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Magnesium in PDB 1h56: Structural and Biochemical Characterization of A New Magnesium Ion Binding Site Near TYR94 in the Restriction Endonuclease Pvuii

Enzymatic activity of Structural and Biochemical Characterization of A New Magnesium Ion Binding Site Near TYR94 in the Restriction Endonuclease Pvuii

All present enzymatic activity of Structural and Biochemical Characterization of A New Magnesium Ion Binding Site Near TYR94 in the Restriction Endonuclease Pvuii:
3.1.21.4;

Protein crystallography data

The structure of Structural and Biochemical Characterization of A New Magnesium Ion Binding Site Near TYR94 in the Restriction Endonuclease Pvuii, PDB code: 1h56 was solved by A.Spyrida, C.Matzen, T.Lanio, A.Jeltsch, A.Simoncsits, A.Athanasiadis, E.Scheuring-Vanamee, M.Kokkinidis, A.Pingoud, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 3.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.180, 105.280, 46.670, 90.00, 90.00, 90.00
R / Rfree (%) 15 / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural and Biochemical Characterization of A New Magnesium Ion Binding Site Near TYR94 in the Restriction Endonuclease Pvuii (pdb code 1h56). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structural and Biochemical Characterization of A New Magnesium Ion Binding Site Near TYR94 in the Restriction Endonuclease Pvuii, PDB code: 1h56:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1h56

Go back to Magnesium Binding Sites List in 1h56
Magnesium binding site 1 out of 2 in the Structural and Biochemical Characterization of A New Magnesium Ion Binding Site Near TYR94 in the Restriction Endonuclease Pvuii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural and Biochemical Characterization of A New Magnesium Ion Binding Site Near TYR94 in the Restriction Endonuclease Pvuii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1

b:81.0
occ:1.00
O A:HOH2014 1.9 73.8 1.0
OE1 A:GLU68 2.4 63.1 1.0
O A:HOH2016 2.7 38.4 1.0
OE2 A:GLU68 2.7 56.6 1.0
CD A:GLU68 2.9 52.2 1.0
OD2 A:ASP58 3.0 53.5 1.0
O A:HOH2025 3.6 52.4 1.0
CE A:LYS70 3.7 39.2 1.0
CG A:ASP58 3.9 42.6 1.0
O A:GLY56 3.9 0.5 1.0
OD1 A:ASP58 4.0 54.9 1.0
OH A:TYR94 4.2 65.0 1.0
CG A:GLU68 4.3 35.3 1.0
NZ A:LYS70 4.3 40.9 1.0
CE1 A:TYR94 4.5 56.9 1.0
CD A:LYS70 4.5 35.1 1.0
N A:LEU69 4.6 17.2 1.0
CZ A:TYR94 4.7 60.5 1.0
O A:LEU69 4.7 20.6 1.0
CB A:GLU68 4.8 23.0 1.0
OE1 A:GLU55 4.9 0.7 1.0
CA A:GLU68 4.9 23.6 1.0

Magnesium binding site 2 out of 2 in 1h56

Go back to Magnesium Binding Sites List in 1h56
Magnesium binding site 2 out of 2 in the Structural and Biochemical Characterization of A New Magnesium Ion Binding Site Near TYR94 in the Restriction Endonuclease Pvuii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural and Biochemical Characterization of A New Magnesium Ion Binding Site Near TYR94 in the Restriction Endonuclease Pvuii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:40.3
occ:1.00
OH B:TYR94 2.3 50.5 1.0
O B:THR82 2.7 59.3 1.0
O B:HOH2013 2.8 64.0 1.0
CB B:HIS83 3.2 61.4 1.0
O B:HOH2005 3.2 60.6 1.0
CG B:HIS83 3.5 66.3 1.0
ND1 B:HIS83 3.5 72.4 1.0
C B:THR82 3.5 51.2 1.0
CZ B:TYR94 3.6 49.9 1.0
NZ B:LYS70 3.7 33.6 1.0
CA B:HIS83 3.7 41.0 1.0
N B:HIS83 4.0 39.2 1.0
CE1 B:TYR94 4.1 45.5 1.0
CE1 B:HIS83 4.4 65.0 1.0
CD2 B:HIS83 4.4 70.2 1.0
CA B:THR82 4.7 45.5 1.0
CE2 B:TYR94 4.7 47.6 1.0
O B:HOH2017 4.7 46.4 1.0
NE2 B:HIS83 4.9 68.8 1.0
CE B:LYS70 4.9 33.4 1.0
OE1 B:GLU68 4.9 60.8 1.0
CG2 B:ILE90 5.0 22.4 1.0

Reference:

A.Spyridaki, C.Matzen, T.Lanio, A.Jeltsch, A.Simoncsits, A.Athanasiadis, E.Scheuring-Vanamee, M.Kokkinidis, A.Pingoud. Structural and Biochemical Characterization of A New Mg(2+) Binding Site Near TYR94 in the Restriction Endonuclease Pvuii. J.Mol.Biol. V. 331 395 2003.
ISSN: ISSN 0022-2836
PubMed: 12888347
DOI: 10.1016/S0022-2836(03)00692-2
Page generated: Mon Dec 14 05:58:39 2020

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