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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

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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

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