Atomistry » Magnesium » PDB 4tyw-4u9h » 4u03
Atomistry »
  Magnesium »
    PDB 4tyw-4u9h »
      4u03 »

Magnesium in PDB 4u03: Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) in Complex with Gtp and 5MTHFGLU2

Enzymatic activity of Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) in Complex with Gtp and 5MTHFGLU2

All present enzymatic activity of Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) in Complex with Gtp and 5MTHFGLU2:
2.7.7.86;

Protein crystallography data

The structure of Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) in Complex with Gtp and 5MTHFGLU2, PDB code: 4u03 was solved by D.Y.Zhu, Y.Xiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.63 / 2.04
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.623, 59.846, 104.053, 90.00, 95.81, 90.00
R / Rfree (%) 18 / 23.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) in Complex with Gtp and 5MTHFGLU2 (pdb code 4u03). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) in Complex with Gtp and 5MTHFGLU2, PDB code: 4u03:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4u03

Go back to Magnesium Binding Sites List in 4u03
Magnesium binding site 1 out of 4 in the Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) in Complex with Gtp and 5MTHFGLU2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) in Complex with Gtp and 5MTHFGLU2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:26.2
occ:1.00
 O2B A:GTP501 2.2 24.6 1.0
OD2 A:ASP131 2.2 48.8 1.0
O3G A:GTP501 2.2 32.0 1.0
O A:HOH750 2.3 27.8 1.0
O2A A:GTP501 2.3 33.6 1.0
OD2 A:ASP133 2.5 37.7 1.0
CG A:ASP131 3.1 51.7 1.0
PB A:GTP501 3.3 28.5 1.0
CG A:ASP133 3.5 40.6 1.0
PG A:GTP501 3.5 32.7 1.0
O A:HOH757 3.5 58.9 1.0
PA A:GTP501 3.6 35.4 1.0
CB A:ASP131 3.7 41.4 1.0
OD1 A:ASP133 3.7 43.0 1.0
O3B A:GTP501 3.7 29.3 1.0
O3A A:GTP501 3.8 32.4 1.0
MG A:MG504 3.8 58.0 1.0
OG A:SER114 3.9 21.4 1.0
C5' A:GTP501 4.0 41.9 1.0
OD1 A:ASP131 4.1 58.2 1.0
O2G A:GTP501 4.3 27.5 1.0
O A:HOH755 4.3 24.4 1.0
N A:SER114 4.3 26.1 1.0
O A:ASP131 4.3 29.9 1.0
O5' A:GTP501 4.4 40.6 1.0
O3' A:GTP502 4.4 61.9 1.0
O A:HOH742 4.5 39.7 1.0
O1G A:GTP501 4.6 27.0 1.0
C A:ASP131 4.6 28.6 1.0
O1B A:GTP501 4.7 32.2 1.0
CA A:GLY113 4.7 23.4 1.0
CA A:ASP131 4.8 30.6 1.0
CB A:ASP133 4.8 33.4 1.0
O1A A:GTP501 4.8 37.0 1.0
CB A:SER114 4.9 20.9 1.0

Magnesium binding site 2 out of 4 in 4u03

Go back to Magnesium Binding Sites List in 4u03
Magnesium binding site 2 out of 4 in the Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) in Complex with Gtp and 5MTHFGLU2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) in Complex with Gtp and 5MTHFGLU2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:58.0
occ:1.00
 O3' A:GTP502 2.0 61.9 1.0
OD2 A:ASP131 2.1 48.8 1.0
OD2 A:ASP193 2.2 41.0 1.0
OD1 A:ASP133 2.3 43.0 1.0
OD1 A:ASP131 2.6 58.2 1.0
CG A:ASP131 2.6 51.7 1.0
O A:HOH757 2.9 58.9 1.0
CG A:ASP193 3.1 36.0 1.0
CG A:ASP133 3.3 40.6 1.0
C3' A:GTP502 3.4 68.6 1.0
CB A:ASP193 3.7 32.0 1.0
OD2 A:ASP133 3.8 37.7 1.0
O2A A:GTP501 3.8 33.6 1.0
MG A:MG503 3.8 26.2 1.0
C4' A:GTP502 3.9 73.1 1.0
O2' A:GTP502 3.9 51.5 1.0
CB A:ASP131 4.0 41.4 1.0
OD1 A:ASP193 4.1 35.1 1.0
NE2 A:HIS191 4.2 33.5 1.0
C2' A:GTP502 4.2 65.3 1.0
C5' A:GTP502 4.4 77.2 1.0
NH2 A:ARG182 4.5 35.9 1.0
CD2 A:HIS191 4.6 35.7 1.0
CB A:ASP133 4.6 33.4 1.0

Magnesium binding site 3 out of 4 in 4u03

Go back to Magnesium Binding Sites List in 4u03
Magnesium binding site 3 out of 4 in the Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) in Complex with Gtp and 5MTHFGLU2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) in Complex with Gtp and 5MTHFGLU2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:27.1
occ:1.00
 O2B B:GTP501 2.2 28.4 1.0
O2A B:GTP501 2.2 37.8 1.0
OD2 B:ASP133 2.4 36.1 1.0
O B:HOH710 2.4 31.3 1.0
O3G B:GTP501 2.5 35.8 1.0
OD2 B:ASP131 2.5 48.3 1.0
PB B:GTP501 3.3 33.7 1.0
CG B:ASP133 3.4 40.3 1.0
PA B:GTP501 3.5 36.4 1.0
CG B:ASP131 3.5 50.4 1.0
O B:HOH714 3.6 46.6 1.0
PG B:GTP501 3.6 33.4 1.0
OD1 B:ASP133 3.7 42.3 1.0
O3A B:GTP501 3.8 36.8 1.0
O3B B:GTP501 3.8 32.4 1.0
O B:HOH706 3.8 33.2 1.0
C5' B:GTP501 3.8 38.5 1.0
OG B:SER114 3.9 25.4 1.0
CB B:ASP131 4.0 39.9 1.0
O5' B:GTP501 4.1 35.6 1.0
N B:SER114 4.1 26.0 1.0
O B:HOH711 4.2 25.3 1.0
O B:ASP131 4.2 31.9 1.0
O2G B:GTP501 4.4 28.6 1.0
CA B:GLY113 4.4 22.3 1.0
MG B:MG504 4.4 52.5 1.0
OD1 B:ASP131 4.5 52.3 1.0
O3' B:GTP502 4.6 40.6 1.0
O B:HOH691 4.6 42.6 1.0
O1B B:GTP501 4.7 35.6 1.0
C B:ASP131 4.7 31.7 1.0
CB B:ASP133 4.7 34.5 1.0
O1A B:GTP501 4.8 38.4 1.0
C B:GLY113 4.8 22.6 1.0
CB B:SER114 4.9 23.3 1.0
O1G B:GTP501 4.9 28.3 1.0
CA B:ASP131 5.0 29.3 1.0

Magnesium binding site 4 out of 4 in 4u03

Go back to Magnesium Binding Sites List in 4u03
Magnesium binding site 4 out of 4 in the Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) in Complex with Gtp and 5MTHFGLU2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Vibrio Cholerae Di-Nucleotide Cyclase (Dncv) in Complex with Gtp and 5MTHFGLU2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:52.5
occ:1.00
 OD2 B:ASP193 1.9 37.0 1.0
O3' B:GTP502 2.1 40.6 1.0
OD1 B:ASP133 2.4 42.3 1.0
OD2 B:ASP131 2.5 48.3 1.0
O B:HOH714 2.7 46.6 1.0
CG B:ASP193 2.7 37.7 1.0
OD1 B:ASP131 3.0 52.3 1.0
CG B:ASP131 3.0 50.4 1.0
CB B:ASP193 3.1 31.0 1.0
C3' B:GTP502 3.3 47.7 1.0
CG B:ASP133 3.6 40.3 1.0
C4' B:GTP502 3.6 49.4 1.0
O2' B:GTP502 3.6 54.4 1.0
OD1 B:ASP193 3.8 39.4 1.0
C2' B:GTP502 4.0 54.7 1.0
NH2 B:ARG182 4.1 36.4 1.0
OD2 B:ASP133 4.2 36.1 1.0
O2A B:GTP501 4.2 37.8 1.0
C5' B:GTP502 4.3 44.0 1.0
CB B:ASP131 4.4 39.9 1.0
MG B:MG503 4.4 27.1 1.0
NE2 B:HIS191 4.5 34.6 1.0
CA B:ASP193 4.5 28.8 1.0
CD2 B:HIS191 4.7 36.9 1.0
CB B:ASP133 4.7 34.5 1.0
O4' B:GTP502 4.8 47.1 1.0
N B:ASP193 4.8 25.4 1.0
O B:HOH706 4.9 33.2 1.0
O3A B:GTP502 4.9 0.8 1.0
O2B B:GTP502 5.0 0.4 1.0

Reference:

D.Zhu, L.Wang, G.Shang, X.Liu, J.Zhu, D.Lu, L.Wang, B.Kan, J.R.Zhang, Y.Xiang. Structural Biochemistry of A Vibrio Cholerae Dinucleotide Cyclase Reveals Cyclase Activity Regulation By Folates. Mol.Cell V. 55 931 2014.
ISSN: ISSN 1097-2765
PubMed: 25201413
DOI: 10.1016/J.MOLCEL.2014.08.001
Page generated: Tue Aug 20 04:22:00 2024

Last articles

Mg in 1XRJ
Mg in 1XRB
Mg in 1XRA
Mg in 1XPU
Mg in 1XR1
Mg in 1XQA
Mg in 1XPY
Mg in 1XPR
Mg in 1XPO
Mg in 1XP7
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy