Iron in PDB 8dw4: Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium

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

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

Protein crystallography data

The structure of Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium, PDB code: 8dw4 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) 54.45 / 2.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.64, 85.55, 141.17, 90, 90, 90
R / Rfree (%) 23.1 / 24.9

Other elements in 8dw4:

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

Sodium (Na) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium (pdb code 8dw4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium, PDB code: 8dw4:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8dw4

Go back to Iron Binding Sites List in 8dw4
Iron binding site 1 out of 4 in the Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:52.7
occ:1.00
 FE1 A:SF4401 0.0 52.7 1.0
SG A:CYS208 2.2 61.8 1.0
S4 A:SF4401 2.3 50.6 1.0
S3 A:SF4401 2.3 61.8 1.0
S2 A:SF4401 2.3 46.9 1.0
HB2 A:CYS208 2.7 71.9 1.0
FE4 A:SF4401 2.7 55.1 1.0
FE2 A:SF4401 2.7 56.3 1.0
FE3 A:SF4401 2.7 55.3 1.0
CB A:CYS208 2.9 61.3 1.0
HB3 A:CYS208 3.1 71.9 1.0
HA A:CYS205 3.5 66.8 1.0
HG23 A:VAL210 3.8 78.8 1.0
HG12 A:VAL197 3.8 64.4 1.0
S1 A:SF4401 3.9 52.1 1.0
HB2 A:CYS198 3.9 61.5 1.0
HA A:GLN211 4.1 83.4 1.0
HB3 A:CYS205 4.2 68.6 1.0
CA A:CYS208 4.4 61.9 1.0
HG22 A:VAL210 4.4 78.8 1.0
HD21 A:LEU193 4.4 60.9 1.0
CA A:CYS205 4.4 61.6 1.0
HA A:CYS208 4.5 72.2 1.0
HG11 A:VAL197 4.5 64.4 1.0
CG2 A:VAL210 4.5 58.4 1.0
CG1 A:VAL197 4.6 63.7 1.0
H A:VAL210 4.6 76.4 1.0
CB A:CYS205 4.6 64.2 1.0
HB2 A:CYS214 4.6 76.9 1.0
HA A:CYS198 4.7 60.1 1.0
SG A:CYS205 4.7 57.4 1.0
CB A:CYS198 4.8 47.6 1.0
HD11 A:LEU193 4.8 63.9 1.0
SG A:CYS214 4.9 71.7 1.0
CA A:GLN211 4.9 89.3 1.0
O A:CYS205 4.9 69.2 1.0
N A:GLN211 4.9 84.8 1.0
HB3 A:GLN211 4.9 85.2 1.0
HG21 A:VAL210 5.0 78.8 1.0
HD21 A:LEU154 5.0 72.1 1.0
C A:VAL210 5.0 63.7 1.0

Iron binding site 2 out of 4 in 8dw4

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Iron binding site 2 out of 4 in the Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:56.3
occ:1.00
 FE2 A:SF4401 0.0 56.3 1.0
SG A:CYS205 2.3 57.4 1.0
S3 A:SF4401 2.3 61.8 1.0
S4 A:SF4401 2.3 50.6 1.0
S1 A:SF4401 2.3 52.1 1.0
HB3 A:CYS205 2.7 68.6 1.0
FE4 A:SF4401 2.7 55.1 1.0
FE1 A:SF4401 2.7 52.7 1.0
FE3 A:SF4401 2.7 55.3 1.0
CB A:CYS205 2.9 64.2 1.0
HA A:CYS205 3.0 66.8 1.0
HB2 A:PHE217 3.4 78.9 1.0
CA A:CYS205 3.5 61.6 1.0
HB2 A:PRO203 3.7 61.2 1.0
HB2 A:CYS205 3.8 68.6 1.0
S2 A:SF4401 3.9 46.9 1.0
HB1 A:ALA222 4.1 69.1 1.0
HB2 A:CYS208 4.2 71.9 1.0
HB2 A:ALA222 4.2 69.1 1.0
N A:CYS205 4.2 58.8 1.0
CB A:PHE217 4.4 79.5 1.0
H A:CYS205 4.4 65.0 1.0
CB A:ALA222 4.5 59.5 1.0
HB3 A:ALA222 4.5 69.1 1.0
CB A:PRO203 4.6 54.3 1.0
HB3 A:CYS208 4.6 71.9 1.0
SG A:CYS214 4.6 71.7 1.0
HD3 A:ARG153 4.7 63.4 1.0
CB A:CYS208 4.7 61.3 1.0
C A:CYS205 4.7 65.7 1.0
HB3 A:PHE217 4.7 78.9 1.0
HA A:CYS198 4.7 60.1 1.0
SG A:CYS208 4.7 61.8 1.0
HB3 A:PRO203 4.8 61.2 1.0
O A:CYS205 4.9 69.2 1.0
CG A:PHE217 4.9 80.9 1.0
HG2 A:PRO203 4.9 62.9 1.0
C A:SER204 5.0 59.0 1.0
HA A:GLN211 5.0 83.4 1.0

Iron binding site 3 out of 4 in 8dw4

Go back to Iron Binding Sites List in 8dw4
Iron binding site 3 out of 4 in the Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:55.3
occ:1.00
 FE3 A:SF4401 0.0 55.3 1.0
S1 A:SF4401 2.3 52.1 1.0
S2 A:SF4401 2.3 46.9 1.0
S4 A:SF4401 2.3 50.6 1.0
SG A:CYS198 2.7 53.2 1.0
FE4 A:SF4401 2.7 55.1 1.0
FE1 A:SF4401 2.7 52.7 1.0
FE2 A:SF4401 2.7 56.3 1.0
HB2 A:CYS198 2.8 61.5 1.0
CB A:CYS198 3.2 47.6 1.0
HD3 A:ARG153 3.2 63.4 1.0
HA A:CYS198 3.4 60.1 1.0
HH11 A:ARG153 3.6 60.8 1.0
CA A:CYS198 3.8 46.2 1.0
S3 A:SF4401 3.9 61.8 1.0
HB3 A:ARG153 4.0 62.7 1.0
HB2 A:ARG153 4.0 62.7 1.0
HB3 A:CYS198 4.0 61.5 1.0
CD A:ARG153 4.0 53.3 1.0
HD2 A:ARG153 4.1 63.4 1.0
HB2 A:PRO203 4.3 61.2 1.0
NH1 A:ARG153 4.3 49.1 1.0
CB A:ARG153 4.4 55.4 1.0
HB1 A:ALA222 4.5 69.1 1.0
HB3 A:PRO203 4.6 61.2 1.0
HA A:VAL150 4.6 59.8 1.0
HG22 A:VAL150 4.6 58.5 1.0
SG A:CYS205 4.7 57.4 1.0
SG A:CYS214 4.7 71.7 1.0
SG A:CYS208 4.7 61.8 1.0
N A:CYS198 4.8 45.0 1.0
HH12 A:ARG153 4.8 60.8 1.0
HG12 A:VAL197 4.8 64.4 1.0
CG A:ARG153 4.8 54.5 1.0
CB A:PRO203 4.9 54.3 1.0
C A:CYS198 5.0 43.0 1.0
H A:CYS198 5.0 58.8 1.0
HA A:CYS205 5.0 66.8 1.0
NE A:ARG153 5.0 54.3 1.0

Iron binding site 4 out of 4 in 8dw4

Go back to Iron Binding Sites List in 8dw4
Iron binding site 4 out of 4 in the Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Abasic Site Product (Ap) Generated By the Enzyme in Crystals By Removal of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:55.1
occ:1.00
 FE4 A:SF4401 0.0 55.1 1.0
SG A:CYS214 2.2 71.7 1.0
S1 A:SF4401 2.3 52.1 1.0
S2 A:SF4401 2.3 46.9 1.0
S3 A:SF4401 2.3 61.8 1.0
FE3 A:SF4401 2.7 55.3 1.0
FE2 A:SF4401 2.7 56.3 1.0
FE1 A:SF4401 2.7 52.7 1.0
HB2 A:CYS214 3.0 76.9 1.0
CB A:CYS214 3.1 75.5 1.0
HB3 A:CYS214 3.3 76.9 1.0
HB2 A:PHE217 3.6 78.9 1.0
HB3 A:ARG153 3.7 62.7 1.0
HD23 A:LEU154 3.9 72.1 1.0
S4 A:SF4401 3.9 50.6 1.0
HB3 A:PHE217 4.1 78.9 1.0
H A:PHE217 4.2 75.8 1.0
HA A:GLN211 4.2 83.4 1.0
CB A:PHE217 4.3 79.5 1.0
HG A:LEU154 4.3 69.7 1.0
HD21 A:LEU154 4.4 72.1 1.0
HB2 A:ARG153 4.4 62.7 1.0
HA A:LEU154 4.4 68.2 1.0
HG23 A:VAL210 4.5 78.8 1.0
SG A:CYS208 4.5 61.8 1.0
HB3 A:ALA216 4.5 74.9 1.0
CD2 A:LEU154 4.5 68.3 1.0
CB A:ARG153 4.5 55.4 1.0
CA A:CYS214 4.6 77.4 1.0
HB3 A:CYS205 4.6 68.6 1.0
HD3 A:ARG153 4.6 63.4 1.0
HB2 A:ALA222 4.7 69.1 1.0
HA A:CYS214 4.8 76.8 1.0
N A:PHE217 4.8 76.1 1.0
SG A:CYS205 4.9 57.4 1.0
O A:VAL210 4.9 63.9 1.0
C A:ARG153 4.9 61.2 1.0
N A:LEU154 4.9 60.6 1.0
O A:ARG153 4.9 65.6 1.0
CG A:LEU154 5.0 64.1 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: Wed Apr 5 08:29:20 2023

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