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Sodium in PDB 4iem: Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+

Enzymatic activity of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+

All present enzymatic activity of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+:
4.2.99.18;

Protein crystallography data

The structure of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+, PDB code: 4iem was solved by S.E.Tsutakawa, C.D.Mol, A.S.Arvai, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.64 / 2.39
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 104.639, 74.090, 112.138, 90.00, 111.98, 90.00
R / Rfree (%) 20.8 / 24.6

Other elements in 4iem:

The structure of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+ also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+ (pdb code 4iem). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+, PDB code: 4iem:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 4iem

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Sodium binding site 1 out of 9 in the Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:50.5
occ:1.00
 O A:TYR269 2.2 32.7 1.0
H A:ASN272 2.3 43.5 1.0
H4' G:DG518 2.9 48.2 1.0
N A:ASN272 3.2 36.3 1.0
HA A:MET270 3.2 43.9 1.0
C A:TYR269 3.3 31.2 1.0
H A:MET271 3.3 43.6 1.0
HA A:ASN272 3.3 43.9 1.0
N A:MET271 3.4 36.3 1.0
C A:MET270 3.4 34.5 1.0
O5' G:DG518 3.6 38.9 1.0
CA A:MET270 3.6 36.6 1.0
CA A:ASN272 3.8 36.5 1.0
C4' G:DG518 3.8 40.1 1.0
N A:MET270 3.9 34.2 1.0
O A:MET270 4.0 34.8 1.0
C5' G:DG518 4.2 27.6 1.0
C A:MET271 4.2 28.6 1.0
CA A:MET271 4.3 26.6 1.0
HB2 A:ASN272 4.3 40.7 1.0
H5' G:DG518 4.3 33.1 1.0
O4' G:DG518 4.4 35.5 1.0
HA A:MET271 4.5 31.9 1.0
H A:ALA273 4.5 32.2 1.0
HA A:TYR269 4.5 36.1 1.0
CA A:TYR269 4.6 30.1 1.0
CB A:ASN272 4.6 33.9 1.0
HB3 A:TYR269 4.6 36.0 1.0
OP1 G:DG518 4.7 26.4 1.0
O3' G:DG518 4.7 39.8 1.0
P G:DG518 4.7 33.4 1.0
H A:MET270 4.8 41.1 1.0
C3' G:DG518 4.8 38.9 1.0
O A:HOH612 4.9 25.2 1.0
C A:ASN272 5.0 28.3 1.0

Sodium binding site 2 out of 9 in 4iem

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Sodium binding site 2 out of 9 in the Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:55.9
occ:1.00
 O A:LEU44 2.4 44.9 1.0
HA A:TYR45 2.8 39.6 1.0
O A:HOH666 3.2 38.2 1.0
HD1 A:TYR262 3.4 42.1 1.0
C A:LEU44 3.5 50.1 1.0
HD1 A:TYR45 3.5 39.4 1.0
CA A:TYR45 3.7 33.0 1.0
HB2 A:TYR262 3.7 46.5 1.0
HB2 A:TYR45 3.8 40.9 1.0
N A:TYR45 4.0 46.4 1.0
CD1 A:TYR262 4.2 35.1 1.0
CB A:TYR45 4.2 34.1 1.0
H A:GLU46 4.3 43.4 1.0
CD1 A:TYR45 4.3 32.8 1.0
O A:PRO261 4.4 42.0 1.0
CB A:TYR262 4.6 38.8 1.0
H A:LEU44 4.7 48.9 1.0
CA A:LEU44 4.8 45.2 1.0
CG A:TYR45 4.8 36.0 1.0
N A:LEU44 4.8 40.7 1.0
HB3 A:TYR262 4.8 46.5 1.0
C A:TYR45 4.8 34.2 1.0
N A:GLU46 4.8 36.2 1.0
HG2 A:PRO261 4.9 47.3 1.0
CG A:TYR262 4.9 39.7 1.0
H A:TYR45 4.9 55.7 1.0
HD2 A:PRO261 4.9 45.2 1.0

Sodium binding site 3 out of 9 in 4iem

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Sodium binding site 3 out of 9 in the Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na601

b:56.4
occ:1.00
 OP2 E:DA504 2.2 45.6 1.0
H3' E:DT503 2.8 55.3 1.0
H2'' E:DT503 2.8 48.3 1.0
H8 E:DA504 2.9 42.8 1.0
H2' E:DT503 3.1 48.3 1.0
O5' E:DA504 3.1 54.5 1.0
P E:DA504 3.1 63.2 1.0
C2' E:DT503 3.2 40.3 1.0
C3' E:DT503 3.3 46.0 1.0
O3' E:DT503 3.6 60.4 1.0
H3' E:DA504 3.7 46.0 1.0
C8 E:DA504 3.9 35.7 1.0
H2' E:DA504 4.3 40.1 1.0
O E:HOH705 4.3 53.8 1.0
C5' E:DA504 4.4 48.6 1.0
OP1 E:DA504 4.5 60.1 1.0
C3' E:DA504 4.5 38.3 1.0
O4' E:DA504 4.6 36.0 1.0
N7 E:DA504 4.6 35.3 1.0
C1' E:DT503 4.7 39.7 1.0
H5' E:DA504 4.7 58.3 1.0
C4' E:DT503 4.7 45.0 1.0
C4' E:DA504 4.7 48.4 1.0
O5' E:DT503 4.8 43.5 1.0
N9 E:DA504 4.8 39.5 1.0
C2' E:DA504 4.8 33.4 1.0
H1' E:DT503 5.0 47.7 1.0

Sodium binding site 4 out of 9 in 4iem

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Sodium binding site 4 out of 9 in the Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na601

b:64.6
occ:1.00
 OP2 F:DC510 2.3 48.0 1.0
H6 F:DC510 2.5 55.5 1.0
C6 F:DC510 3.3 46.3 1.0
H5 F:DC510 3.3 50.8 1.0
O5' F:DC510 3.4 53.3 1.0
H2' F:DC510 3.4 60.9 1.0
P F:DC510 3.4 54.3 1.0
H2'' F:DT509 3.4 58.4 1.0
H2' F:DT509 3.5 58.4 1.0
C5 F:DC510 3.7 42.4 1.0
C2' F:DT509 3.8 48.7 1.0
H3' F:DT509 4.0 59.5 1.0
C3' F:DT509 4.3 49.6 1.0
C2' F:DC510 4.3 50.7 1.0
O3' F:DT509 4.3 57.8 1.0
N1 F:DC510 4.4 38.8 1.0
O F:HOH709 4.6 54.1 1.0
OP1 F:DC510 4.6 52.3 1.0
C5' F:DC510 4.7 46.9 1.0
C1' F:DC510 4.7 46.8 1.0
H3' F:DC510 4.7 63.2 1.0
O4' F:DC510 4.7 46.7 1.0
H2'' F:DC510 5.0 60.9 1.0
C3' F:DC510 5.0 52.7 1.0

Sodium binding site 5 out of 9 in 4iem

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Sodium binding site 5 out of 9 in the Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:81.3
occ:1.00
 HE2 B:TYR257 1.6 0.1 1.0
CE2 B:TYR257 2.3 87.6 1.0
O B:SER298 2.5 70.9 1.0
HZ2 B:LYS299 2.5 89.4 1.0
OH B:TYR257 2.5 89.2 1.0
HA B:LYS299 2.8 92.1 1.0
CZ B:TYR257 2.8 87.4 1.0
HD3 B:LYS299 3.0 98.2 1.0
HE2 B:LYS299 3.0 89.3 1.0
HD2 B:PRO48 3.0 0.8 1.0
OD1 B:ASP47 3.2 79.7 1.0
NZ B:LYS299 3.2 74.5 1.0
CE B:LYS299 3.4 74.4 1.0
CD2 B:TYR257 3.5 84.8 1.0
HE1 B:PHE253 3.5 83.3 1.0
C B:SER298 3.5 69.5 1.0
HZ3 B:LYS299 3.5 89.4 1.0
HD1 B:PHE253 3.6 84.0 1.0
CD B:LYS299 3.6 81.8 1.0
HD2 B:TYR257 3.7 0.8 1.0
CA B:LYS299 3.7 76.8 1.0
OD1 B:ASP297 3.8 74.5 1.0
CD B:PRO48 3.9 84.9 1.0
HZ1 B:LYS299 3.9 89.4 1.0
CE1 B:PHE253 4.0 69.4 1.0
CD1 B:PHE253 4.1 70.0 1.0
HD3 B:PRO48 4.1 0.8 1.0
N B:LYS299 4.1 73.4 1.0
CE1 B:TYR257 4.1 81.6 1.0
HG2 B:PRO48 4.1 81.7 1.0
CG B:ASP47 4.2 87.3 1.0
H B:SER298 4.2 98.3 1.0
HD2 B:LYS299 4.3 98.2 1.0
HE3 B:LYS299 4.3 89.3 1.0
H B:ILE300 4.4 73.4 1.0
OH B:TYR45 4.4 69.3 1.0
C B:LYS299 4.5 73.1 1.0
HH B:TYR45 4.5 83.2 1.0
HG13 B:ILE300 4.5 65.8 1.0
OD2 B:ASP47 4.5 81.1 1.0
CG B:LYS299 4.5 85.7 1.0
HG2 B:LYS299 4.5 0.9 1.0
CG B:PRO48 4.6 68.0 1.0
CG B:TYR257 4.6 88.1 1.0
CB B:LYS299 4.6 83.9 1.0
HE1 B:TYR257 4.7 98.0 1.0
N B:ILE300 4.7 61.2 1.0
CG B:ASP297 4.7 72.7 1.0
CA B:SER298 4.8 71.8 1.0
HA B:ASP47 4.8 0.8 1.0
N B:SER298 4.8 82.0 1.0
CD1 B:TYR257 4.9 84.8 1.0
HB3 B:LYS299 4.9 0.7 1.0
H B:LYS299 4.9 88.0 1.0
HB3 B:SER298 5.0 82.9 1.0

Sodium binding site 6 out of 9 in 4iem

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Sodium binding site 6 out of 9 in the Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:79.1
occ:1.00
 OD1 B:ASP189 2.2 71.3 1.0
HH21 B:ARG185 2.6 88.9 1.0
O B:GLU236 2.8 74.3 1.0
CG B:ASP189 3.0 66.2 1.0
HA B:GLU236 3.1 88.8 1.0
HG22 B:VAL213 3.1 0.5 1.0
OD2 B:ASP189 3.1 69.1 1.0
NH2 B:ARG185 3.1 74.1 1.0
HG23 B:VAL213 3.2 0.5 1.0
HA3 B:GLY239 3.3 0.4 1.0
HE B:ARG185 3.4 68.5 1.0
HB3 B:GLU236 3.5 85.6 1.0
HH22 B:ARG185 3.5 88.9 1.0
CG2 B:VAL213 3.6 85.4 1.0
C B:GLU236 3.6 70.3 1.0
CA B:GLU236 3.7 74.0 1.0
H B:PHE240 3.8 92.1 1.0
CZ B:ARG185 3.8 69.7 1.0
N B:PHE240 3.8 76.7 1.0
HB2 B:PHE240 3.9 94.3 1.0
NE B:ARG185 3.9 57.1 1.0
C B:GLY239 3.9 79.1 1.0
CA B:GLY239 4.0 85.3 1.0
CB B:GLU236 4.1 71.3 1.0
HG21 B:VAL213 4.1 0.5 1.0
HG2 B:GLU236 4.3 93.1 1.0
H B:GLY239 4.4 0.5 1.0
CB B:ASP189 4.4 63.3 1.0
O B:GLY239 4.4 77.3 1.0
HA B:PHE240 4.4 97.4 1.0
CA B:PHE240 4.5 81.2 1.0
HB3 B:ASP189 4.5 76.0 1.0
HG12 B:VAL213 4.5 80.8 1.0
N B:GLY239 4.6 84.6 1.0
CB B:PHE240 4.6 78.6 1.0
O B:HOH514 4.6 46.8 1.0
HA2 B:GLY239 4.7 0.4 1.0
CB B:VAL213 4.7 81.5 1.0
CG B:GLU236 4.8 77.6 1.0
HG3 B:ARG185 4.8 84.7 1.0
HB B:VAL213 4.8 97.8 1.0
NH1 B:ARG185 4.8 71.8 1.0
HB2 B:ASP189 4.9 76.0 1.0
HB2 B:GLU236 4.9 85.6 1.0
N B:ARG237 4.9 74.1 1.0
O B:GLN235 4.9 76.2 1.0
HG11 B:VAL172 5.0 66.5 1.0
HD1 B:PHE240 5.0 90.5 1.0

Sodium binding site 7 out of 9 in 4iem

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Sodium binding site 7 out of 9 in the Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:72.1
occ:1.00
 O B:ASP189 2.2 78.7 1.0
HB2 B:ARG193 2.5 92.4 1.0
HD13 B:LEU243 2.5 90.5 1.0
HA B:ASP189 3.0 80.6 1.0
H B:ARG193 3.1 92.8 1.0
C B:ASP189 3.2 75.3 1.0
HB2 B:LEU243 3.2 0.1 1.0
HB3 B:PHE192 3.2 83.0 1.0
CB B:ARG193 3.4 77.0 1.0
CD1 B:LEU243 3.4 75.5 1.0
CA B:ASP189 3.5 67.2 1.0
N B:ARG193 3.5 77.4 1.0
HD12 B:LEU243 3.6 90.5 1.0
HD2 B:PHE192 3.6 74.8 1.0
HB3 B:ASP189 3.7 76.0 1.0
HB3 B:ARG193 3.7 92.4 1.0
O B:HOH514 3.8 46.8 1.0
CA B:ARG193 3.9 77.7 1.0
HA B:ARG193 3.9 93.2 1.0
HD11 B:LEU243 4.0 90.5 1.0
O B:GLY239 4.0 77.3 1.0
CB B:ASP189 4.0 63.3 1.0
CB B:LEU243 4.0 85.9 1.0
HD22 B:LEU243 4.1 96.1 1.0
HD3 B:ARG193 4.1 96.2 1.0
CB B:PHE192 4.1 69.2 1.0
CG B:LEU243 4.2 78.7 1.0
CG B:ASP189 4.3 66.2 1.0
N B:GLU190 4.4 71.8 1.0
CD2 B:PHE192 4.4 62.3 1.0
C B:PHE192 4.4 77.3 1.0
CG B:ARG193 4.5 74.5 1.0
HG3 B:ARG193 4.5 89.4 1.0
HA B:GLU190 4.5 89.0 1.0
H B:PHE192 4.5 91.5 1.0
HB3 B:LEU243 4.6 0.1 1.0
OD2 B:ASP189 4.6 69.1 1.0
HB2 B:PHE192 4.6 83.0 1.0
CD2 B:LEU243 4.7 80.1 1.0
CD B:ARG193 4.8 80.2 1.0
CG B:PHE192 4.8 61.6 1.0
CA B:PHE192 4.8 78.2 1.0
HA B:LEU243 4.8 0.0 1.0
O B:TRP188 4.8 57.9 1.0
N B:ASP189 4.8 65.6 1.0
OD1 B:ASP189 4.9 71.3 1.0
CA B:GLU190 4.9 74.2 1.0
HB2 B:ASP189 4.9 76.0 1.0
HD12 B:LEU196 5.0 80.7 1.0
CA B:LEU243 5.0 83.3 1.0

Sodium binding site 8 out of 9 in 4iem

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Sodium binding site 8 out of 9 in the Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:78.5
occ:1.00
 HD22 D:ASN222 2.0 81.0 1.0
OP2 O:DT509 2.3 64.3 1.0
ND2 D:ASN222 2.8 67.5 1.0
H3' O:DA508 3.0 69.0 1.0
HG21 D:VAL278 3.3 59.8 1.0
HD21 D:ASN222 3.3 81.0 1.0
HG11 D:VAL278 3.5 54.6 1.0
P O:DT509 3.6 58.4 1.0
CG D:ASN222 3.7 60.1 1.0
OD1 D:ASN222 3.7 67.1 1.0
C3' O:DA508 3.8 57.5 1.0
HG22 D:VAL278 3.8 59.8 1.0
CG2 D:VAL278 3.9 49.8 1.0
HG13 D:VAL278 4.0 54.6 1.0
H2' O:DA508 4.0 69.6 1.0
H2'' O:DA508 4.0 69.6 1.0
O3' O:DA508 4.1 66.0 1.0
CG1 D:VAL278 4.1 45.5 1.0
C2' O:DA508 4.1 58.0 1.0
OP1 O:DT509 4.3 58.9 1.0
CB D:VAL278 4.7 51.4 1.0
HG2 D:ARG221 4.7 67.9 1.0
HG23 D:VAL278 4.7 59.8 1.0
O5' O:DT509 4.7 54.0 1.0
O5' O:DA508 4.8 42.8 1.0
HG12 D:VAL278 5.0 54.6 1.0
HG3 D:ARG221 5.0 67.9 1.0

Sodium binding site 9 out of 9 in 4iem

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Sodium binding site 9 out of 9 in the Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na601

b:56.6
occ:1.00
 OP2 N:DA504 2.4 60.9 1.0
H8 N:DA504 2.7 71.8 1.0
H2'' N:DT503 3.0 66.4 1.0
O5' N:DA504 3.0 70.0 1.0
H3' N:DT503 3.2 77.1 1.0
P N:DA504 3.2 76.2 1.0
H2' N:DT503 3.3 66.4 1.0
C2' N:DT503 3.4 55.3 1.0
H3' N:DA504 3.4 58.4 1.0
C3' N:DT503 3.6 64.3 1.0
C8 N:DA504 3.7 59.9 1.0
H2' N:DA504 3.9 58.7 1.0
O3' N:DT503 3.9 68.7 1.0
C3' N:DA504 4.2 48.7 1.0
C5' N:DA504 4.3 55.5 1.0
C2' N:DA504 4.4 48.9 1.0
O4' N:DA504 4.5 52.0 1.0
N7 N:DA504 4.5 57.0 1.0
C4' N:DA504 4.6 50.8 1.0
N9 N:DA504 4.6 58.1 1.0
OP1 N:DA504 4.6 81.5 1.0
H5' N:DA504 4.7 66.6 1.0
C1' N:DA504 4.8 51.6 1.0
C1' N:DT503 4.9 54.4 1.0
H5'' N:DA504 5.0 66.6 1.0

Reference:

S.E.Tsutakawa, D.S.Shin, C.D.Mol, T.Izumi, A.S.Arvai, A.K.Mantha, B.Szczesny, I.N.Ivanov, D.J.Hosfield, B.Maiti, M.E.Pique, K.A.Frankel, K.Hitomi, R.P.Cunningham, S.Mitra, J.A.Tainer. Conserved Structural Chemistry For Incision Activity in Structurally Non-Homologous Apurinic/Apyrimidinic Endonuclease APE1 and Endonuclease IV Dna Repair Enzymes. J.Biol.Chem. V. 288 8445 2013.
ISSN: ISSN 0021-9258
PubMed: 23355472
DOI: 10.1074/JBC.M112.422774
Page generated: Mon Oct 7 15:59:40 2024

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