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Iron in PDB 6u7t: Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G)

Enzymatic activity of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G)

All present enzymatic activity of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G):
3.2.2.31;

Protein crystallography data

The structure of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G), PDB code: 6u7t was solved by V.L.O'shea Murray, S.Cao, 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) 41.33 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.800, 86.490, 140.580, 90.00, 90.00, 90.00
R / Rfree (%) 26.1 / 27

Other elements in 6u7t:

The structure of Muty Adenine Glycosylase Bound to Dna Containing A 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 Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G) (pdb code 6u7t). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G), PDB code: 6u7t:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6u7t

Go back to Iron Binding Sites List in 6u7t
Iron binding site 1 out of 4 in the Muty Adenine Glycosylase Bound to Dna Containing A 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 Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:45.4
occ:1.00
 FE1 A:SF4401 0.0 45.4 1.0
S3 A:SF4401 2.2 50.6 1.0
S2 A:SF4401 2.3 37.2 1.0
S4 A:SF4401 2.3 43.7 1.0
SG A:CYS208 2.3 55.5 1.0
FE2 A:SF4401 2.7 46.0 1.0
FE4 A:SF4401 2.7 49.8 1.0
FE3 A:SF4401 2.7 37.2 0.7
HB2 A:CYS208 2.8 52.4 1.0
CB A:CYS208 3.0 43.7 1.0
HB3 A:CYS208 3.1 52.4 1.0
HA A:CYS205 3.5 52.5 1.0
HB2 A:CYS198 3.8 41.1 1.0
S1 A:SF4401 3.8 49.8 1.0
HG23 A:VAL210 3.9 65.0 1.0
HA A:GLN211 4.0 68.0 1.0
HB2 A:CYS214 4.2 65.8 1.0
HG22 A:VAL210 4.2 65.0 1.0
HG12 A:VAL197 4.2 53.4 1.0
HG11 A:VAL197 4.3 53.4 1.0
HB3 A:CYS205 4.3 60.3 1.0
CA A:CYS205 4.4 43.8 1.0
CA A:CYS208 4.5 50.7 1.0
CG2 A:VAL210 4.5 54.1 1.0
HD11 A:LEU193 4.5 49.7 1.0
CB A:CYS198 4.6 34.2 1.0
H A:VAL210 4.6 67.3 1.0
HB3 A:CYS214 4.6 65.8 1.0
HB3 A:GLN211 4.6 70.0 1.0
SG A:CYS198 4.6 43.6 1.0
HA A:CYS208 4.7 60.8 1.0
CB A:CYS205 4.7 50.2 1.0
CA A:GLN211 4.7 56.7 1.0
CB A:CYS214 4.7 54.9 1.0
HA A:CYS198 4.7 44.0 1.0
O A:VAL210 4.8 59.3 1.0
CG1 A:VAL197 4.8 44.5 1.0
N A:GLN211 4.8 55.0 1.0
C A:VAL210 4.8 54.1 1.0
O A:CYS205 4.8 39.5 1.0
SG A:CYS205 4.9 40.5 1.0
HD2 A:PRO209 4.9 54.1 1.0
SG A:CYS214 4.9 53.6 1.0
HD21 A:LEU193 5.0 50.2 1.0

Iron binding site 2 out of 4 in 6u7t

Go back to Iron Binding Sites List in 6u7t
Iron binding site 2 out of 4 in the Muty Adenine Glycosylase Bound to Dna Containing A 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 Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:46.0
occ:1.00
 FE2 A:SF4401 0.0 46.0 1.0
S3 A:SF4401 2.2 50.6 1.0
S4 A:SF4401 2.3 43.7 1.0
SG A:CYS205 2.3 40.5 1.0
S1 A:SF4401 2.3 49.8 1.0
HB3 A:CYS205 2.5 60.3 1.0
HA A:CYS205 2.7 52.5 1.0
FE1 A:SF4401 2.7 45.4 1.0
CB A:CYS205 2.7 50.2 1.0
FE4 A:SF4401 2.8 49.8 1.0
FE3 A:SF4401 2.8 37.2 0.7
CA A:CYS205 3.2 43.8 1.0
HB2 A:CYS205 3.7 60.3 1.0
HB2 A:PHE217 3.7 65.1 1.0
HB2 A:PRO203 3.8 42.4 1.0
S2 A:SF4401 3.9 37.2 1.0
N A:CYS205 4.0 45.6 1.0
HB2 A:CYS208 4.0 52.4 1.0
HB3 A:CYS208 4.2 52.4 1.0
H A:CYS205 4.2 54.7 1.0
HG2 A:PRO203 4.2 44.2 1.0
SG A:CYS214 4.2 53.6 1.0
C A:CYS205 4.4 45.1 1.0
CB A:CYS208 4.4 43.7 1.0
HB1 A:ALA222 4.4 54.9 1.0
HB2 A:ALA222 4.5 54.9 1.0
HB3 A:CYS214 4.5 65.8 1.0
HA A:GLN211 4.6 68.0 1.0
O A:CYS205 4.6 39.5 1.0
CB A:PRO203 4.6 35.3 1.0
CB A:PHE217 4.7 54.2 1.0
HB2 A:CYS214 4.7 65.8 1.0
SG A:CYS208 4.7 55.5 1.0
CG A:PRO203 4.7 36.8 1.0
HG3 A:PRO203 4.8 44.2 1.0
CB A:CYS214 4.8 54.9 1.0
C A:SER204 4.8 46.6 1.0
HD1 A:PHE217 4.9 74.5 1.0
CB A:ALA222 4.9 45.8 1.0
HD3 A:ARG153 4.9 43.9 1.0
HA A:CYS198 4.9 44.0 1.0
SG A:CYS198 5.0 43.6 1.0

Iron binding site 3 out of 4 in 6u7t

Go back to Iron Binding Sites List in 6u7t
Iron binding site 3 out of 4 in the Muty Adenine Glycosylase Bound to Dna Containing A 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 Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:37.2
occ:0.69
 FE3 A:SF4401 0.0 37.2 0.7
S2 A:SF4401 2.2 37.2 1.0
S1 A:SF4401 2.3 49.8 1.0
SG A:CYS198 2.3 43.6 1.0
S4 A:SF4401 2.3 43.7 1.0
FE4 A:SF4401 2.6 49.8 1.0
FE1 A:SF4401 2.7 45.4 1.0
FE2 A:SF4401 2.8 46.0 1.0
HB2 A:CYS198 2.9 41.1 1.0
HD3 A:ARG153 3.1 43.9 1.0
CB A:CYS198 3.1 34.2 1.0
HA A:CYS198 3.4 44.0 1.0
HH11 A:ARG153 3.6 46.8 1.0
HB2 A:PRO203 3.8 42.4 1.0
CA A:CYS198 3.8 36.7 1.0
S3 A:SF4401 3.8 50.6 1.0
HB3 A:CYS198 4.0 41.1 1.0
CD A:ARG153 4.0 36.6 1.0
HB3 A:ARG153 4.0 49.8 1.0
HD2 A:ARG153 4.1 43.9 1.0
HB2 A:ARG153 4.2 49.8 1.0
NH1 A:ARG153 4.3 39.0 1.0
HB3 A:PRO203 4.4 42.4 1.0
CB A:ARG153 4.5 41.5 1.0
CB A:PRO203 4.5 35.3 1.0
HG3 A:PRO203 4.5 44.2 1.0
SG A:CYS205 4.6 40.5 1.0
SG A:CYS214 4.7 53.6 1.0
HA A:VAL150 4.7 44.5 1.0
HH12 A:ARG153 4.7 46.8 1.0
CG A:ARG153 4.7 38.7 1.0
HB1 A:ALA222 4.7 54.9 1.0
HA A:CYS205 4.8 52.5 1.0
C A:CYS198 4.8 33.6 1.0
N A:CYS198 4.8 34.5 1.0
HB2 A:CYS208 4.9 52.4 1.0
SG A:CYS208 4.9 55.5 1.0
HG2 A:PRO203 4.9 44.2 1.0
CG A:PRO203 4.9 36.8 1.0
NE A:ARG153 4.9 39.2 1.0
HG2 A:ARG153 4.9 46.5 1.0
HB2 A:CYS214 4.9 65.8 1.0
HG13 A:VAL150 5.0 48.9 1.0
HG12 A:VAL197 5.0 53.4 1.0

Iron binding site 4 out of 4 in 6u7t

Go back to Iron Binding Sites List in 6u7t
Iron binding site 4 out of 4 in the Muty Adenine Glycosylase Bound to Dna Containing A 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 Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:49.8
occ:1.00
 FE4 A:SF4401 0.0 49.8 1.0
S1 A:SF4401 2.2 49.8 1.0
S2 A:SF4401 2.3 37.2 1.0
S3 A:SF4401 2.3 50.6 1.0
SG A:CYS214 2.3 53.6 1.0
HB2 A:CYS214 2.4 65.8 1.0
FE3 A:SF4401 2.6 37.2 0.7
FE1 A:SF4401 2.7 45.4 1.0
CB A:CYS214 2.7 54.9 1.0
FE2 A:SF4401 2.8 46.0 1.0
HB3 A:CYS214 3.0 65.8 1.0
HD23 A:LEU154 3.5 54.0 1.0
HB3 A:ARG153 3.6 49.8 1.0
S4 A:SF4401 3.9 43.7 1.0
HB2 A:PHE217 4.0 65.1 1.0
CA A:CYS214 4.2 57.9 1.0
HA A:CYS214 4.3 69.5 1.0
HA A:GLN211 4.3 68.0 1.0
CD2 A:LEU154 4.3 45.0 1.0
HD3 A:ARG153 4.4 43.9 1.0
H A:PHE217 4.4 58.5 1.0
CB A:ARG153 4.4 41.5 1.0
HD21 A:LEU154 4.4 54.0 1.0
HB2 A:ARG153 4.4 49.8 1.0
HG A:LEU154 4.5 56.1 1.0
HA A:LEU154 4.6 55.3 1.0
HB3 A:ALA216 4.6 55.3 1.0
HG23 A:VAL210 4.7 65.0 1.0
SG A:CYS198 4.7 43.6 1.0
HB3 A:CYS205 4.7 60.3 1.0
SG A:CYS208 4.8 55.5 1.0
SG A:CYS205 4.9 40.5 1.0
CB A:PHE217 4.9 54.2 1.0
O A:VAL210 5.0 59.3 1.0
H A:CYS214 5.0 67.5 1.0
HB3 A:PHE217 5.0 65.1 1.0

Reference:

R.D.Woods, V.L.O'shea, A.Chu, S.Cao, J.L.Richards, M.P.Horvath, S.S.David. Structure and Stereochemistry of the Base Excision Repair Glycosylase Muty Reveal A Mechanism Similar to Retaining Glycosidases. Nucleic Acids Res. V. 44 801 2016.
ISSN: ESSN 1362-4962
PubMed: 26673696
DOI: 10.1093/NAR/GKV1469
Page generated: Wed Aug 7 12:04:09 2024

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