Atomistry » Magnesium » PDB 3u8u-3umo » 3u8u
Atomistry »
  Magnesium »
    PDB 3u8u-3umo »
      3u8u »

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

Go back to Magnesium Binding Sites List in 3u8u
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy