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Lead in PDB 1e9n: A Second Divalent Metal Ion in the Active Site of A New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, APE1, and Its Implications For the Catalytic Mechanism

Enzymatic activity of A Second Divalent Metal Ion in the Active Site of A New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, APE1, and Its Implications For the Catalytic Mechanism

All present enzymatic activity of A Second Divalent Metal Ion in the Active Site of A New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, APE1, and Its Implications For the Catalytic Mechanism:
4.2.99.18;

Protein crystallography data

The structure of A Second Divalent Metal Ion in the Active Site of A New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, APE1, and Its Implications For the Catalytic Mechanism, PDB code: 1e9n was solved by P.T.Beernink, B.W.Segelke, B.Rupp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 137.522, 45.016, 125.702, 90.00, 108.03, 90.00
R / Rfree (%) 18.6 / 25.2

Lead Binding Sites:

The binding sites of Lead atom in the A Second Divalent Metal Ion in the Active Site of A New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, APE1, and Its Implications For the Catalytic Mechanism (pdb code 1e9n). This binding sites where shown within 5.0 Angstroms radius around Lead atom.
In total 4 binding sites of Lead where determined in the A Second Divalent Metal Ion in the Active Site of A New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, APE1, and Its Implications For the Catalytic Mechanism, PDB code: 1e9n:
Jump to Lead binding site number: 1; 2; 3; 4;

Lead binding site 1 out of 4 in 1e9n

Go back to Lead Binding Sites List in 1e9n
Lead binding site 1 out of 4 in the A Second Divalent Metal Ion in the Active Site of A New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, APE1, and Its Implications For the Catalytic Mechanism


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 1 of A Second Divalent Metal Ion in the Active Site of A New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, APE1, and Its Implications For the Catalytic Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pb1319

b:63.3
occ:1.00
 OE1 A:GLU96 2.0 85.2 1.0
O A:HOH2164 2.8 26.3 1.0
CD A:GLU96 3.1 28.9 1.0
O A:HOH2165 3.2 39.5 1.0
O A:HOH2163 3.3 38.9 1.0
O A:HOH2024 3.4 38.9 1.0
O A:HOH2038 3.4 40.3 1.0
OD1 A:ASP70 3.5 43.2 1.0
OE2 A:GLU96 3.7 89.2 1.0
O A:HOH2080 4.1 30.0 1.0
CG A:GLU96 4.2 48.0 1.0
CG A:ASP70 4.3 49.4 1.0
OD2 A:ASP308 4.3 39.7 1.0
ND2 A:ASN68 4.6 24.3 1.0
OH A:TYR171 4.6 45.9 1.0
OD1 A:ASP308 4.6 29.6 1.0
CB A:ASP70 4.7 37.4 1.0
OD1 A:ASN68 4.9 35.9 1.0
CG A:ASP308 4.9 27.8 1.0
CB A:GLU96 5.0 29.7 1.0

Lead binding site 2 out of 4 in 1e9n

Go back to Lead Binding Sites List in 1e9n
Lead binding site 2 out of 4 in the A Second Divalent Metal Ion in the Active Site of A New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, APE1, and Its Implications For the Catalytic Mechanism


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 2 of A Second Divalent Metal Ion in the Active Site of A New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, APE1, and Its Implications For the Catalytic Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pb1320

b:56.4
occ:1.00
 OD2 A:ASP210 2.8 37.4 1.0
O A:HOH2080 2.9 30.0 1.0
ND2 A:ASN212 3.0 20.6 1.0
NE2 A:HIS309 3.0 21.4 1.0
OD1 A:ASP210 3.2 14.7 1.0
CG A:ASP210 3.3 23.4 1.0
CE1 A:HIS309 3.3 20.1 1.0
OD1 A:ASN212 3.7 24.3 1.0
CG A:ASN212 3.7 32.5 1.0
CD1 A:LEU282 3.8 28.2 1.0
CD2 A:HIS309 4.3 26.8 1.0
OD1 A:ASN68 4.4 35.9 1.0
O A:HOH2165 4.6 39.5 1.0
CE1 A:TYR171 4.6 35.1 1.0
ND1 A:HIS309 4.6 23.8 1.0
CB A:ASP210 4.7 23.6 1.0
CB A:LEU282 5.0 28.2 1.0

Lead binding site 3 out of 4 in 1e9n

Go back to Lead Binding Sites List in 1e9n
Lead binding site 3 out of 4 in the A Second Divalent Metal Ion in the Active Site of A New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, APE1, and Its Implications For the Catalytic Mechanism


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 3 of A Second Divalent Metal Ion in the Active Site of A New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, APE1, and Its Implications For the Catalytic Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pb1319

b:53.9
occ:1.00
 OD2 B:ASP210 2.7 33.8 1.0
NE2 B:HIS309 3.0 20.0 1.0
ND2 B:ASN212 3.1 16.8 1.0
OD1 B:ASP210 3.1 12.0 1.0
O B:HOH2076 3.1 24.1 1.0
CG B:ASP210 3.3 20.9 1.0
CE1 B:HIS309 3.3 17.8 1.0
CD1 B:LEU282 3.7 25.8 1.0
OD1 B:ASN212 3.8 23.9 1.0
CG B:ASN212 3.8 29.1 1.0
ND2 B:ASN68 4.0 23.7 1.0
CD2 B:HIS309 4.3 24.1 1.0
ND1 B:HIS309 4.6 20.2 1.0
CE1 B:TYR171 4.7 31.2 1.0
CB B:ASP210 4.7 21.1 1.0
O B:HOH2078 4.8 57.2 1.0
O B:HOH2101 4.9 27.3 1.0
CB B:LEU282 4.9 25.1 1.0
CG B:LEU282 4.9 29.4 1.0

Lead binding site 4 out of 4 in 1e9n

Go back to Lead Binding Sites List in 1e9n
Lead binding site 4 out of 4 in the A Second Divalent Metal Ion in the Active Site of A New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, APE1, and Its Implications For the Catalytic Mechanism


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 4 of A Second Divalent Metal Ion in the Active Site of A New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, APE1, and Its Implications For the Catalytic Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pb1320

b:58.0
occ:1.00
 OE1 B:GLU96 2.0 85.4 1.0
O B:HOH2178 2.9 20.3 1.0
CD B:GLU96 3.1 27.1 1.0
OE2 B:GLU96 3.7 89.3 1.0
OD1 B:ASP70 3.7 43.6 1.0
O B:HOH2076 4.1 24.1 1.0
OH B:TYR171 4.2 42.9 1.0
CG B:GLU96 4.3 46.7 1.0
OD2 B:ASP308 4.3 36.6 1.0
ND2 B:ASN68 4.5 23.7 1.0
CG B:ASP70 4.5 49.3 1.0
OD1 B:ASN68 4.5 31.5 1.0
OD1 B:ASP308 4.6 28.1 1.0
CB B:ASP70 4.9 38.2 1.0
CG B:ASP308 4.9 25.9 1.0
CG B:ASN68 4.9 36.3 1.0

Reference:

P.T.Beernink, B.W.Segelke, M.Z.Hadi, J.P.Erzberger, D.M.Wilson Iii, B.Rupp. Two Divalent Metal Ions in the Active Site of A New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, APE1: Implications For the Catalytic Mechanism J.Mol.Biol. V. 307 1023 2001.
ISSN: ISSN 0022-2836
PubMed: 11286553
DOI: 10.1006/JMBI.2001.4529
Page generated: Thu Oct 10 09:59:35 2024

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