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Iron in PDB 8dw7: Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G)

Enzymatic activity of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G)

All present enzymatic activity of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G):
3.2.2.31;

Protein crystallography data

The structure of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G), PDB code: 8dw7 was solved by M.Demir, L.P.Russelburg, M.P.Horvath, S.S.David, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.80 / 1.96
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.89, 137.21, 74.16, 90, 101, 90
R / Rfree (%) 20.3 / 23.4

Other elements in 8dw7:

The structure of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G) also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G) (pdb code 8dw7). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G), PDB code: 8dw7:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8dw7

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Iron binding site 1 out of 8 in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:51.9
occ:1.00
FE1 A:SF4401 0.0 51.9 1.0
SG A:CYS208 2.2 53.4 1.0
S3 A:SF4401 2.2 57.9 1.0
S2 A:SF4401 2.3 50.1 1.0
S4 A:SF4401 2.3 52.4 1.0
FE4 A:SF4401 2.7 53.3 1.0
FE3 A:SF4401 2.7 49.0 1.0
FE2 A:SF4401 2.7 56.8 1.0
HB2 A:CYS208 3.0 57.9 1.0
CB A:CYS208 3.1 57.5 1.0
HB3 A:CYS208 3.2 57.9 1.0
HG23 A:VAL210 3.6 48.7 1.0
HA A:CYS205 3.6 63.2 1.0
HB2 A:CYS198 3.8 44.9 1.0
S1 A:SF4401 3.9 52.8 1.0
HA A:GLN211 3.9 57.2 1.0
HG12 A:VAL197 4.0 50.1 1.0
HG22 A:VAL210 4.2 48.7 1.0
HD21 A:LEU193 4.3 46.0 1.0
HB2 A:CYS214 4.3 54.1 1.0
CG2 A:VAL210 4.3 49.7 1.0
HB3 A:CYS205 4.5 61.9 1.0
HB2 A:GLN211 4.5 62.4 1.0
H A:VAL210 4.5 51.7 1.0
CA A:CYS208 4.5 56.8 1.0
CA A:CYS205 4.5 63.2 1.0
N A:GLN211 4.6 58.9 1.0
HD11 A:LEU193 4.6 51.5 1.0
CB A:CYS198 4.6 48.2 1.0
HG11 A:VAL197 4.6 50.1 1.0
CA A:GLN211 4.6 58.6 1.0
HA A:CYS208 4.7 56.5 1.0
H A:GLN211 4.7 59.7 1.0
CG1 A:VAL197 4.7 51.1 1.0
SG A:CYS198 4.8 49.6 1.0
SG A:CYS214 4.8 53.4 1.0
HG21 A:VAL210 4.8 48.7 1.0
C A:VAL210 4.8 56.0 1.0
CB A:CYS205 4.8 63.3 1.0
HD21 A:LEU154 4.9 44.1 1.0
CB A:CYS214 4.9 56.3 1.0

Iron binding site 2 out of 8 in 8dw7

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Iron binding site 2 out of 8 in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:56.8
occ:1.00
FE2 A:SF4401 0.0 56.8 1.0
S1 A:SF4401 2.3 52.8 1.0
S3 A:SF4401 2.3 57.9 1.0
S4 A:SF4401 2.3 52.4 1.0
SG A:CYS205 2.5 61.0 1.0
FE3 A:SF4401 2.7 49.0 1.0
FE4 A:SF4401 2.7 53.3 1.0
FE1 A:SF4401 2.7 51.9 1.0
HB3 A:CYS205 2.9 61.9 1.0
HA A:CYS205 2.9 63.2 1.0
CB A:CYS205 3.1 63.3 1.0
HB2 A:PRO203 3.3 57.2 1.0
CA A:CYS205 3.4 63.2 1.0
S2 A:SF4401 3.9 50.1 1.0
HB2 A:PHE217 3.9 67.3 1.0
HB2 A:CYS205 4.0 61.9 1.0
N A:CYS205 4.0 60.4 1.0
H A:CYS205 4.0 59.1 1.0
HB2 A:CYS208 4.1 57.9 1.0
CB A:PRO203 4.2 57.1 1.0
HG2 A:PRO203 4.4 61.4 1.0
HB3 A:CYS208 4.5 57.9 1.0
HB3 A:PRO203 4.6 57.2 1.0
HD1 A:PHE217 4.6 72.0 1.0
HB2 A:CYS198 4.6 44.9 1.0
CB A:CYS208 4.6 57.5 1.0
HA A:CYS198 4.6 44.5 1.0
SG A:CYS208 4.7 53.4 1.0
SG A:CYS214 4.7 53.4 1.0
HG3 A:PRO203 4.7 61.4 1.0
CG A:PRO203 4.7 60.5 1.0
HB2 A:ALA222 4.7 63.0 1.0
HD3 A:ARG153 4.7 46.7 1.0
C A:CYS205 4.7 66.1 1.0
HB1 A:ALA222 4.8 63.0 1.0
SG A:CYS198 4.8 49.6 1.0
CB A:PHE217 4.9 68.0 1.0
C A:SER204 4.9 60.9 1.0

Iron binding site 3 out of 8 in 8dw7

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Iron binding site 3 out of 8 in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:49.0
occ:1.00
FE3 A:SF4401 0.0 49.0 1.0
S1 A:SF4401 2.2 52.8 1.0
SG A:CYS198 2.3 49.6 1.0
S4 A:SF4401 2.3 52.4 1.0
S2 A:SF4401 2.3 50.1 1.0
HB2 A:CYS198 2.6 44.9 1.0
FE4 A:SF4401 2.7 53.3 1.0
FE2 A:SF4401 2.7 56.8 1.0
FE1 A:SF4401 2.7 51.9 1.0
CB A:CYS198 2.9 48.2 1.0
HA A:CYS198 3.5 44.5 1.0
HD3 A:ARG153 3.5 46.7 1.0
HB3 A:CYS198 3.7 44.9 1.0
HH11 A:ARG153 3.7 48.9 1.0
CA A:CYS198 3.8 48.3 1.0
S3 A:SF4401 3.8 57.9 1.0
HD2 A:ARG153 4.0 46.7 1.0
HB2 A:PRO203 4.0 57.2 1.0
CD A:ARG153 4.2 47.3 1.0
HB3 A:ARG153 4.3 47.5 1.0
HB2 A:ARG153 4.3 47.5 1.0
HB3 A:PRO203 4.3 57.2 1.0
NH1 A:ARG153 4.5 47.7 1.0
HA A:VAL150 4.6 40.2 1.0
HG12 A:VAL197 4.6 50.1 1.0
CB A:PRO203 4.6 57.1 1.0
CB A:ARG153 4.7 48.5 1.0
SG A:CYS214 4.7 53.4 1.0
HG22 A:VAL150 4.7 44.4 1.0
SG A:CYS208 4.7 53.4 1.0
N A:CYS198 4.8 51.3 1.0
HD21 A:LEU193 4.8 46.0 1.0
HG13 A:VAL150 4.8 49.8 1.0
C A:CYS198 4.9 49.1 1.0
SG A:CYS205 4.9 61.0 1.0
HH12 A:ARG153 4.9 48.9 1.0
HA A:CYS205 5.0 63.2 1.0

Iron binding site 4 out of 8 in 8dw7

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Iron binding site 4 out of 8 in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:53.3
occ:1.00
FE4 A:SF4401 0.0 53.3 1.0
S2 A:SF4401 2.2 50.1 1.0
SG A:CYS214 2.3 53.4 1.0
S1 A:SF4401 2.3 52.8 1.0
S3 A:SF4401 2.3 57.9 1.0
FE3 A:SF4401 2.7 49.0 1.0
FE1 A:SF4401 2.7 51.9 1.0
FE2 A:SF4401 2.7 56.8 1.0
HB2 A:CYS214 2.9 54.1 1.0
CB A:CYS214 3.1 56.3 1.0
HB3 A:CYS214 3.4 54.1 1.0
HB2 A:PHE217 3.5 67.3 1.0
HD23 A:LEU154 3.7 44.1 1.0
HB3 A:ARG153 3.7 47.5 1.0
S4 A:SF4401 3.9 52.4 1.0
H A:PHE217 4.1 65.4 1.0
HA A:GLN211 4.3 57.2 1.0
CB A:PHE217 4.4 68.0 1.0
HD21 A:LEU154 4.4 44.1 1.0
HB2 A:ARG153 4.5 47.5 1.0
HB3 A:PHE217 4.5 67.3 1.0
CD2 A:LEU154 4.5 47.1 1.0
HD3 A:ARG153 4.5 46.7 1.0
CA A:CYS214 4.5 57.6 1.0
CB A:ARG153 4.5 48.5 1.0
HG A:LEU154 4.6 44.4 1.0
HA A:CYS214 4.6 55.5 1.0
HB3 A:ALA216 4.6 56.5 1.0
HG23 A:VAL210 4.6 48.7 1.0
SG A:CYS198 4.7 49.6 1.0
SG A:CYS208 4.7 53.4 1.0
HB3 A:CYS205 4.8 61.9 1.0
N A:PHE217 4.8 66.7 1.0
HA A:LEU154 4.8 47.8 1.0
SG A:CYS205 4.9 61.0 1.0

Iron binding site 5 out of 8 in 8dw7

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Iron binding site 5 out of 8 in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:48.7
occ:1.00
FE1 D:SF4401 0.0 48.7 1.0
S3 D:SF4401 2.2 51.1 1.0
S2 D:SF4401 2.3 44.5 1.0
S4 D:SF4401 2.3 48.2 1.0
SG D:CYS208 2.3 51.2 1.0
FE2 D:SF4401 2.7 52.6 1.0
FE4 D:SF4401 2.7 48.5 1.0
FE3 D:SF4401 2.8 44.3 1.0
HB2 D:CYS208 3.0 54.6 1.0
CB D:CYS208 3.1 55.3 1.0
HB3 D:CYS208 3.3 54.6 1.0
HA D:CYS205 3.5 64.9 1.0
HG23 D:VAL210 3.7 49.1 1.0
S1 D:SF4401 3.9 49.1 1.0
HA D:GLN211 3.9 56.1 1.0
HB2 D:CYS198 3.9 42.6 1.0
HG12 D:VAL197 4.1 47.6 1.0
HG22 D:VAL210 4.3 49.1 1.0
HD21 D:LEU193 4.3 41.5 1.0
HB2 D:CYS214 4.3 52.7 1.0
CG2 D:VAL210 4.4 48.4 1.0
HB3 D:CYS205 4.5 61.6 1.0
CA D:CYS205 4.5 62.5 1.0
HD11 D:LEU193 4.5 45.6 1.0
CA D:CYS208 4.6 56.5 1.0
HG11 D:VAL197 4.6 47.6 1.0
HB2 D:GLN211 4.6 61.5 1.0
H D:VAL210 4.6 50.1 1.0
CA D:GLN211 4.7 57.8 1.0
SG D:CYS198 4.7 46.4 1.0
N D:GLN211 4.7 57.2 1.0
CB D:CYS198 4.7 44.5 1.0
HA D:CYS208 4.8 55.7 1.0
CG1 D:VAL197 4.8 48.4 1.0
CB D:CYS205 4.8 60.9 1.0
SG D:CYS214 4.8 48.8 1.0
H D:GLN211 4.9 56.2 1.0
HG21 D:VAL210 4.9 49.1 1.0
SG D:CYS205 4.9 56.9 1.0
C D:VAL210 4.9 53.7 1.0
CB D:CYS214 5.0 52.3 1.0
HD21 D:LEU154 5.0 42.0 1.0
HA D:CYS198 5.0 44.2 1.0

Iron binding site 6 out of 8 in 8dw7

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Iron binding site 6 out of 8 in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:52.6
occ:1.00
FE2 D:SF4401 0.0 52.6 1.0
S4 D:SF4401 2.2 48.2 1.0
S3 D:SF4401 2.2 51.1 1.0
S1 D:SF4401 2.3 49.1 1.0
SG D:CYS205 2.4 56.9 1.0
FE1 D:SF4401 2.7 48.7 1.0
FE4 D:SF4401 2.7 48.5 1.0
FE3 D:SF4401 2.8 44.3 1.0
HA D:CYS205 2.8 64.9 1.0
HB3 D:CYS205 3.0 61.6 1.0
CB D:CYS205 3.1 60.9 1.0
CA D:CYS205 3.4 62.5 1.0
HB2 D:PRO203 3.4 54.5 1.0
HB2 D:PHE217 3.8 60.6 1.0
S2 D:SF4401 3.8 44.5 1.0
N D:CYS205 3.9 60.7 1.0
H D:CYS205 3.9 61.5 1.0
HB2 D:CYS205 4.0 61.6 1.0
HB2 D:CYS208 4.1 54.6 1.0
CB D:PRO203 4.3 53.4 1.0
HD2 D:PHE217 4.3 63.9 1.0
HG2 D:PRO203 4.4 52.6 1.0
HB3 D:CYS208 4.6 54.6 1.0
CB D:CYS208 4.6 55.3 1.0
HA D:CYS198 4.6 44.2 1.0
HB3 D:PRO203 4.6 54.5 1.0
SG D:CYS208 4.7 51.2 1.0
SG D:CYS198 4.7 46.4 1.0
CG D:PRO203 4.7 52.9 1.0
HB2 D:ALA222 4.7 57.5 1.0
C D:CYS205 4.7 66.9 1.0
HG3 D:PRO203 4.7 52.6 1.0
HD3 D:ARG153 4.8 45.0 1.0
C D:SER204 4.8 58.6 1.0
SG D:CYS214 4.8 48.8 1.0
CB D:PHE217 4.8 58.4 1.0
HG12 D:VAL197 4.8 47.6 1.0
HB2 D:CYS198 4.8 42.6 1.0
HB1 D:ALA222 4.8 57.5 1.0

Iron binding site 7 out of 8 in 8dw7

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Iron binding site 7 out of 8 in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:44.3
occ:1.00
FE3 D:SF4401 0.0 44.3 1.0
SG D:CYS198 2.2 46.4 1.0
S2 D:SF4401 2.2 44.5 1.0
S1 D:SF4401 2.3 49.1 1.0
S4 D:SF4401 2.3 48.2 1.0
FE4 D:SF4401 2.7 48.5 1.0
HB2 D:CYS198 2.7 42.6 1.0
FE1 D:SF4401 2.8 48.7 1.0
FE2 D:SF4401 2.8 52.6 1.0
CB D:CYS198 3.0 44.5 1.0
HD3 D:ARG153 3.4 45.0 1.0
HA D:CYS198 3.4 44.2 1.0
HH11 D:ARG153 3.7 47.4 1.0
HB3 D:CYS198 3.8 42.6 1.0
CA D:CYS198 3.8 46.2 1.0
S3 D:SF4401 3.9 51.1 1.0
HD2 D:ARG153 3.9 45.0 1.0
HB2 D:PRO203 4.0 54.5 1.0
HB3 D:ARG153 4.0 41.9 1.0
CD D:ARG153 4.1 45.9 1.0
HB2 D:ARG153 4.3 41.9 1.0
HB3 D:PRO203 4.4 54.5 1.0
NH1 D:ARG153 4.5 47.9 1.0
HG22 D:VAL150 4.5 39.3 1.0
CB D:ARG153 4.6 43.9 1.0
HA D:VAL150 4.6 37.1 1.0
CB D:PRO203 4.6 53.4 1.0
HG12 D:VAL197 4.7 47.6 1.0
SG D:CYS214 4.7 48.8 1.0
SG D:CYS208 4.8 51.2 1.0
N D:CYS198 4.8 47.8 1.0
HD21 D:LEU193 4.8 41.5 1.0
CG D:ARG153 4.9 45.5 1.0
C D:CYS198 4.9 45.6 1.0
SG D:CYS205 5.0 56.9 1.0
HH12 D:ARG153 5.0 47.4 1.0
HB1 D:ALA222 5.0 57.5 1.0

Iron binding site 8 out of 8 in 8dw7

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Iron binding site 8 out of 8 in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing the Transition State Analog 1N Paired with D(8-Oxo-G) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:48.5
occ:1.00
FE4 D:SF4401 0.0 48.5 1.0
S2 D:SF4401 2.2 44.5 1.0
S1 D:SF4401 2.2 49.1 1.0
SG D:CYS214 2.3 48.8 1.0
S3 D:SF4401 2.3 51.1 1.0
FE3 D:SF4401 2.7 44.3 1.0
FE1 D:SF4401 2.7 48.7 1.0
FE2 D:SF4401 2.7 52.6 1.0
HB2 D:CYS214 2.9 52.7 1.0
CB D:CYS214 3.1 52.3 1.0
HB3 D:CYS214 3.4 52.7 1.0
HB2 D:PHE217 3.6 60.6 1.0
HB3 D:ARG153 3.7 41.9 1.0
HD23 D:LEU154 3.7 42.0 1.0
S4 D:SF4401 3.8 48.2 1.0
H D:PHE217 4.0 60.5 1.0
HB3 D:PHE217 4.2 60.6 1.0
CB D:PHE217 4.3 58.4 1.0
HA D:GLN211 4.4 56.1 1.0
HD3 D:ARG153 4.5 45.0 1.0
HD21 D:LEU154 4.5 42.0 1.0
CD2 D:LEU154 4.5 42.6 1.0
HB3 D:ALA216 4.5 57.3 1.0
CA D:CYS214 4.6 53.0 1.0
CB D:ARG153 4.6 43.9 1.0
HG D:LEU154 4.7 44.2 1.0
SG D:CYS198 4.7 46.4 1.0
HB2 D:ARG153 4.7 41.9 1.0
HA D:CYS214 4.7 53.8 1.0
N D:PHE217 4.7 57.3 1.0
HA D:LEU154 4.7 44.1 1.0
HB3 D:CYS205 4.7 61.6 1.0
HG23 D:VAL210 4.8 49.1 1.0
SG D:CYS205 4.8 56.9 1.0
HB2 D:ALA222 4.9 57.5 1.0
SG D:CYS208 4.9 51.2 1.0

Reference:

M.Demir, L.P.Russelburg, J.Lin, C.H.Trasvina-Arenas, B.Huang, P.K.Yuen, M.P.Horvath, S.S.David. Structural Snapshots of Base Excision Mechanism By Dna Glycosylase Muty Reveal Retention of Stereochemistry For Abasic Site Product Formation To Be Published.
Page generated: Sat Aug 10 00:24:50 2024

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