Atomistry » Zinc » PDB 5ve9-5vmy » 5vgm
Atomistry »
  Zinc »
    PDB 5ve9-5vmy »
      5vgm »

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: Mon Oct 28 12:56:02 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy