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

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

All present enzymatic activity of Human Mutyh 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 Human Mutyh Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with D(8-Oxo-G), PDB code: 8fay was solved by C.H.Trasvina-Arenas, W.J.Lin, M.Demir, A.J.Fisher, 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) 60.28 / 1.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.686, 116.422, 118.378, 90, 90, 90
R / Rfree (%) 18.1 / 20.9

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 8fay

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Iron binding site 1 out of 8 in the Human Mutyh 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 Human Mutyh 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:Fe601

b:33.0
occ:1.00
 FE1 A:SF4601 0.0 33.0 1.0
SG A:CYS300 2.2 32.0 1.0
S4 A:SF4601 2.3 36.2 1.0
S2 A:SF4601 2.3 34.5 1.0
S3 A:SF4601 2.4 33.2 1.0
FE3 A:SF4601 2.7 34.5 1.0
FE2 A:SF4601 2.7 33.5 1.0
FE4 A:SF4601 2.8 34.0 1.0
HB2 A:CYS300 3.1 41.7 1.0
CB A:CYS300 3.1 34.7 1.0
HB3 A:CYS300 3.2 41.7 1.0
HA A:CYS297 3.6 39.4 1.0
HG23 A:VAL302 3.6 47.9 1.0
HB2 A:CYS290 3.9 43.1 1.0
S1 A:SF4601 3.9 33.1 1.0
HA A:GLU303 4.0 41.6 1.0
HG22 A:VAL302 4.0 47.9 1.0
HG12 A:VAL289 4.1 38.4 1.0
HD21 A:LEU285 4.2 44.4 1.0
HB2 A:CYS306 4.3 44.2 1.0
CG2 A:VAL302 4.3 39.9 1.0
H A:VAL302 4.5 39.2 1.0
CA A:CYS297 4.5 32.8 1.0
HB2 A:GLU303 4.6 47.0 1.0
CA A:CYS300 4.6 36.3 1.0
HD11 A:LEU285 4.6 45.3 1.0
HB3 A:CYS297 4.6 37.2 1.0
CB A:CYS290 4.7 35.9 1.0
N A:GLU303 4.7 37.2 1.0
SG A:CYS290 4.7 32.2 1.0
CA A:GLU303 4.7 34.7 1.0
HG21 A:VAL302 4.7 47.9 1.0
HB3 A:CYS306 4.8 44.2 1.0
H A:GLU303 4.8 44.6 1.0
CB A:CYS306 4.8 36.8 1.0
SG A:CYS297 4.9 33.1 1.0
HA A:CYS300 4.9 43.6 1.0
SG A:CYS306 4.9 33.2 1.0
HG11 A:VAL289 4.9 38.4 1.0
CB A:CYS297 4.9 31.0 1.0
CG1 A:VAL289 4.9 32.0 1.0
C A:VAL302 4.9 34.9 1.0
HA A:CYS290 5.0 38.3 1.0

Iron binding site 2 out of 8 in 8fay

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Iron binding site 2 out of 8 in the Human Mutyh 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 Human Mutyh 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:Fe601

b:33.5
occ:1.00
 FE2 A:SF4601 0.0 33.5 1.0
S1 A:SF4601 2.2 33.1 1.0
SG A:CYS290 2.3 32.2 1.0
S3 A:SF4601 2.3 33.2 1.0
S4 A:SF4601 2.3 36.2 1.0
FE4 A:SF4601 2.7 34.0 1.0
FE3 A:SF4601 2.7 34.5 1.0
FE1 A:SF4601 2.7 33.0 1.0
HB2 A:CYS290 2.8 43.1 1.0
CB A:CYS290 3.1 35.9 1.0
HD3 A:ARG245 3.4 44.0 1.0
HA A:CYS290 3.5 38.3 1.0
HH11 A:ARG245 3.7 41.3 1.0
CA A:CYS290 3.9 31.9 1.0
S2 A:SF4601 3.9 34.5 1.0
HD2 A:ARG245 3.9 44.0 1.0
HB3 A:CYS290 3.9 43.1 1.0
HB2 A:ARG245 4.0 45.4 1.0
CD A:ARG245 4.1 36.7 1.0
HB3 A:ARG245 4.2 45.4 1.0
HB2 A:PRO295 4.2 44.7 1.0
HA A:VAL242 4.4 40.2 1.0
NH1 A:ARG245 4.5 34.4 1.0
CB A:ARG245 4.5 37.8 1.0
HG22 A:VAL242 4.6 43.1 1.0
HB3 A:PRO295 4.7 44.7 1.0
SG A:CYS300 4.7 32.0 1.0
HG21 A:VAL355 4.7 43.1 1.0
SG A:CYS306 4.8 33.2 1.0
HG12 A:VAL289 4.8 38.4 1.0
N A:CYS290 4.9 32.6 1.0
SG A:CYS297 4.9 33.1 1.0
CB A:PRO295 4.9 37.2 1.0
C A:CYS290 4.9 33.4 1.0
HG23 A:VAL246 4.9 47.0 1.0
HH12 A:ARG245 4.9 41.3 1.0
CG A:ARG245 5.0 37.0 1.0
HG13 A:VAL242 5.0 40.4 1.0
HD21 A:LEU285 5.0 44.4 1.0

Iron binding site 3 out of 8 in 8fay

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Iron binding site 3 out of 8 in the Human Mutyh 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 Human Mutyh 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:Fe601

b:34.5
occ:1.00
 FE3 A:SF4601 0.0 34.5 1.0
S2 A:SF4601 2.3 34.5 1.0
S4 A:SF4601 2.3 36.2 1.0
S1 A:SF4601 2.3 33.1 1.0
SG A:CYS306 2.4 33.2 1.0
FE1 A:SF4601 2.7 33.0 1.0
FE2 A:SF4601 2.7 33.5 1.0
FE4 A:SF4601 2.8 34.0 1.0
HB2 A:CYS306 2.9 44.2 1.0
CB A:CYS306 3.1 36.8 1.0
HB3 A:CYS306 3.2 44.2 1.0
HB2 A:ARG309 3.4 46.6 1.0
S3 A:SF4601 3.9 33.2 1.0
HB3 A:ARG245 3.9 45.4 1.0
H A:ARG309 4.0 46.6 1.0
HG22 A:VAL246 4.1 47.0 1.0
CB A:ARG309 4.2 38.8 1.0
HB3 A:ARG309 4.2 46.6 1.0
HA A:GLU303 4.3 41.6 1.0
HG23 A:VAL246 4.3 47.0 1.0
HB2 A:ARG245 4.4 45.4 1.0
HG11 A:VAL355 4.4 44.9 1.0
HG23 A:VAL302 4.5 47.9 1.0
HB3 A:ALA308 4.5 37.0 1.0
CA A:CYS306 4.5 38.1 1.0
HA A:VAL246 4.6 48.0 1.0
CB A:ARG245 4.6 37.8 1.0
HD3 A:ARG245 4.7 44.0 1.0
N A:ARG309 4.7 38.9 1.0
CG2 A:VAL246 4.7 39.2 1.0
SG A:CYS300 4.7 32.0 1.0
HA A:CYS306 4.8 45.7 1.0
SG A:CYS290 4.8 32.2 1.0
SG A:CYS297 4.8 33.1 1.0
HG2 A:ARG309 4.9 46.5 1.0
HB3 A:CYS297 4.9 37.2 1.0
HB A:VAL355 5.0 46.6 1.0

Iron binding site 4 out of 8 in 8fay

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Iron binding site 4 out of 8 in the Human Mutyh 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 Human Mutyh 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:Fe601

b:34.0
occ:1.00
 FE4 A:SF4601 0.0 34.0 1.0
S3 A:SF4601 2.2 33.2 1.0
S1 A:SF4601 2.3 33.1 1.0
S2 A:SF4601 2.3 34.5 1.0
SG A:CYS297 2.3 33.1 1.0
FE2 A:SF4601 2.7 33.5 1.0
FE3 A:SF4601 2.8 34.5 1.0
FE1 A:SF4601 2.8 33.0 1.0
HA A:CYS297 3.0 39.4 1.0
HB3 A:CYS297 3.2 37.2 1.0
CB A:CYS297 3.2 31.0 1.0
CA A:CYS297 3.5 32.8 1.0
HB2 A:PRO295 3.6 44.7 1.0
HG21 A:VAL355 3.6 43.1 1.0
HG11 A:VAL355 3.9 44.9 1.0
HB2 A:ARG309 3.9 46.6 1.0
S4 A:SF4601 4.0 36.2 1.0
H A:CYS297 4.0 38.0 1.0
HD3 A:ARG309 4.1 45.3 1.0
HB2 A:CYS297 4.1 37.2 1.0
N A:CYS297 4.1 31.7 1.0
HB2 A:CYS300 4.4 41.7 1.0
CB A:PRO295 4.5 37.2 1.0
CG2 A:VAL355 4.5 35.9 1.0
HB3 A:CYS300 4.5 41.7 1.0
HG2 A:PRO295 4.6 40.0 1.0
HA A:CYS290 4.7 38.3 1.0
CG1 A:VAL355 4.7 37.4 1.0
HD3 A:ARG245 4.8 44.0 1.0
SG A:CYS300 4.8 32.0 1.0
SG A:CYS290 4.8 32.2 1.0
CB A:CYS300 4.8 34.7 1.0
HB3 A:PRO295 4.8 44.7 1.0
HG23 A:VAL355 4.8 43.1 1.0
CB A:ARG309 4.8 38.8 1.0
SG A:CYS306 4.8 33.2 1.0
HB A:VAL355 4.8 46.6 1.0
C A:CYS297 4.8 37.9 1.0
HB2 A:CYS290 4.9 43.1 1.0
HG3 A:PRO295 4.9 40.0 1.0
O D:HOH799 4.9 40.5 1.0
CG A:PRO295 4.9 33.3 1.0
CD A:ARG309 5.0 37.7 1.0
CB A:VAL355 5.0 38.8 1.0

Iron binding site 5 out of 8 in 8fay

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Iron binding site 5 out of 8 in the Human Mutyh 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 5 of Human Mutyh 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
D:Fe601

b:32.3
occ:1.00
 FE1 D:SF4601 0.0 32.3 1.0
S4 D:SF4601 2.2 34.3 1.0
SG D:CYS300 2.3 32.4 1.0
S3 D:SF4601 2.3 32.6 1.0
S2 D:SF4601 2.3 34.1 1.0
FE2 D:SF4601 2.6 32.0 1.0
FE3 D:SF4601 2.7 32.8 1.0
FE4 D:SF4601 2.8 34.0 1.0
HB2 D:CYS300 3.0 46.5 1.0
CB D:CYS300 3.1 38.7 1.0
HB3 D:CYS300 3.2 46.5 1.0
HA D:CYS297 3.7 35.8 1.0
HB2 D:CYS290 3.8 34.5 1.0
S1 D:SF4601 3.9 35.6 1.0
HG23 D:VAL302 3.9 41.2 1.0
HA D:GLU303 4.0 45.7 1.0
HG12 D:VAL289 4.1 39.8 1.0
HG22 D:VAL302 4.2 41.2 1.0
HD21 D:LEU285 4.2 42.9 1.0
HB2 D:CYS306 4.4 36.2 1.0
CG2 D:VAL302 4.5 34.4 1.0
CA D:CYS300 4.5 32.7 1.0
CB D:CYS290 4.6 28.8 1.0
H D:VAL302 4.6 41.9 1.0
CA D:CYS297 4.6 29.8 1.0
SG D:CYS290 4.7 31.8 1.0
N D:GLU303 4.8 41.5 1.0
HA D:CYS300 4.8 39.2 1.0
CA D:GLU303 4.8 38.1 1.0
HD11 D:LEU285 4.8 45.9 1.0
HA D:CYS290 4.8 36.5 1.0
HG11 D:VAL289 4.9 39.8 1.0
CG1 D:VAL289 4.9 33.2 1.0
SG D:CYS306 4.9 35.8 1.0
HB3 D:CYS306 4.9 36.2 1.0
SG D:CYS297 4.9 32.2 1.0
HB2 D:GLU303 4.9 42.7 1.0
CB D:CYS306 4.9 30.1 1.0
H D:GLU303 4.9 49.9 1.0
HG21 D:VAL302 5.0 41.2 1.0
C D:VAL302 5.0 34.9 1.0
HB3 D:CYS297 5.0 36.3 1.0
HD2 D:PRO301 5.0 41.0 1.0

Iron binding site 6 out of 8 in 8fay

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Iron binding site 6 out of 8 in the Human Mutyh 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 6 of Human Mutyh 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
D:Fe601

b:32.0
occ:1.00
 FE2 D:SF4601 0.0 32.0 1.0
S4 D:SF4601 2.2 34.3 1.0
S3 D:SF4601 2.3 32.6 1.0
SG D:CYS290 2.3 31.8 1.0
S1 D:SF4601 2.4 35.6 1.0
FE1 D:SF4601 2.6 32.3 1.0
FE3 D:SF4601 2.7 32.8 1.0
HB2 D:CYS290 2.7 34.5 1.0
FE4 D:SF4601 2.8 34.0 1.0
CB D:CYS290 3.0 28.8 1.0
HA D:CYS290 3.4 36.5 1.0
HD3 D:ARG245 3.5 47.4 1.0
HH11 D:ARG245 3.7 37.4 1.0
CA D:CYS290 3.8 30.4 1.0
S2 D:SF4601 3.8 34.1 1.0
HB3 D:CYS290 3.8 34.5 1.0
HD2 D:ARG245 4.0 47.4 1.0
HB2 D:ARG245 4.2 37.9 1.0
CD D:ARG245 4.2 39.5 1.0
HB2 D:PRO295 4.2 44.2 1.0
HB3 D:ARG245 4.3 37.9 1.0
HA D:VAL242 4.4 37.1 1.0
NH1 D:ARG245 4.5 31.2 1.0
CB D:ARG245 4.6 31.6 1.0
SG D:CYS300 4.6 32.4 1.0
HG22 D:VAL242 4.7 38.8 1.0
HG23 D:VAL246 4.7 47.5 1.0
HG12 D:VAL289 4.7 39.8 1.0
HB3 D:PRO295 4.7 44.2 1.0
N D:CYS290 4.7 33.2 1.0
HG21 D:VAL355 4.8 45.1 1.0
SG D:CYS306 4.8 35.8 1.0
C D:CYS290 4.9 32.1 1.0
HD21 D:LEU285 4.9 42.9 1.0
SG D:CYS297 4.9 32.2 1.0
CB D:PRO295 4.9 36.8 1.0
HH12 D:ARG245 4.9 37.4 1.0
HG13 D:VAL242 4.9 38.7 1.0
HB2 D:CYS300 5.0 46.5 1.0
HA D:CYS297 5.0 35.8 1.0

Iron binding site 7 out of 8 in 8fay

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Iron binding site 7 out of 8 in the Human Mutyh 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 7 of Human Mutyh 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
D:Fe601

b:32.8
occ:1.00
 FE3 D:SF4601 0.0 32.8 1.0
S2 D:SF4601 2.2 34.1 1.0
S1 D:SF4601 2.3 35.6 1.0
S4 D:SF4601 2.3 34.3 1.0
SG D:CYS306 2.4 35.8 1.0
FE1 D:SF4601 2.7 32.3 1.0
FE2 D:SF4601 2.7 32.0 1.0
FE4 D:SF4601 2.7 34.0 1.0
HB2 D:CYS306 3.0 36.2 1.0
CB D:CYS306 3.2 30.1 1.0
HB3 D:CYS306 3.3 36.2 1.0
HB2 D:ARG309 3.4 36.6 1.0
HB3 D:ARG245 3.8 37.9 1.0
S3 D:SF4601 3.9 32.6 1.0
HG22 D:VAL246 4.0 47.5 1.0
HG23 D:VAL246 4.0 47.5 1.0
HB3 D:ARG309 4.1 36.6 1.0
H D:ARG309 4.1 43.3 1.0
CB D:ARG309 4.2 30.5 1.0
HG11 D:VAL355 4.3 40.5 1.0
HA D:GLU303 4.4 45.7 1.0
HB2 D:ARG245 4.4 37.9 1.0
CG2 D:VAL246 4.5 39.5 1.0
HB3 D:ALA308 4.5 46.5 1.0
CB D:ARG245 4.6 31.6 1.0
HD3 D:ARG245 4.6 47.4 1.0
CA D:CYS306 4.6 36.3 1.0
HG23 D:VAL302 4.7 41.2 1.0
HA D:VAL246 4.7 38.3 1.0
SG D:CYS300 4.8 32.4 1.0
SG D:CYS290 4.8 31.8 1.0
SG D:CYS297 4.8 32.2 1.0
N D:ARG309 4.8 36.1 1.0
HG2 D:ARG309 4.8 41.8 1.0
HA D:CYS306 4.9 43.6 1.0
HB D:VAL355 4.9 49.8 1.0

Iron binding site 8 out of 8 in 8fay

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Iron binding site 8 out of 8 in the Human Mutyh 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 8 of Human Mutyh 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
D:Fe601

b:34.0
occ:1.00
 FE4 D:SF4601 0.0 34.0 1.0
S1 D:SF4601 2.2 35.6 1.0
S2 D:SF4601 2.3 34.1 1.0
SG D:CYS297 2.3 32.2 1.0
S3 D:SF4601 2.3 32.6 1.0
FE3 D:SF4601 2.7 32.8 1.0
FE2 D:SF4601 2.8 32.0 1.0
FE1 D:SF4601 2.8 32.3 1.0
HA D:CYS297 2.9 35.8 1.0
CB D:CYS297 3.3 30.2 1.0
HB3 D:CYS297 3.3 36.3 1.0
CA D:CYS297 3.5 29.8 1.0
HG21 D:VAL355 3.6 45.1 1.0
HB2 D:PRO295 3.7 44.2 1.0
HG11 D:VAL355 3.7 40.5 1.0
HB2 D:ARG309 3.8 36.6 1.0
S4 D:SF4601 4.0 34.3 1.0
H D:CYS297 4.0 35.4 1.0
N D:CYS297 4.1 29.5 1.0
HB2 D:CYS297 4.1 36.3 1.0
HD3 D:ARG309 4.3 45.2 1.0
HB2 D:CYS300 4.3 46.5 1.0
HG2 D:PRO295 4.5 46.1 1.0
CG2 D:VAL355 4.5 37.6 1.0
HB3 D:CYS300 4.5 46.5 1.0
CB D:PRO295 4.6 36.8 1.0
CG1 D:VAL355 4.6 33.8 1.0
HA D:CYS290 4.7 36.5 1.0
CB D:ARG309 4.7 30.5 1.0
HB D:VAL355 4.7 49.8 1.0
CB D:CYS300 4.7 38.7 1.0
HD3 D:ARG245 4.8 47.4 1.0
C D:CYS297 4.8 33.6 1.0
SG D:CYS290 4.8 31.8 1.0
HG2 D:ARG309 4.8 41.8 1.0
SG D:CYS300 4.8 32.4 1.0
SG D:CYS306 4.8 35.8 1.0
HG23 D:VAL355 4.8 45.1 1.0
CG D:PRO295 4.9 38.4 1.0
HG3 D:PRO295 4.9 46.1 1.0
CB D:VAL355 4.9 41.5 1.0
HB3 D:PRO295 4.9 44.2 1.0
HB2 D:CYS290 4.9 34.5 1.0

Reference:

C.H.Trasvina-Arenas, C.H.Trasvina-Arenas, W.J.Lin, M.Demir, A.J.Fisher, S.S.David, M.P.Horvath. N/A N/A.
Page generated: Sat Aug 10 03:35:29 2024

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