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Magnesium in PDB 2isi: Crystal Structure of APE1 From Homo Sapiens in A New Crystal Form Complexed with A Ligand

Enzymatic activity of Crystal Structure of APE1 From Homo Sapiens in A New Crystal Form Complexed with A Ligand

All present enzymatic activity of Crystal Structure of APE1 From Homo Sapiens in A New Crystal Form Complexed with A Ligand:
4.2.99.18;

Protein crystallography data

The structure of Crystal Structure of APE1 From Homo Sapiens in A New Crystal Form Complexed with A Ligand, PDB code: 2isi was solved by R.Agarwal, M.D.Naidu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.13 / 2.76
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.347, 92.392, 94.006, 90.00, 121.38, 90.00
R / Rfree (%) 22.8 / 28.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of APE1 From Homo Sapiens in A New Crystal Form Complexed with A Ligand (pdb code 2isi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of APE1 From Homo Sapiens in A New Crystal Form Complexed with A Ligand, PDB code: 2isi:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 2isi

Go back to Magnesium Binding Sites List in 2isi
Magnesium binding site 1 out of 3 in the Crystal Structure of APE1 From Homo Sapiens in A New Crystal Form Complexed with A Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of APE1 From Homo Sapiens in A New Crystal Form Complexed with A Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:46.4
occ:1.00
OE2 A:GLU96 2.2 49.8 1.0
O A:HOH414 2.3 54.5 1.0
OE1 A:GLU96 2.5 51.0 1.0
OD1 A:ASP70 2.5 53.4 1.0
CD A:GLU96 2.6 48.9 1.0
CG A:ASP70 3.6 53.1 1.0
CB A:ASP70 4.0 51.8 1.0
CG A:GLU96 4.1 47.9 1.0
CA A:ASP70 4.1 51.8 1.0
OD2 A:ASP308 4.2 39.3 1.0
OD1 A:ASP308 4.2 40.8 1.0
OD2 A:ASP70 4.6 53.6 1.0
ND2 A:ASN68 4.6 54.5 1.0
CG A:ASP308 4.6 41.9 1.0
OD1 A:ASN68 4.6 55.0 1.0
OH A:TYR171 4.7 45.7 1.0
CB A:GLU96 4.8 46.7 1.0

Magnesium binding site 2 out of 3 in 2isi

Go back to Magnesium Binding Sites List in 2isi
Magnesium binding site 2 out of 3 in the Crystal Structure of APE1 From Homo Sapiens in A New Crystal Form Complexed with A Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of APE1 From Homo Sapiens in A New Crystal Form Complexed with A Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:53.4
occ:1.00
OD1 B:ASP70 2.4 60.7 1.0
OE1 B:GLU96 2.8 69.7 1.0
CG B:ASP70 3.3 60.2 1.0
CD B:GLU96 3.3 68.8 1.0
CB B:ASP70 3.6 59.6 1.0
CG B:GLU96 3.7 66.8 1.0
CA B:ASP70 3.8 57.7 1.0
ND2 B:ASN68 4.0 48.2 1.0
OE2 B:GLU96 4.1 69.9 1.0
OD1 B:ASP308 4.1 54.4 1.0
OD1 B:ASN68 4.2 47.9 1.0
OD2 B:ASP308 4.2 52.1 1.0
CB B:GLU96 4.4 63.2 1.0
OD2 B:ASP70 4.4 59.9 1.0
CG B:ASN68 4.5 48.0 1.0
CG B:ASP308 4.6 51.8 1.0
N B:ASP70 4.7 54.9 1.0
C B:ASP70 4.7 59.1 1.0
O B:ASP70 4.8 59.4 1.0
NZ B:LYS98 4.9 58.1 1.0
OH B:TYR171 5.0 57.8 1.0

Magnesium binding site 3 out of 3 in 2isi

Go back to Magnesium Binding Sites List in 2isi
Magnesium binding site 3 out of 3 in the Crystal Structure of APE1 From Homo Sapiens in A New Crystal Form Complexed with A Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of APE1 From Homo Sapiens in A New Crystal Form Complexed with A Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:66.3
occ:1.00
OE1 C:GLU96 2.2 66.2 1.0
OD1 C:ASP70 2.3 62.2 1.0
CG C:ASP70 2.9 62.1 1.0
CD C:GLU96 3.1 64.7 1.0
CB C:ASP70 3.4 60.6 1.0
OE2 C:GLU96 3.5 62.7 1.0
OD2 C:ASP308 3.6 51.2 1.0
ND2 C:ASN68 3.7 59.4 1.0
OD2 C:ASP70 3.8 61.1 1.0
OD1 C:ASP308 4.0 50.7 1.0
CG C:ASP308 4.3 52.1 1.0
CA C:ASP70 4.3 58.9 1.0
CG C:GLU96 4.3 64.2 1.0
CG C:ASN68 4.6 59.6 1.0
OD1 C:ASN68 4.6 62.2 1.0
NE2 C:HIS309 4.9 59.0 1.0
CB C:GLU96 5.0 64.1 1.0

Reference:

R.Agarwal, M.D.Naidu. Crystal Structure of HAPE1 in A New Crystal Form with A Bound Ligand: Implications on Catalytic Mechanism and Its Inhibition To Be Published.
Page generated: Mon Dec 14 07:27:42 2020

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