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Chlorine 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:

Magnesium (Mg) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Human Apurinic/Apyridinimic Endonuclease, APE1 in A New Crystal Form, PDB code: 3u8u:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3u8u

Go back to Chlorine Binding Sites List in 3u8u
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl320

b:36.0
occ:1.00
 NH2 A:ARG156 3.1 24.3 1.0
O A:HOH544 3.2 45.6 1.0
N A:ASN174 3.2 22.2 1.0
O A:HOH372 3.4 27.8 1.0
OH A:TYR171 3.4 30.2 1.0
NH1 A:ARG156 3.5 22.4 1.0
CZ A:TYR171 3.6 24.8 1.0
CB A:ASN174 3.7 25.6 1.0
CZ A:ARG156 3.8 24.5 1.0
CE2 A:TYR171 3.8 22.8 1.0
O A:HOH362 3.8 19.0 1.0
CA A:PRO173 3.8 22.4 1.0
C A:PRO173 4.0 23.6 1.0
CA A:ASN174 4.1 23.7 1.0
O A:VAL172 4.2 18.6 1.0
CE1 A:TYR171 4.4 25.6 1.0
OD1 A:ASN212 4.4 23.6 1.0
O A:HOH395 4.6 31.8 1.0
CD2 A:TYR171 4.7 24.5 1.0
CB A:PRO173 4.8 25.0 1.0
OG A:SER129 4.8 40.0 1.0
N A:PRO173 4.8 22.7 1.0
C A:VAL172 4.9 20.9 1.0
O A:ASN174 4.9 24.1 1.0

Chlorine binding site 2 out of 4 in 3u8u

Go back to Chlorine Binding Sites List in 3u8u
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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:Cl320

b:45.6
occ:1.00
 N B:ASN174 3.2 28.5 1.0
NH2 B:ARG156 3.3 24.6 1.0
O B:HOH567 3.4 34.2 1.0
NH1 B:ARG156 3.5 28.5 1.0
CB B:ASN174 3.5 29.7 1.0
CZ B:ARG156 3.8 25.8 1.0
CE2 B:TYR171 3.9 26.8 1.0
O B:HOH480 3.9 29.6 1.0
OH B:TYR171 3.9 26.6 1.0
CA B:ASN174 4.0 29.1 1.0
CZ B:TYR171 4.0 30.0 1.0
CA B:PRO173 4.1 26.2 1.0
C B:PRO173 4.1 27.3 1.0
O B:VAL172 4.3 24.1 1.0
CD2 B:TYR171 4.7 24.8 1.0
OD1 B:ASN212 4.7 30.6 1.0
O B:TYR128 4.7 41.5 1.0
CE1 B:TYR171 4.8 27.5 1.0
CG B:ASN174 4.9 33.4 1.0
N B:PRO173 4.9 25.4 1.0
O B:ASN174 5.0 29.7 1.0
C B:VAL172 5.0 23.6 1.0

Chlorine binding site 3 out of 4 in 3u8u

Go back to Chlorine Binding Sites List in 3u8u
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl 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:Cl320

b:34.7
occ:1.00
 NH2 C:ARG156 3.1 26.8 1.0
N C:ASN174 3.2 26.7 1.0
O C:HOH359 3.2 32.5 1.0
O C:HOH744 3.3 42.2 1.0
NH1 C:ARG156 3.3 23.6 1.0
CZ C:ARG156 3.7 26.8 1.0
CE2 C:TYR171 3.8 26.8 1.0
CB C:ASN174 3.8 30.5 1.0
O C:HOH334 3.8 26.9 1.0
OH C:TYR171 3.8 31.7 1.0
CA C:PRO173 3.9 26.4 1.0
CZ C:TYR171 3.9 28.7 1.0
C C:PRO173 4.1 26.8 1.0
CA C:ASN174 4.1 28.6 1.0
OH C:TYR128 4.1 43.6 1.0
O C:VAL172 4.1 21.6 1.0
CD2 C:TYR171 4.5 26.2 1.0
OD1 C:ASN212 4.6 29.8 1.0
CZ C:TYR128 4.7 46.6 1.0
CE1 C:TYR128 4.7 49.4 1.0
CE1 C:TYR171 4.8 24.0 1.0
CB C:PRO173 4.9 26.3 1.0
N C:PRO173 4.9 23.8 1.0
C C:VAL172 4.9 22.7 1.0
NE C:ARG156 5.0 27.0 1.0

Chlorine binding site 4 out of 4 in 3u8u

Go back to Chlorine Binding Sites List in 3u8u
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl 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
F:Cl320

b:40.9
occ:1.00
 O F:HOH361 2.9 43.0 1.0
NH2 F:ARG156 3.1 34.7 1.0
N F:ASN174 3.4 28.7 1.0
NH1 F:ARG156 3.5 32.1 1.0
CE2 F:TYR171 3.7 28.0 1.0
CZ F:ARG156 3.8 30.5 1.0
CB F:ASN174 3.8 33.0 1.0
OH F:TYR171 3.8 33.8 1.0
CZ F:TYR171 3.9 36.6 1.0
CA F:PRO173 4.0 26.6 1.0
O F:HOH349 4.0 24.3 1.0
OH F:TYR128 4.1 51.9 1.0
C F:PRO173 4.2 28.9 1.0
CA F:ASN174 4.2 31.2 1.0
O F:VAL172 4.3 24.1 1.0
CD2 F:TYR171 4.6 30.0 1.0
CZ F:TYR128 4.6 47.8 1.0
CE1 F:TYR128 4.7 45.2 1.0
OD1 F:ASN212 4.7 32.3 1.0
CE1 F:TYR171 4.8 32.1 1.0
N F:PRO173 4.9 25.0 1.0
CB F:PRO173 4.9 24.5 1.0
C F:VAL172 5.0 24.6 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: Fri Jul 11 11:09:11 2025

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