39 5.0 45.9 1.0

Zinc binding site 3 out of 4 in 5vgm

Go back to Zinc Binding Sites List in 5vgm
Zinc binding site 3 out of 4 in the Crystal Structure of Dihydroorotase Pyrc From Vibrio Cholerae in Complex with Zinc at 1.95 A Resolution.


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 Dihydroorotase Pyrc From Vibrio Cholerae in Complex with Zinc at 1.95 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:54.0
occ:1.00
 OQ2 B:KCX98 1.9 62.2 1.0
O B:HOH556 2.0 59.6 1.0
NE2 B:HIS173 2.1 30.1 1.0
ND1 B:HIS135 2.1 38.8 1.0
CE1 B:HIS135 3.0 42.8 1.0
CX B:KCX98 3.0 51.6 1.0
CE1 B:HIS173 3.1 29.8 1.0
CD2 B:HIS173 3.1 33.9 1.0
CG B:HIS135 3.2 41.0 1.0
ZN B:ZN402 3.3 46.2 1.0
OQ1 B:KCX98 3.3 51.7 1.0
CB B:HIS135 3.6 40.0 1.0
CE1 B:HIS13 4.0 40.0 1.0
NE2 B:HIS135 4.1 43.2 1.0
NZ B:KCX98 4.2 54.4 1.0
ND1 B:HIS173 4.2 33.0 1.0
NE2 B:HIS13 4.2 34.4 1.0
CG B:HIS173 4.2 32.7 1.0
CD2 B:HIS135 4.3 41.6 1.0
CE1 B:TYR100 4.4 50.1 1.0
O B:LEU218 4.4 51.4 1.0
CA B:HIS135 4.5 39.0 1.0
CE B:KCX98 4.5 51.0 1.0
OD1 B:ASP246 4.5 42.9 1.0
OD2 B:ASP246 4.5 37.5 1.0
CG B:ASP246 4.8 38.2 1.0

Zinc binding site 4 out of 4 in 5vgm

Go back to Zinc Binding Sites List in 5vgm
Zinc binding site 4 out of 4 in the Crystal Structure of Dihydroorotase Pyrc From Vibrio Cholerae in Complex with Zinc at 1.95 A Resolution.


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 Dihydroorotase Pyrc From Vibrio Cholerae in Complex with Zinc at 1.95 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:46.2
occ:1.00
 O B:HOH556 2.0 59.6 1.0
OQ1 B:KCX98 2.0 51.7 1.0
OD1 B:ASP246 2.1 42.9 1.0
NE2 B:HIS15 2.1 39.0 1.0
NE2 B:HIS13 2.1 34.4 1.0
CX B:KCX98 3.0 51.6 1.0
CE1 B:HIS15 3.1 44.0 1.0
CE1 B:HIS13 3.1 40.0 1.0
CG B:ASP246 3.1 38.2 1.0
CD2 B:HIS13 3.1 37.8 1.0
CD2 B:HIS15 3.2 35.0 1.0
ZN B:ZN401 3.3 54.0 1.0
OQ2 B:KCX98 3.3 62.2 1.0
OD2 B:ASP246 3.7 37.5 1.0
NZ B:KCX98 4.1 54.4 1.0
CD2 B:HIS173 4.2 33.9 1.0
ND1 B:HIS13 4.2 40.1 1.0
ND1 B:HIS15 4.2 36.2 1.0
NE2 B:HIS173 4.3 30.1 1.0
CG B:HIS13 4.3 39.0 1.0
CG B:HIS15 4.3 36.4 1.0
CB B:ASP246 4.3 35.0 1.0
CG B:MET39 4.4 39.9 1.0
OH B:TYR100 4.7 48.5 1.0
CA B:ASP246 4.8 30.9 1.0
CB B:MET39 5.0 35.8 1.0

Reference:

J.Lipowska, C.D.Miks, K.Kwon, L.Shuvalova, H.Zheng, K.Lewinski, D.R.Cooper, I.G.Shabalin, W.Minor. Pyrimidine Biosynthesis in Pathogens - Structures and Analysis of Dihydroorotases From Yersinia Pestis and Vibrio Cholerae. Int.J.Biol.Macromol. V. 136 1176 2019.
ISSN: ISSN 0141-8130
PubMed: 31207330
DOI: 10.1016/J.IJBIOMAC.2019.05.149
Page generated: Wed Dec 16 11:09:23 2020

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