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Manganese in PDB 5dg0: Human APE1 Phosphorothioate Substrate Complex with MN2+

Enzymatic activity of Human APE1 Phosphorothioate Substrate Complex with MN2+

All present enzymatic activity of Human APE1 Phosphorothioate Substrate Complex with MN2+:
4.2.99.18;

Protein crystallography data

The structure of Human APE1 Phosphorothioate Substrate Complex with MN2+, PDB code: 5dg0 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) 23.95 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.365, 60.601, 73.316, 83.12, 80.68, 89.04
R / Rfree (%) 16.6 / 20.5

Other elements in 5dg0:

The structure of Human APE1 Phosphorothioate Substrate Complex with MN2+ also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Human APE1 Phosphorothioate Substrate Complex with MN2+ (pdb code 5dg0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Human APE1 Phosphorothioate Substrate Complex with MN2+, PDB code: 5dg0:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 5dg0

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Manganese binding site 1 out of 7 in the Human APE1 Phosphorothioate Substrate Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human APE1 Phosphorothioate Substrate Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:31.8
occ:0.55
 OE2 A:GLU96 2.1 46.5 1.0
OD1 A:ASP70 2.2 27.5 1.0
O A:HOH504 2.2 37.5 1.0
O A:HOH527 2.2 27.9 1.0
O A:HOH516 2.3 37.9 1.0
CG A:ASP70 2.9 31.5 1.0
CD A:GLU96 3.0 27.8 1.0
OE1 A:GLU96 3.3 20.3 1.0
CB A:ASP70 3.4 21.4 1.0
CA A:ASP70 3.7 18.8 1.0
O A:HOH519 3.8 27.9 1.0
OD1 A:ASP308 3.9 17.3 1.0
OD2 A:ASP70 3.9 24.8 1.0
SP3 P:48Z11 4.1 24.0 0.6
OD2 A:ASP308 4.2 16.6 1.0
CG A:GLU96 4.2 27.6 1.0
OP1 P:48Z11 4.3 21.9 0.4
CE A:LYS98 4.4 30.8 1.0
CG A:ASP308 4.5 15.8 1.0
C A:ASP70 4.6 17.4 1.0
OD1 A:ASN68 4.6 14.4 1.0
N A:ASP70 4.8 12.4 1.0
O A:ASP70 4.9 20.2 1.0
CB A:GLU96 5.0 20.6 1.0
O3' P:OMC10 5.0 20.8 0.3
NZ A:LYS98 5.0 33.8 1.0

Manganese binding site 2 out of 7 in 5dg0

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Manganese binding site 2 out of 7 in the Human APE1 Phosphorothioate Substrate Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human APE1 Phosphorothioate Substrate Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:86.1
occ:1.00
 O A:HOH604 2.2 19.8 1.0
O A:HOH631 3.0 44.4 1.0
O A:HOH620 3.3 41.3 1.0
O A:HOH575 3.6 36.3 1.0
O A:HOH667 4.0 24.3 1.0
O A:HOH560 4.1 18.1 1.0
O A:ASP47 4.2 20.8 1.0
O A:PRO48 4.4 17.0 1.0
O A:HOH695 4.5 20.6 1.0
CA A:PRO49 4.5 18.2 1.0
C A:PRO48 4.8 20.8 1.0
N A:PRO49 4.9 21.4 1.0
OD1 A:ASP50 4.9 17.4 1.0

Manganese binding site 3 out of 7 in 5dg0

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Manganese binding site 3 out of 7 in the Human APE1 Phosphorothioate Substrate Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Human APE1 Phosphorothioate Substrate Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:73.4
occ:1.00
 O A:GLY225 2.9 25.6 1.0
ND2 A:ASN229 3.4 42.4 1.0
N7 P:DG13 3.6 31.7 1.0
O6 P:DG13 3.6 39.5 1.0
O A:HOH580 3.9 27.4 1.0
C A:GLY225 4.0 24.3 1.0
OD1 A:ASN226 4.1 33.9 1.0
CG A:ASN229 4.2 41.9 1.0
C5 P:DG13 4.3 29.2 1.0
C6 P:DG13 4.3 33.4 1.0
O4 V:DT8 4.4 41.2 1.0
OD1 A:ASN229 4.5 39.2 1.0
C8 P:DG13 4.7 23.5 1.0
C6 P:DC12 4.7 40.2 1.0
C2' P:DC12 4.8 25.3 1.0
CA A:GLY225 4.8 30.1 1.0
CA A:ASN226 4.8 19.9 1.0
N A:ASN226 4.9 19.4 1.0
CG A:ASN226 4.9 21.8 1.0
O V:HOH122 4.9 43.2 1.0
N6 P:DA14 5.0 35.8 1.0

Manganese binding site 4 out of 7 in 5dg0

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Manganese binding site 4 out of 7 in the Human APE1 Phosphorothioate Substrate Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Human APE1 Phosphorothioate Substrate Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:87.3
occ:1.00
 O B:HOH504 2.0 44.3 1.0
O B:HOH591 2.0 55.8 1.0
OD1 B:ASN229 2.2 27.2 1.0
O B:HOH624 2.2 58.4 1.0
O B:HOH637 2.3 49.8 1.0
CG B:ASN229 3.3 28.9 1.0
O B:LYS228 3.7 23.9 1.0
O B:HOH611 3.8 39.8 1.0
CA B:ASN229 4.0 20.4 1.0
N B:GLY178 4.1 32.4 1.0
CB B:ASN229 4.2 18.4 1.0
ND2 B:ASN229 4.3 25.6 1.0
CA B:GLY178 4.4 30.9 1.0
C B:LYS228 4.5 25.8 1.0
O B:HOH552 4.5 35.4 1.0
N B:ASN229 4.6 21.3 1.0

Manganese binding site 5 out of 7 in 5dg0

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Manganese binding site 5 out of 7 in the Human APE1 Phosphorothioate Substrate Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Human APE1 Phosphorothioate Substrate Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:70.6
occ:1.00
 O P:HOH234 2.1 44.0 1.0
N7 P:DG1 2.3 36.7 1.0
C8 P:DG1 3.1 33.9 1.0
C5 P:DG1 3.5 30.6 1.0
O6 P:DG1 3.9 32.1 1.0
C6 P:DG1 4.1 31.8 1.0
N4 P:DC2 4.3 25.5 1.0
N9 P:DG1 4.3 30.2 1.0
C4 P:DG1 4.5 32.8 1.0
C5 P:DC2 4.9 27.6 1.0
C4 P:DC2 5.0 29.6 1.0

Manganese binding site 6 out of 7 in 5dg0

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Manganese binding site 6 out of 7 in the Human APE1 Phosphorothioate Substrate Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Human APE1 Phosphorothioate Substrate Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn102

b:71.3
occ:1.00
 N7 P:DG4 2.3 25.8 1.0
C8 P:DG4 3.1 23.8 1.0
C5 P:DG4 3.4 24.2 1.0
O V:HOH121 3.5 41.9 1.0
O P:HOH231 3.6 36.0 1.0
O P:HOH215 3.6 39.5 1.0
O P:HOH222 3.7 42.8 1.0
O6 P:DG4 3.9 24.9 1.0
C6 P:DG4 4.0 23.6 1.0
N9 P:DG4 4.3 22.6 1.0
N6 P:DA5 4.3 24.1 1.0
C4 P:DG4 4.5 25.1 1.0
C6 P:DT3 4.5 23.8 1.0
C5 P:DT3 4.7 26.3 1.0
C7 P:DT3 4.7 23.0 1.0
C2' P:DT3 4.8 24.0 1.0

Manganese binding site 7 out of 7 in 5dg0

Go back to Manganese Binding Sites List in 5dg0
Manganese binding site 7 out of 7 in the Human APE1 Phosphorothioate Substrate Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Human APE1 Phosphorothioate Substrate Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn103

b:85.9
occ:1.00
 O P:HOH205 2.2 39.0 1.0
N7 P:DG16 2.9 44.7 1.0
C8 P:DG16 3.8 47.1 1.0
C2' P:DC15 3.9 53.9 1.0
C5 P:DG16 4.0 40.4 1.0
O P:HOH230 4.0 38.1 1.0
C6 P:DC15 4.1 40.7 1.0
O6 P:DG16 4.1 40.9 1.0
C6 P:DG16 4.5 42.4 1.0
O6 P:DG17 4.5 35.2 1.0
C5 P:DC15 4.5 37.4 1.0
N1 P:DC15 4.6 45.8 1.0
C1' P:DC15 4.8 47.5 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 Oct 5 23:54:36 2024

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