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Chlorine in PDB 5dfj: Human APE1 E96Q/D210N Mismatch Substrate Complex

Enzymatic activity of Human APE1 E96Q/D210N Mismatch Substrate Complex

All present enzymatic activity of Human APE1 E96Q/D210N Mismatch Substrate Complex:
4.2.99.18;

Protein crystallography data

The structure of Human APE1 E96Q/D210N Mismatch Substrate Complex, PDB code: 5dfj was solved by B.D.Freudenthal, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.45 / 1.85
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.462, 60.668, 73.161, 82.78, 80.28, 89.20
R / Rfree (%) 15.9 / 20

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Human APE1 E96Q/D210N Mismatch Substrate Complex (pdb code 5dfj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Human APE1 E96Q/D210N Mismatch Substrate Complex, PDB code: 5dfj:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5dfj

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Chlorine binding site 1 out of 8 in the Human APE1 E96Q/D210N Mismatch Substrate Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human APE1 E96Q/D210N Mismatch Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:27.2
occ:1.00
 N A:SER129 3.2 16.1 1.0
O P:HOH126 3.2 38.5 1.0
NE2 A:GLN96 3.3 30.9 1.0
OH A:TYR171 3.4 31.0 1.0
CE A:LYS98 3.7 25.4 1.0
O A:HOH601 3.8 25.5 1.0
CA A:TYR128 3.8 20.4 1.0
CG A:GLN96 3.8 20.7 1.0
C5' P:DT10 3.8 23.0 0.5
CB A:TYR128 3.8 18.8 1.0
CD1 A:TYR128 3.9 25.4 1.0
C A:TYR128 4.0 17.9 1.0
CD A:GLN96 4.0 28.1 1.0
CZ A:TYR171 4.0 28.2 1.0
CE2 A:TYR171 4.1 27.2 1.0
CA A:SER129 4.1 18.0 1.0
C4' P:DT10 4.2 26.1 0.5
CG A:TYR128 4.4 23.8 1.0
NZ A:LYS98 4.5 30.5 1.0
C5' P:DT10 4.7 23.7 0.5
CG A:LYS98 4.7 19.7 1.0
OG A:SER129 4.8 27.7 1.0
CD A:LYS98 4.9 18.7 1.0
OP1 P:DT10 4.9 26.4 0.5
O4' P:DT10 4.9 23.2 0.5

Chlorine binding site 2 out of 8 in 5dfj

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Chlorine binding site 2 out of 8 in the Human APE1 E96Q/D210N Mismatch Substrate Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human APE1 E96Q/D210N Mismatch Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:32.8
occ:1.00
 NE1 A:TRP188 3.2 18.3 1.0
O A:HOH622 3.2 21.4 1.0
O A:HOH678 3.2 16.3 1.0
NH1 A:ARG156 3.3 16.8 0.4
CB A:GLU154 3.7 23.0 1.0
CD A:ARG156 3.8 18.9 0.4
CB A:ARG156 3.9 14.5 0.4
CG A:GLU154 3.9 27.7 1.0
CE2 A:TRP188 4.0 19.5 1.0
CG A:ARG156 4.1 17.4 0.4
CZ2 A:TRP188 4.2 19.6 1.0
CB A:ARG156 4.2 14.4 0.6
CG1 A:ILE146 4.2 19.6 1.0
CD1 A:TRP188 4.3 18.7 1.0
CZ A:ARG156 4.3 21.6 0.4
CD A:ARG156 4.4 21.3 0.6
NE A:ARG156 4.5 19.6 0.4
CD1 A:ILE146 4.6 24.6 1.0
OE2 A:GLU149 4.6 23.2 1.0
CG2 A:ILE146 4.7 20.3 1.0
CG A:ARG156 4.7 16.1 0.6
CG2 A:VAL157 4.8 18.1 1.0
N A:ILE146 4.9 16.1 1.0
CA A:GLY145 5.0 15.0 1.0

Chlorine binding site 3 out of 8 in 5dfj

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Chlorine binding site 3 out of 8 in the Human APE1 E96Q/D210N Mismatch Substrate Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human APE1 E96Q/D210N Mismatch Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:30.2
occ:1.00
 O A:HOH706 2.8 21.3 1.0
O A:ASP283 2.9 15.0 1.0
O A:HOH638 2.9 14.7 1.0
NH1 A:ARG281 3.0 17.0 1.0
CB A:PHE253 3.6 16.9 1.0
CD A:ARG281 3.7 14.7 1.0
CA A:TYR284 3.8 15.9 1.0
C A:ASP283 4.0 14.4 1.0
CZ A:ARG281 4.0 15.2 1.0
CG A:ARG281 4.1 13.8 1.0
CG A:PHE253 4.2 14.3 1.0
NE A:ARG281 4.3 13.8 1.0
N A:TYR284 4.3 13.4 1.0
CD2 A:TYR284 4.5 11.1 1.0
N A:PHE285 4.5 14.7 1.0
CB A:TYR284 4.6 14.4 1.0
C A:TYR284 4.6 14.5 1.0
CG A:TYR284 4.6 13.7 1.0
OD1 A:ASP251 4.6 15.9 1.0
CG2 A:ILE312 4.7 14.5 1.0
CD1 A:ILE312 4.7 14.4 1.0
CD2 A:PHE253 4.7 12.3 1.0
CG1 A:ILE300 4.8 17.2 1.0
CD1 A:ILE300 4.8 19.8 1.0
CD1 A:PHE253 4.8 16.0 1.0
OG A:SER298 4.8 15.5 1.0
CA A:PHE253 4.9 14.2 1.0

Chlorine binding site 4 out of 8 in 5dfj

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Chlorine binding site 4 out of 8 in the Human APE1 E96Q/D210N Mismatch Substrate Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human APE1 E96Q/D210N Mismatch Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:33.4
occ:1.00
 O A:HOH800 2.7 23.4 1.0
ND1 A:HIS215 2.7 15.6 1.0
O A:HOH583 2.7 18.5 1.0
OD2 A:ASP251 2.8 15.6 1.0
CE1 A:HIS215 3.6 19.4 1.0
CG A:ASP251 3.7 15.5 1.0
CG A:HIS215 3.7 16.4 1.0
CB A:ASP251 3.8 16.5 1.0
CB A:HIS215 3.9 17.9 1.0
NH2 A:ARG281 4.0 14.7 1.0
CE1 A:PHE240 4.0 19.8 1.0
CB A:ARG254 4.0 17.9 1.0
CG A:ARG254 4.1 20.6 1.0
O A:HOH781 4.3 20.5 1.0
OD2 A:ASP219 4.5 17.9 1.0
CZ A:PHE240 4.6 16.1 1.0
CD1 A:LEU244 4.7 19.4 1.0
NE2 A:HIS215 4.8 18.8 1.0
OD1 A:ASP251 4.8 15.9 1.0
CD2 A:HIS215 4.9 16.9 1.0
CD1 A:PHE240 4.9 15.2 1.0

Chlorine binding site 5 out of 8 in 5dfj

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Chlorine binding site 5 out of 8 in the Human APE1 E96Q/D210N Mismatch Substrate Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Human APE1 E96Q/D210N Mismatch Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:32.4
occ:1.00
 NZ A:LYS299 2.7 15.5 1.0
O A:SER298 2.8 14.4 1.0
OD1 A:ASP47 2.8 17.8 1.0
CE2 A:TYR257 3.3 15.1 1.0
CE A:LYS299 3.3 20.5 1.0
OD2 A:ASP47 3.4 15.0 1.0
CG A:ASP47 3.4 18.0 1.0
CA A:LYS299 3.6 14.6 1.0
CZ A:TYR257 3.6 16.8 1.0
OH A:TYR257 3.6 17.4 1.0
CD A:LYS299 3.7 14.1 1.0
C A:SER298 3.7 13.8 1.0
OD1 A:ASP297 3.8 16.3 1.0
CE1 A:PHE253 3.9 17.0 1.0
CD A:PRO48 4.0 18.6 1.0
CD2 A:TYR257 4.1 16.9 1.0
N A:LYS299 4.1 14.1 1.0
O A:HOH636 4.1 19.8 1.0
CG A:PRO48 4.2 20.0 1.0
CD1 A:PHE253 4.2 16.0 1.0
N A:ILE300 4.4 15.6 1.0
CB A:LYS299 4.4 17.3 1.0
C A:LYS299 4.5 13.5 1.0
OH A:TYR45 4.5 18.5 1.0
CG A:ASP297 4.5 15.5 1.0
OD2 A:ASP297 4.6 15.8 1.0
CE1 A:TYR257 4.7 18.3 1.0
CG A:LYS299 4.7 16.7 1.0
O A:PRO48 4.7 16.1 1.0
N A:PRO48 4.7 17.4 1.0
CB A:ASP47 4.8 16.8 1.0
N A:SER298 5.0 14.5 1.0
CA A:SER298 5.0 16.6 1.0

Chlorine binding site 6 out of 8 in 5dfj

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Chlorine binding site 6 out of 8 in the Human APE1 E96Q/D210N Mismatch Substrate Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Human APE1 E96Q/D210N Mismatch Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:36.8
occ:1.00
 O A:HOH702 2.9 21.9 1.0
N B:GLN117 3.1 16.2 1.0
O B:HOH611 3.3 20.6 1.0
O B:GLN117 3.4 19.3 1.0
CA B:HIS116 3.7 12.2 1.0
CD2 A:TYR144 3.8 14.7 1.0
C B:HIS116 3.8 17.2 1.0
O B:SER115 3.9 18.4 1.0
CA B:GLN117 4.0 17.3 1.0
C B:GLN117 4.1 20.3 1.0
CB A:TYR144 4.3 16.6 1.0
O B:HOH564 4.4 37.4 1.0
CB B:HIS116 4.4 16.0 1.0
CG A:TYR144 4.5 14.9 1.0
O B:HOH538 4.6 25.9 1.0
CB B:GLN117 4.6 14.3 1.0
N B:HIS116 4.7 14.3 1.0
C B:SER115 4.7 17.6 1.0
ND1 B:HIS116 4.7 17.7 1.0
CE2 A:TYR144 4.7 17.0 1.0
CZ B:TYR118 4.8 18.8 1.0
N A:TYR144 4.8 16.9 1.0
CE1 B:TYR118 4.9 16.4 1.0
OH B:TYR118 4.9 22.6 1.0
O A:TYR144 5.0 16.9 1.0
O B:HIS116 5.0 17.4 1.0
CG B:HIS116 5.0 14.8 1.0

Chlorine binding site 7 out of 8 in 5dfj

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Chlorine binding site 7 out of 8 in the Human APE1 E96Q/D210N Mismatch Substrate Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Human APE1 E96Q/D210N Mismatch Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:35.6
occ:1.00
 N B:ARG156 3.2 18.1 1.0
O B:HOH507 3.2 32.1 1.0
N B:VAL157 3.4 15.9 1.0
CA B:GLY145 3.6 22.7 1.0
CA B:ARG156 3.8 15.7 1.0
CB B:ARG156 3.9 18.2 1.0
N B:GLY155 4.0 34.1 1.0
C B:ARG156 4.0 16.7 1.0
CB B:VAL157 4.2 19.6 1.0
C B:GLY155 4.2 20.8 1.0
N B:GLY145 4.2 19.0 1.0
CA B:GLY155 4.3 26.0 1.0
CA B:VAL157 4.3 15.3 1.0
O B:VAL157 4.4 17.4 1.0
CG2 B:VAL157 4.4 18.0 1.0
N B:GLN153 4.5 63.1 1.0
C B:GLY145 4.5 28.4 1.0
N B:ILE146 4.6 21.5 1.0
CG B:ARG156 4.6 21.6 1.0
N B:GLU154 4.7 50.8 1.0
C B:GLU154 4.8 36.0 1.0
C B:VAL157 4.9 15.1 1.0

Chlorine binding site 8 out of 8 in 5dfj

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Chlorine binding site 8 out of 8 in the Human APE1 E96Q/D210N Mismatch Substrate Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Human APE1 E96Q/D210N Mismatch Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Cl101

b:60.6
occ:1.00
 C5' V:DG12 3.1 26.5 1.0
N A:MET271 3.4 27.7 1.0
O3' V:DG11 3.4 64.0 1.0
CA A:MET270 3.9 23.9 1.0
C4' V:DG11 3.9 59.1 1.0
C4' V:DG12 4.0 32.4 1.0
O5' V:DG12 4.0 39.2 1.0
CB A:MET270 4.1 27.5 1.0
C A:MET270 4.1 28.3 1.0
P V:DG12 4.2 55.2 1.0
OP1 V:DG12 4.2 59.5 1.0
CA A:MET271 4.2 26.9 1.0
C3' V:DG11 4.3 57.7 1.0
CG A:MET270 4.4 33.1 1.0
O4' V:DG12 4.4 28.9 1.0
CG A:MET271 4.5 36.1 1.0
C5' V:DG11 4.6 57.4 1.0
O A:HOH608 4.6 37.0 1.0
O4' V:DG11 4.9 53.0 1.0

Reference:

B.D.Freudenthal, W.A.Beard, M.J.Cuneo, N.S.Dyrkheeva, S.H.Wilson. Capturing Snapshots of APE1 Processing Dna Damage. Nat.Struct.Mol.Biol. V. 22 924 2015.
ISSN: ESSN 1545-9985
PubMed: 26458045
DOI: 10.1038/NSMB.3105
Page generated: Sat Jul 12 01:14:05 2025

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