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Iron in PDB 8dvy: Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate

Enzymatic activity of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate

All present enzymatic activity of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate:
3.2.2.31;

Protein crystallography data

The structure of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate, PDB code: 8dvy 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) 70.35 / 2.36
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.86, 85.48, 140.71, 90, 90, 90
R / Rfree (%) 24.7 / 27.4

Other elements in 8dvy:

The structure of Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate (pdb code 8dvy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate, PDB code: 8dvy:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8dvy

Go back to Iron Binding Sites List in 8dvy
Iron binding site 1 out of 4 in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate


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 D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:48.7
occ:1.00
 FE1 A:SF4401 0.0 48.7 1.0
S4 A:SF4401 2.3 51.8 1.0
S3 A:SF4401 2.3 48.6 1.0
S2 A:SF4401 2.3 46.3 1.0
SG A:CYS208 2.3 65.5 1.0
FE3 A:SF4401 2.7 52.9 1.0
FE2 A:SF4401 2.7 47.6 1.0
FE4 A:SF4401 2.7 52.5 1.0
HB2 A:CYS208 3.0 80.1 1.0
CB A:CYS208 3.1 66.7 1.0
HB3 A:CYS208 3.3 80.1 1.0
HG23 A:VAL210 3.5 85.5 1.0
HA A:CYS205 3.7 80.5 1.0
S1 A:SF4401 3.9 46.2 1.0
HB2 A:CYS198 4.0 64.9 1.0
HA A:GLN211 4.0 88.5 1.0
HG11 A:VAL197 4.2 71.0 1.0
HB2 A:CYS214 4.3 93.4 1.0
CG2 A:VAL210 4.3 71.2 1.0
HG22 A:VAL210 4.3 85.5 1.0
H A:VAL210 4.4 85.1 1.0
HD21 A:LEU193 4.4 70.5 1.0
HD11 A:LEU193 4.5 68.7 1.0
HB3 A:CYS205 4.5 79.7 1.0
HG12 A:VAL197 4.6 71.0 1.0
CA A:CYS208 4.6 69.1 1.0
SG A:CYS205 4.6 52.0 1.0
CA A:CYS205 4.6 67.0 1.0
C A:VAL210 4.7 74.0 1.0
N A:GLN211 4.7 72.8 1.0
HG21 A:VAL210 4.8 85.5 1.0
O A:VAL210 4.8 71.9 1.0
CB A:CYS198 4.8 54.0 1.0
HA A:CYS208 4.8 83.0 1.0
CA A:GLN211 4.8 73.6 1.0
CB A:CYS205 4.8 66.3 1.0
SG A:CYS214 4.8 79.2 1.0
SG A:CYS198 4.9 57.1 1.0
CG1 A:VAL197 4.9 59.1 1.0
CB A:CYS214 4.9 77.7 1.0
HB3 A:CYS214 4.9 93.4 1.0
HA A:CYS198 5.0 59.2 1.0
HD2 A:PRO209 5.0 79.4 1.0
HD21 A:LEU154 5.0 84.2 1.0

Iron binding site 2 out of 4 in 8dvy

Go back to Iron Binding Sites List in 8dvy
Iron binding site 2 out of 4 in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate


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 D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:47.6
occ:1.00
 FE2 A:SF4401 0.0 47.6 1.0
SG A:CYS205 2.0 52.0 1.0
S3 A:SF4401 2.2 48.6 1.0
S4 A:SF4401 2.3 51.8 1.0
S1 A:SF4401 2.3 46.2 1.0
FE4 A:SF4401 2.7 52.5 1.0
FE1 A:SF4401 2.7 48.7 1.0
FE3 A:SF4401 2.8 52.9 1.0
HB3 A:CYS205 2.8 79.7 1.0
CB A:CYS205 2.9 66.3 1.0
HA A:CYS205 3.0 80.5 1.0
CA A:CYS205 3.4 67.0 1.0
HB2 A:PHE217 3.7 90.7 1.0
HB2 A:PRO203 3.8 63.4 1.0
HB2 A:CYS205 3.8 79.7 1.0
S2 A:SF4401 3.9 46.3 1.0
HB2 A:CYS208 4.1 80.1 1.0
N A:CYS205 4.2 64.4 1.0
H A:CYS205 4.3 77.4 1.0
HB3 A:CYS208 4.4 80.1 1.0
HB1 A:ALA222 4.4 75.5 1.0
HB2 A:ALA222 4.4 75.5 1.0
SG A:CYS214 4.5 79.2 1.0
CB A:CYS208 4.6 66.7 1.0
CB A:PRO203 4.6 52.7 1.0
C A:CYS205 4.7 67.2 1.0
CB A:PHE217 4.7 75.5 1.0
HG2 A:PRO203 4.7 65.6 1.0
SG A:CYS208 4.7 65.5 1.0
HD3 A:ARG153 4.7 66.9 1.0
HA A:GLN211 4.8 88.5 1.0
CB A:ALA222 4.8 62.9 1.0
HA A:CYS198 4.9 59.2 1.0
O A:CYS205 4.9 62.7 1.0
HB3 A:CYS214 4.9 93.4 1.0
HB3 A:PRO203 4.9 63.4 1.0
SG A:CYS198 5.0 57.1 1.0

Iron binding site 3 out of 4 in 8dvy

Go back to Iron Binding Sites List in 8dvy
Iron binding site 3 out of 4 in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate


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 D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:52.9
occ:1.00
 FE3 A:SF4401 0.0 52.9 1.0
S2 A:SF4401 2.3 46.3 1.0
S1 A:SF4401 2.3 46.2 1.0
S4 A:SF4401 2.3 51.8 1.0
SG A:CYS198 2.4 57.1 1.0
FE4 A:SF4401 2.7 52.5 1.0
FE1 A:SF4401 2.7 48.7 1.0
FE2 A:SF4401 2.8 47.6 1.0
HB2 A:CYS198 2.9 64.9 1.0
CB A:CYS198 3.2 54.0 1.0
HD3 A:ARG153 3.2 66.9 1.0
HH11 A:ARG153 3.4 60.9 1.0
HA A:CYS198 3.5 59.2 1.0
S3 A:SF4401 3.8 48.6 1.0
CA A:CYS198 4.0 49.2 1.0
HB3 A:CYS198 4.0 64.9 1.0
HD2 A:ARG153 4.0 66.9 1.0
CD A:ARG153 4.0 55.6 1.0
HB2 A:ARG153 4.1 71.1 1.0
HB3 A:ARG153 4.1 71.1 1.0
NH1 A:ARG153 4.2 50.7 1.0
HB2 A:PRO203 4.2 63.4 1.0
SG A:CYS205 4.4 52.0 1.0
CB A:ARG153 4.5 59.1 1.0
HB3 A:PRO203 4.5 63.4 1.0
HH12 A:ARG153 4.6 60.9 1.0
SG A:CYS214 4.6 79.2 1.0
HA A:VAL150 4.6 59.2 1.0
HG22 A:VAL150 4.7 61.5 1.0
HB1 A:ALA222 4.8 75.5 1.0
CB A:PRO203 4.8 52.7 1.0
SG A:CYS208 4.8 65.5 1.0
N A:CYS198 4.9 48.3 1.0
CG A:ARG153 4.9 55.9 1.0
NE A:ARG153 5.0 54.2 1.0

Iron binding site 4 out of 4 in 8dvy

Go back to Iron Binding Sites List in 8dvy
Iron binding site 4 out of 4 in the Dna Glycosylase Muty Variant N146S in Complex with Dna Containing D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate


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 D(8- Oxo-G) Paired with An Enzyme-Generated Abasic Site Product (Ap) and Crystalized with Calcium Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:52.5
occ:1.00
 FE4 A:SF4401 0.0 52.5 1.0
SG A:CYS214 2.2 79.2 1.0
S1 A:SF4401 2.3 46.2 1.0
S3 A:SF4401 2.3 48.6 1.0
S2 A:SF4401 2.3 46.3 1.0
FE3 A:SF4401 2.7 52.9 1.0
FE2 A:SF4401 2.7 47.6 1.0
FE1 A:SF4401 2.7 48.7 1.0
HB2 A:CYS214 2.8 93.4 1.0
CB A:CYS214 2.9 77.7 1.0
HB3 A:CYS214 3.2 93.4 1.0
HB3 A:ARG153 3.7 71.1 1.0
HD23 A:LEU154 3.8 84.2 1.0
S4 A:SF4401 3.9 51.8 1.0
HB2 A:PHE217 3.9 90.7 1.0
HB2 A:ARG153 4.3 71.1 1.0
HA A:GLN211 4.4 88.5 1.0
H A:PHE217 4.4 87.4 1.0
CA A:CYS214 4.4 73.1 1.0
HD3 A:ARG153 4.4 66.9 1.0
CB A:ARG153 4.4 59.1 1.0
HA A:LEU154 4.5 74.4 1.0
HG A:LEU154 4.5 76.7 1.0
HB3 A:ALA216 4.6 84.5 1.0
HA A:CYS214 4.6 87.9 1.0
SG A:CYS205 4.6 52.0 1.0
CD2 A:LEU154 4.6 70.1 1.0
HD21 A:LEU154 4.6 84.2 1.0
HG23 A:VAL210 4.7 85.5 1.0
HB3 A:PHE217 4.7 90.7 1.0
CB A:PHE217 4.7 75.5 1.0
SG A:CYS208 4.8 65.5 1.0
HB3 A:CYS205 4.8 79.7 1.0
C A:ARG153 4.9 62.0 1.0
SG A:CYS198 4.9 57.1 1.0
O A:VAL210 5.0 71.9 1.0
HB2 A:ALA222 5.0 75.5 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 00:18:53 2024

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