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Iron in PDB 8dwe: Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine

Enzymatic activity of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine

All present enzymatic activity of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine:
3.2.2.31;

Protein crystallography data

The structure of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine, PDB code: 8dwe was solved by L.P.Russelburg, M.Demir, S.S.David, M.P.Horvath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.12 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.63, 137.96, 74.49, 90, 101, 90
R / Rfree (%) 19.2 / 23.4

Other elements in 8dwe:

The structure of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine (pdb code 8dwe). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine, PDB code: 8dwe:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8dwe

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Iron binding site 1 out of 8 in the Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:50.8
occ:1.00
FE1 A:SF4401 0.0 50.8 1.0
S2 A:SF4401 2.2 48.7 1.0
S3 A:SF4401 2.3 56.7 1.0
S4 A:SF4401 2.3 52.6 1.0
SG A:CYS208 2.4 49.6 1.0
FE3 A:SF4401 2.7 49.3 1.0
FE4 A:SF4401 2.7 47.4 1.0
FE2 A:SF4401 2.8 57.1 1.0
HB2 A:CYS208 3.0 64.0 1.0
CB A:CYS208 3.1 55.3 1.0
HB3 A:CYS208 3.3 64.0 1.0
HA A:CYS205 3.6 70.8 1.0
HG23 A:VAL210 3.8 56.0 1.0
S1 A:SF4401 3.9 55.2 1.0
HB2 A:CYS198 3.9 55.1 1.0
HA A:GLN211 4.0 68.7 1.0
HG12 A:VAL197 4.2 56.8 1.0
HB2 A:CYS214 4.3 55.7 1.0
HG22 A:VAL210 4.3 56.0 1.0
HD21 A:LEU193 4.4 54.6 1.0
CG2 A:VAL210 4.5 47.7 1.0
HD11 A:LEU193 4.5 54.7 1.0
H A:VAL210 4.5 57.9 1.0
CA A:CYS208 4.5 55.7 1.0
CA A:CYS205 4.5 61.7 1.0
HB3 A:CYS205 4.6 69.9 1.0
HA A:CYS208 4.7 63.9 1.0
CB A:CYS198 4.7 47.8 1.0
HG11 A:VAL197 4.7 56.8 1.0
N A:GLN211 4.8 55.9 1.0
HB2 A:GLN211 4.8 70.8 1.0
CA A:GLN211 4.8 58.4 1.0
SG A:CYS198 4.8 48.6 1.0
HD21 A:LEU154 4.9 50.3 1.0
CG1 A:VAL197 4.9 50.2 1.0
HD2 A:PRO209 4.9 61.3 1.0
SG A:CYS214 4.9 52.1 1.0
CB A:CYS205 4.9 61.2 1.0
H A:GLN211 4.9 66.3 1.0
CB A:CYS214 4.9 46.8 1.0
C A:VAL210 4.9 55.3 1.0
HA A:CYS198 5.0 54.8 1.0
HG21 A:VAL210 5.0 56.0 1.0

Iron binding site 2 out of 8 in 8dwe

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Iron binding site 2 out of 8 in the Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:57.1
occ:1.00
FE2 A:SF4401 0.0 57.1 1.0
S1 A:SF4401 2.2 55.2 1.0
S4 A:SF4401 2.2 52.6 1.0
S3 A:SF4401 2.3 56.7 1.0
SG A:CYS205 2.5 53.9 1.0
FE3 A:SF4401 2.7 49.3 1.0
FE4 A:SF4401 2.7 47.4 1.0
FE1 A:SF4401 2.8 50.8 1.0
HA A:CYS205 2.9 70.8 1.0
HB3 A:CYS205 3.1 69.9 1.0
CB A:CYS205 3.2 61.2 1.0
HB2 A:PRO203 3.4 67.8 1.0
CA A:CYS205 3.4 61.7 1.0
S2 A:SF4401 3.9 48.7 1.0
H A:CYS205 3.9 63.4 1.0
N A:CYS205 4.0 55.3 1.0
HB2 A:PHE217 4.0 74.7 1.0
HB2 A:CYS205 4.1 69.9 1.0
HB2 A:CYS208 4.1 64.0 1.0
CB A:PRO203 4.3 55.9 1.0
HG2 A:PRO203 4.4 71.8 1.0
HB3 A:CYS208 4.6 64.0 1.0
HB3 A:PRO203 4.6 67.8 1.0
HB1 A:ALA222 4.6 70.1 1.0
HA A:CYS198 4.7 54.8 1.0
CB A:CYS208 4.7 55.3 1.0
HD1 A:PHE217 4.7 82.3 1.0
HD3 A:ARG153 4.7 58.5 1.0
C A:CYS205 4.8 67.0 1.0
CG A:PRO203 4.8 59.7 1.0
HB2 A:CYS198 4.8 55.1 1.0
SG A:CYS214 4.8 52.1 1.0
HB2 A:ALA222 4.8 70.1 1.0
HG3 A:PRO203 4.8 71.8 1.0
SG A:CYS208 4.8 49.6 1.0
C A:SER204 4.9 51.4 1.0
SG A:CYS198 4.9 48.6 1.0
CB A:PHE217 5.0 63.9 1.0

Iron binding site 3 out of 8 in 8dwe

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Iron binding site 3 out of 8 in the Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:49.3
occ:1.00
FE3 A:SF4401 0.0 49.3 1.0
S1 A:SF4401 2.3 55.2 1.0
S2 A:SF4401 2.3 48.7 1.0
S4 A:SF4401 2.3 52.6 1.0
SG A:CYS198 2.4 48.6 1.0
FE1 A:SF4401 2.7 50.8 1.0
FE2 A:SF4401 2.7 57.1 1.0
FE4 A:SF4401 2.7 47.4 1.0
HB2 A:CYS198 2.7 55.1 1.0
CB A:CYS198 3.1 47.8 1.0
HD3 A:ARG153 3.4 58.5 1.0
HA A:CYS198 3.5 54.8 1.0
S3 A:SF4401 3.8 56.7 1.0
CA A:CYS198 3.9 47.8 1.0
HB3 A:CYS198 3.9 55.1 1.0
HH11 A:ARG153 3.9 57.8 1.0
HB2 A:PRO203 4.1 67.8 1.0
HD2 A:ARG153 4.2 58.5 1.0
HB3 A:ARG153 4.2 56.0 1.0
CD A:ARG153 4.2 50.6 1.0
HB2 A:ARG153 4.3 56.0 1.0
HB3 A:PRO203 4.4 67.8 1.0
HA A:VAL150 4.5 50.9 1.0
HG22 A:VAL150 4.6 52.0 1.0
NH1 A:ARG153 4.6 50.0 1.0
CB A:ARG153 4.7 48.5 1.0
CB A:PRO203 4.7 55.9 1.0
HG12 A:VAL197 4.8 56.8 1.0
N A:CYS198 4.8 48.9 1.0
SG A:CYS208 4.8 49.6 1.0
SG A:CYS214 4.8 52.1 1.0
C A:CYS198 4.9 47.3 1.0
HA A:CYS205 4.9 70.8 1.0

Iron binding site 4 out of 8 in 8dwe

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Iron binding site 4 out of 8 in the Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:47.4
occ:1.00
FE4 A:SF4401 0.0 47.4 1.0
S2 A:SF4401 2.3 48.7 1.0
S3 A:SF4401 2.3 56.7 1.0
S1 A:SF4401 2.3 55.2 1.0
SG A:CYS214 2.4 52.1 1.0
FE1 A:SF4401 2.7 50.8 1.0
FE3 A:SF4401 2.7 49.3 1.0
FE2 A:SF4401 2.7 57.1 1.0
HB2 A:CYS214 2.9 55.7 1.0
CB A:CYS214 3.1 46.8 1.0
HB3 A:CYS214 3.3 55.7 1.0
HB2 A:PHE217 3.6 74.7 1.0
HB3 A:ARG153 3.8 56.0 1.0
S4 A:SF4401 3.9 52.6 1.0
HD23 A:LEU154 3.9 50.3 1.0
H A:PHE217 4.2 63.5 1.0
HA A:GLN211 4.4 68.7 1.0
HB3 A:PHE217 4.4 74.7 1.0
CB A:PHE217 4.4 63.9 1.0
HD21 A:LEU154 4.5 50.3 1.0
CA A:CYS214 4.5 54.5 1.0
HD3 A:ARG153 4.6 58.5 1.0
CD2 A:LEU154 4.6 43.3 1.0
HB2 A:ARG153 4.6 56.0 1.0
CB A:ARG153 4.6 48.5 1.0
HA A:CYS214 4.7 64.8 1.0
HG A:LEU154 4.7 54.2 1.0
HB3 A:ALA216 4.7 63.2 1.0
HA A:LEU154 4.8 58.7 1.0
HG23 A:VAL210 4.8 56.0 1.0
N A:PHE217 4.9 53.6 1.0
HB3 A:CYS205 4.9 69.9 1.0
SG A:CYS205 4.9 53.9 1.0
SG A:CYS208 4.9 49.6 1.0
SG A:CYS198 4.9 48.6 1.0

Iron binding site 5 out of 8 in 8dwe

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Iron binding site 5 out of 8 in the Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:48.9
occ:1.00
FE1 D:SF4401 0.0 48.9 1.0
S4 D:SF4401 2.2 49.4 1.0
S2 D:SF4401 2.3 42.5 1.0
S3 D:SF4401 2.3 53.8 1.0
SG D:CYS208 2.4 51.8 1.0
FE3 D:SF4401 2.7 42.1 1.0
FE2 D:SF4401 2.7 49.2 1.0
FE4 D:SF4401 2.7 45.5 1.0
HB2 D:CYS208 3.0 60.7 1.0
CB D:CYS208 3.2 53.5 1.0
HB3 D:CYS208 3.3 60.7 1.0
HA D:CYS205 3.6 69.4 1.0
HG23 D:VAL210 3.7 54.6 1.0
S1 D:SF4401 3.9 45.5 1.0
HB2 D:CYS198 4.0 57.9 1.0
HA D:GLN211 4.0 61.8 1.0
HG12 D:VAL197 4.1 57.1 1.0
HD21 D:LEU193 4.2 48.1 1.0
HB2 D:CYS214 4.2 58.1 1.0
HG22 D:VAL210 4.3 54.6 1.0
CG2 D:VAL210 4.4 45.6 1.0
CA D:CYS205 4.5 59.9 1.0
HD11 D:LEU193 4.5 53.7 1.0
HB2 D:GLN211 4.6 63.3 1.0
CA D:CYS208 4.6 52.2 1.0
HB3 D:CYS205 4.6 62.9 1.0
HG11 D:VAL197 4.7 57.1 1.0
SG D:CYS198 4.7 48.1 1.0
CA D:GLN211 4.7 52.5 1.0
CB D:CYS198 4.7 49.8 1.0
N D:GLN211 4.8 50.4 1.0
H D:VAL210 4.8 54.6 1.0
SG D:CYS214 4.8 47.1 1.0
HA D:CYS208 4.8 58.5 1.0
HD21 D:LEU154 4.8 50.5 1.0
HG21 D:VAL210 4.8 54.6 1.0
CG1 D:VAL197 4.8 50.8 1.0
SG D:CYS205 4.9 55.6 1.0
CB D:CYS214 4.9 50.6 1.0
H D:GLN211 4.9 59.7 1.0
CB D:CYS205 4.9 54.6 1.0
HA D:CYS198 5.0 52.4 1.0
HG3 D:GLN211 5.0 69.0 1.0
HB3 D:CYS214 5.0 58.1 1.0

Iron binding site 6 out of 8 in 8dwe

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Iron binding site 6 out of 8 in the Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:49.2
occ:1.00
FE2 D:SF4401 0.0 49.2 1.0
S3 D:SF4401 2.2 53.8 1.0
S4 D:SF4401 2.3 49.4 1.0
S1 D:SF4401 2.3 45.5 1.0
SG D:CYS205 2.4 55.6 1.0
FE4 D:SF4401 2.7 45.5 1.0
FE1 D:SF4401 2.7 48.9 1.0
FE3 D:SF4401 2.8 42.1 1.0
HA D:CYS205 2.9 69.4 1.0
HB3 D:CYS205 3.1 62.9 1.0
CB D:CYS205 3.2 54.6 1.0
HB2 D:PRO203 3.4 64.5 1.0
CA D:CYS205 3.5 59.9 1.0
HB2 D:PHE217 3.7 65.9 1.0
S2 D:SF4401 3.9 42.5 1.0
N D:CYS205 4.0 53.9 1.0
H D:CYS205 4.1 62.3 1.0
HB2 D:CYS205 4.1 62.9 1.0
HD1 D:PHE217 4.2 71.1 1.0
HB2 D:CYS208 4.3 60.7 1.0
CB D:PRO203 4.3 55.4 1.0
HG2 D:PRO203 4.4 57.3 1.0
HB1 D:ALA222 4.4 64.3 1.0
HB2 D:ALA222 4.5 64.3 1.0
HB3 D:PRO203 4.6 64.5 1.0
SG D:CYS214 4.6 47.1 1.0
HB3 D:CYS208 4.6 60.7 1.0
CB D:PHE217 4.7 57.5 1.0
HD3 D:ARG153 4.7 55.0 1.0
HA D:CYS198 4.7 52.4 1.0
CG D:PRO203 4.7 49.8 1.0
SG D:CYS198 4.8 48.1 1.0
HG3 D:PRO203 4.8 57.3 1.0
CB D:CYS208 4.8 53.5 1.0
C D:CYS205 4.8 60.4 1.0
CD1 D:PHE217 4.8 62.9 1.0
CB D:ALA222 4.8 59.9 1.0
SG D:CYS208 4.9 51.8 1.0
C D:SER204 4.9 49.7 1.0
HG3 D:GLN211 4.9 69.0 1.0
HB2 D:CYS198 5.0 57.9 1.0
HB3 D:ALA222 5.0 64.3 1.0

Iron binding site 7 out of 8 in 8dwe

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Iron binding site 7 out of 8 in the Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:42.1
occ:1.00
FE3 D:SF4401 0.0 42.1 1.0
SG D:CYS198 2.2 48.1 1.0
S2 D:SF4401 2.3 42.5 1.0
S4 D:SF4401 2.3 49.4 1.0
S1 D:SF4401 2.3 45.5 1.0
FE1 D:SF4401 2.7 48.9 1.0
FE4 D:SF4401 2.7 45.5 1.0
HB2 D:CYS198 2.8 57.9 1.0
FE2 D:SF4401 2.8 49.2 1.0
CB D:CYS198 3.0 49.8 1.0
HD3 D:ARG153 3.4 55.0 1.0
HA D:CYS198 3.5 52.4 1.0
CA D:CYS198 3.8 45.6 1.0
HB3 D:CYS198 3.8 57.9 1.0
S3 D:SF4401 3.8 53.8 1.0
HH11 D:ARG153 3.9 53.9 1.0
HB2 D:PRO203 4.1 64.5 1.0
HD2 D:ARG153 4.1 55.0 1.0
HB3 D:ARG153 4.2 55.9 1.0
HB2 D:ARG153 4.2 55.9 1.0
CD D:ARG153 4.2 46.9 1.0
HB3 D:PRO203 4.4 64.5 1.0
HG22 D:VAL150 4.6 49.7 1.0
CB D:ARG153 4.6 47.7 1.0
HA D:VAL150 4.6 46.3 1.0
NH1 D:ARG153 4.7 46.1 1.0
HG12 D:VAL197 4.7 57.1 1.0
SG D:CYS214 4.7 47.1 1.0
CB D:PRO203 4.7 55.4 1.0
HD21 D:LEU193 4.8 48.1 1.0
N D:CYS198 4.8 49.4 1.0
SG D:CYS208 4.8 51.8 1.0
HB1 D:ALA222 4.9 64.3 1.0
CG D:ARG153 5.0 46.0 1.0
C D:CYS198 5.0 46.9 1.0
HG13 D:VAL150 5.0 54.2 1.0
SG D:CYS205 5.0 55.6 1.0
HA D:CYS205 5.0 69.4 1.0

Iron binding site 8 out of 8 in 8dwe

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Iron binding site 8 out of 8 in the Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Adenine Glycosylase Muty Variant E43Q in Complex with Dna Containing D(8-Oxo-G) Paired with Substrate Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:45.5
occ:1.00
FE4 D:SF4401 0.0 45.5 1.0
SG D:CYS214 2.2 47.1 1.0
S1 D:SF4401 2.3 45.5 1.0
S2 D:SF4401 2.3 42.5 1.0
S3 D:SF4401 2.3 53.8 1.0
FE3 D:SF4401 2.7 42.1 1.0
FE2 D:SF4401 2.7 49.2 1.0
FE1 D:SF4401 2.7 48.9 1.0
HB2 D:CYS214 2.9 58.1 1.0
CB D:CYS214 3.1 50.6 1.0
HB3 D:CYS214 3.3 58.1 1.0
HB2 D:PHE217 3.5 65.9 1.0
HB3 D:ARG153 3.7 55.9 1.0
HD23 D:LEU154 3.8 50.5 1.0
S4 D:SF4401 3.8 49.4 1.0
H D:PHE217 4.1 68.1 1.0
HB3 D:PHE217 4.2 65.9 1.0
CB D:PHE217 4.3 57.5 1.0
HA D:GLN211 4.4 61.8 1.0
HB2 D:ARG153 4.4 55.9 1.0
HD21 D:LEU154 4.4 50.5 1.0
HD3 D:ARG153 4.5 55.0 1.0
CA D:CYS214 4.5 59.0 1.0
CB D:ARG153 4.5 47.7 1.0
CD2 D:LEU154 4.6 41.1 1.0
HA D:CYS214 4.6 68.1 1.0
HA D:LEU154 4.6 53.3 1.0
HG D:LEU154 4.6 53.1 1.0
HB3 D:ALA216 4.7 68.5 1.0
SG D:CYS198 4.7 48.1 1.0
N D:PHE217 4.7 58.6 1.0
HG23 D:VAL210 4.8 54.6 1.0
SG D:CYS205 4.8 55.6 1.0
HB2 D:ALA222 4.8 64.3 1.0
SG D:CYS208 5.0 51.8 1.0
HB3 D:CYS205 5.0 62.9 1.0

Reference:

L.P.Russelburg, M.Demir, K.Cedeno, S.S.David, M.P.Horvath. Structural Basis For Base Engagement and Stereochemistry Revealed By Alteration of Catalytic Residue GLU43 in Dna Repair Glycosylase Muty To Be Published.
Page generated: Sat Aug 10 00:27:34 2024

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