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Magnesium in PDB 3u8u: Crystal Structure of Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form

Enzymatic activity of Crystal Structure of Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form

All present enzymatic activity of Crystal Structure of Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form:
4.2.99.18;

Protein crystallography data

The structure of Crystal Structure of Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form, PDB code: 3u8u 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) 40.71 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 95.840, 97.284, 132.150, 90.00, 90.91, 90.00
R / Rfree (%) 19.8 / 24.3

Other elements in 3u8u:

The structure of Crystal Structure of Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form (pdb code 3u8u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form, PDB code: 3u8u:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3u8u

Go back to Magnesium Binding Sites List in 3u8u
Magnesium binding site 1 out of 6 in the Crystal Structure of Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form


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 Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg319

b:31.6
occ:1.00
 OE1 A:GLU96 2.1 27.8 1.0
O A:HOH689 2.1 29.4 1.0
O A:HOH670 2.1 22.3 1.0
OD1 A:ASP70 2.2 23.4 1.0
O A:HOH708 2.2 32.9 1.0
CD A:GLU96 3.0 30.2 1.0
CG A:ASP70 3.2 22.9 1.0
OE2 A:GLU96 3.3 40.8 1.0
CB A:ASP70 3.8 23.2 1.0
CA A:ASP70 4.0 23.5 1.0
OD1 A:ASP308 4.0 23.3 1.0
OD2 A:ASP70 4.1 28.3 1.0
OD2 A:ASP308 4.1 24.9 1.0
CG A:GLU96 4.3 30.5 1.0
OD1 A:ASN68 4.4 18.7 1.0
NZ A:LYS98 4.4 38.6 1.0
CG A:ASP308 4.5 23.5 1.0
CE A:LYS98 4.8 36.3 1.0
ND2 A:ASN68 4.9 20.9 1.0
N A:ASP70 4.9 24.0 1.0
C A:ASP70 5.0 25.1 1.0
OH A:TYR171 5.0 30.2 1.0
CB A:GLU96 5.0 23.5 1.0

Magnesium binding site 2 out of 6 in 3u8u

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Magnesium binding site 2 out of 6 in the Crystal Structure of Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form


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 Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg319

b:37.9
occ:1.00
 O B:HOH779 2.1 34.7 1.0
OE2 B:GLU96 2.1 30.4 1.0
O B:HOH733 2.1 38.4 1.0
O B:HOH714 2.1 24.9 1.0
OD1 B:ASP70 2.1 31.4 1.0
CD B:GLU96 2.9 34.0 1.0
OE1 B:GLU96 3.1 39.9 1.0
CG B:ASP70 3.2 33.2 1.0
CB B:ASP70 3.7 27.8 1.0
CA B:ASP70 3.9 27.8 1.0
OD1 B:ASP308 4.2 26.1 1.0
OD2 B:ASP70 4.2 36.3 1.0
OD2 B:ASP308 4.2 31.1 1.0
OD1 B:ASN68 4.2 28.8 1.0
CG B:GLU96 4.3 31.1 1.0
O B:HOH563 4.4 30.2 1.0
NZ B:LYS98 4.6 35.3 1.0
CG B:ASP308 4.6 31.4 1.0
CB B:GLU96 4.7 26.4 1.0
N B:ASP70 4.8 27.0 1.0
ND2 B:ASN68 4.8 26.9 1.0
CE B:LYS98 4.9 29.8 1.0
OH B:TYR171 4.9 26.6 1.0
C B:ASP70 4.9 29.1 1.0
CG B:ASN68 5.0 28.2 1.0

Magnesium binding site 3 out of 6 in 3u8u

Go back to Magnesium Binding Sites List in 3u8u
Magnesium binding site 3 out of 6 in the Crystal Structure of Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form


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 Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg319

b:33.1
occ:1.00
 OE1 C:GLU96 2.1 30.6 1.0
OD1 C:ASP70 2.1 24.2 1.0
O C:HOH700 2.1 27.4 1.0
O C:HOH876 2.1 29.4 1.0
O C:HOH656 2.2 31.4 1.0
O C:HOH657 2.2 19.4 1.0
CD C:GLU96 2.9 33.9 1.0
OE2 C:GLU96 3.0 44.0 1.0
CG C:ASP70 3.1 26.3 1.0
CB C:ASP70 3.7 24.3 1.0
CA C:ASP70 3.9 25.0 1.0
OD2 C:ASP70 4.0 25.0 1.0
NZ C:LYS98 4.1 36.5 1.0
OD1 C:ASP308 4.1 22.1 1.0
OD2 C:ASP308 4.1 28.8 1.0
CG C:GLU96 4.2 30.4 1.0
OD1 C:ASN68 4.4 24.1 1.0
CG C:ASP308 4.5 23.1 1.0
CE C:LYS98 4.7 31.9 1.0
OD2 B:ASP124 4.7 62.8 1.0
CB C:GLU96 4.8 24.7 1.0
C C:ASP70 4.8 25.6 1.0
N C:ASP70 4.8 23.6 1.0

Magnesium binding site 4 out of 6 in 3u8u

Go back to Magnesium Binding Sites List in 3u8u
Magnesium binding site 4 out of 6 in the Crystal Structure of Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg319

b:46.3
occ:1.00
 OE1 D:GLU96 2.1 33.0 1.0
OD1 D:ASP70 2.2 31.1 1.0
O D:HOH717 2.3 24.8 1.0
CD D:GLU96 2.8 32.2 1.0
OE2 D:GLU96 2.8 43.0 1.0
CG D:ASP70 3.2 33.4 1.0
OD2 D:ASP308 3.8 33.3 1.0
O D:HOH491 4.0 27.8 1.0
OD2 D:ASP70 4.0 34.4 1.0
CB D:ASP70 4.0 30.0 1.0
OD1 D:ASP308 4.0 32.6 1.0
CG D:GLU96 4.3 29.4 1.0
CA D:ASP70 4.4 31.2 1.0
CG D:ASP308 4.4 32.5 1.0
OD1 D:ASN68 4.6 35.0 1.0
OH D:TYR171 4.8 34.6 1.0
NZ D:LYS98 4.8 43.0 1.0
CB D:GLU96 4.9 29.4 1.0

Magnesium binding site 5 out of 6 in 3u8u

Go back to Magnesium Binding Sites List in 3u8u
Magnesium binding site 5 out of 6 in the Crystal Structure of Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg319

b:23.8
occ:1.00
 OE1 E:GLU96 2.1 23.4 1.0
OD1 E:ASP70 2.1 24.4 1.0
O E:HOH660 2.1 20.7 1.0
O E:HOH658 2.1 16.9 1.0
O E:HOH653 2.1 24.4 1.0
O E:HOH659 2.1 18.3 1.0
CG E:ASP70 3.0 24.1 1.0
CD E:GLU96 3.0 26.6 1.0
OE2 E:GLU96 3.4 32.5 1.0
CB E:ASP70 3.7 21.3 1.0
OD2 E:ASP70 3.8 22.7 1.0
CA E:ASP70 3.9 23.2 1.0
OD2 E:ASP308 3.9 26.9 1.0
NZ E:LYS98 4.1 31.4 1.0
OD1 E:ASP308 4.1 23.8 1.0
CG E:GLU96 4.3 25.4 1.0
CG E:ASP308 4.4 21.2 1.0
O E:HOH654 4.5 27.5 1.0
CE E:LYS98 4.5 27.2 1.0
OD1 E:ASN68 4.6 18.3 1.0
C E:ASP70 4.8 22.8 1.0
N E:ASP70 4.9 20.1 1.0

Magnesium binding site 6 out of 6 in 3u8u

Go back to Magnesium Binding Sites List in 3u8u
Magnesium binding site 6 out of 6 in the Crystal Structure of Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg319

b:35.9
occ:1.00
 O F:HOH663 2.1 27.2 1.0
OD1 F:ASP70 2.1 21.4 1.0
O F:HOH665 2.1 33.5 1.0
O F:HOH662 2.2 33.2 1.0
OE2 F:GLU96 2.2 20.0 1.0
O F:HOH664 2.3 27.3 1.0
CD F:GLU96 2.9 20.0 1.0
OE1 F:GLU96 2.9 20.0 1.0
CG F:ASP70 3.1 28.3 1.0
CB F:ASP70 3.8 24.3 1.0
OD2 F:ASP70 3.9 30.0 1.0
OD2 F:ASP308 4.0 27.3 1.0
CA F:ASP70 4.0 27.4 1.0
O F:HOH413 4.3 45.7 1.0
O F:HOH454 4.3 27.6 1.0
OD1 F:ASP308 4.3 30.5 1.0
CG F:GLU96 4.3 20.0 1.0
OD1 F:ASN68 4.5 23.6 1.0
NZ F:LYS98 4.5 37.0 1.0
CG F:ASP308 4.6 28.4 1.0
CE F:LYS98 4.6 33.3 1.0
CB F:GLU96 5.0 20.0 1.0
C F:ASP70 5.0 26.6 1.0

Reference:

R.Agarwal, M.D.Naidu. Crystal Structure of Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form To Be Published.
Page generated: Thu Aug 15 12:26:51 2024

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