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Iron in PDB 7ef9: Crystal Structure of Mouse Mutyh in Complex with Dna Containing Ap Site Analogue:8-Oxog (Form II)

Enzymatic activity of Crystal Structure of Mouse Mutyh in Complex with Dna Containing Ap Site Analogue:8-Oxog (Form II)

All present enzymatic activity of Crystal Structure of Mouse Mutyh in Complex with Dna Containing Ap Site Analogue:8-Oxog (Form II):
3.2.2.31;

Protein crystallography data

The structure of Crystal Structure of Mouse Mutyh in Complex with Dna Containing Ap Site Analogue:8-Oxog (Form II), PDB code: 7ef9 was solved by T.Nakamura, Y.Nakabeppu, Y.Yamagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.53 / 1.97
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 71.66, 108.496, 158.527, 90, 90, 90
R / Rfree (%) 17.8 / 19.7

Other elements in 7ef9:

The structure of Crystal Structure of Mouse Mutyh in Complex with Dna Containing Ap Site Analogue:8-Oxog (Form II) also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Mouse Mutyh in Complex with Dna Containing Ap Site Analogue:8-Oxog (Form II) (pdb code 7ef9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Mouse Mutyh in Complex with Dna Containing Ap Site Analogue:8-Oxog (Form II), PDB code: 7ef9:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7ef9

Go back to Iron Binding Sites List in 7ef9
Iron binding site 1 out of 4 in the Crystal Structure of Mouse Mutyh in Complex with Dna Containing Ap Site Analogue:8-Oxog (Form II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Mouse Mutyh in Complex with Dna Containing Ap Site Analogue:8-Oxog (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:41.4
occ:1.00
 FE1 A:SF4501 0.0 41.4 1.0
S3 A:SF4501 2.3 44.1 1.0
S4 A:SF4501 2.3 42.1 1.0
SG A:CYS271 2.3 46.4 1.0
S2 A:SF4501 2.3 42.0 1.0
FE3 A:SF4501 2.7 43.6 1.0
FE2 A:SF4501 2.7 40.7 1.0
FE4 A:SF4501 2.7 48.4 1.0
CB A:CYS271 3.0 46.2 1.0
S1 A:SF4501 3.9 40.0 1.0
CG2 A:VAL273 4.3 44.3 1.0
CA A:CYS271 4.4 47.1 1.0
CA A:CYS268 4.7 56.9 1.0
SG A:CYS261 4.7 41.5 1.0
CA A:GLN274 4.8 52.6 1.0
SG A:CYS277 4.8 48.1 1.0
CB A:CYS261 4.8 39.2 1.0
SG A:CYS268 4.8 52.7 1.0
N A:GLN274 4.8 55.0 1.0
C A:VAL273 5.0 50.1 1.0

Iron binding site 2 out of 4 in 7ef9

Go back to Iron Binding Sites List in 7ef9
Iron binding site 2 out of 4 in the Crystal Structure of Mouse Mutyh in Complex with Dna Containing Ap Site Analogue:8-Oxog (Form II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Mouse Mutyh in Complex with Dna Containing Ap Site Analogue:8-Oxog (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:40.7
occ:1.00
 FE2 A:SF4501 0.0 40.7 1.0
S4 A:SF4501 2.2 42.1 1.0
S3 A:SF4501 2.3 44.1 1.0
S1 A:SF4501 2.3 40.0 1.0
SG A:CYS261 2.3 41.5 1.0
FE3 A:SF4501 2.7 43.6 1.0
FE1 A:SF4501 2.7 41.4 1.0
FE4 A:SF4501 2.8 48.4 1.0
CB A:CYS261 3.2 39.2 1.0
S2 A:SF4501 3.9 42.0 1.0
CA A:CYS261 3.9 42.0 1.0
CD A:ARG216 4.1 41.3 1.0
CB A:ARG216 4.6 40.0 1.0
NH1 A:ARG216 4.6 44.3 1.0
SG A:CYS277 4.7 48.1 1.0
SG A:CYS271 4.7 46.4 1.0
CB A:PRO266 4.8 51.9 1.0
SG A:CYS268 4.9 52.7 1.0
N A:CYS261 4.9 44.7 1.0
CG A:ARG216 5.0 46.8 1.0

Iron binding site 3 out of 4 in 7ef9

Go back to Iron Binding Sites List in 7ef9
Iron binding site 3 out of 4 in the Crystal Structure of Mouse Mutyh in Complex with Dna Containing Ap Site Analogue:8-Oxog (Form II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Mouse Mutyh in Complex with Dna Containing Ap Site Analogue:8-Oxog (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:43.6
occ:1.00
 FE3 A:SF4501 0.0 43.6 1.0
S1 A:SF4501 2.3 40.0 1.0
S4 A:SF4501 2.3 42.1 1.0
S2 A:SF4501 2.3 42.0 1.0
SG A:CYS277 2.3 48.1 1.0
FE2 A:SF4501 2.7 40.7 1.0
FE1 A:SF4501 2.7 41.4 1.0
FE4 A:SF4501 2.7 48.4 1.0
CB A:CYS277 3.2 49.1 1.0
S3 A:SF4501 3.8 44.1 1.0
CB A:TYR280 4.4 55.2 1.0
CB A:ARG216 4.6 40.0 1.0
CA A:CYS277 4.7 53.3 1.0
N A:TYR280 4.7 47.9 1.0
SG A:CYS268 4.7 52.7 1.0
SG A:CYS271 4.8 46.4 1.0
CG2 A:VAL217 4.8 39.9 1.0
SG A:CYS261 4.8 41.5 1.0
CB A:ALA279 4.9 48.3 1.0

Iron binding site 4 out of 4 in 7ef9

Go back to Iron Binding Sites List in 7ef9
Iron binding site 4 out of 4 in the Crystal Structure of Mouse Mutyh in Complex with Dna Containing Ap Site Analogue:8-Oxog (Form II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Mouse Mutyh in Complex with Dna Containing Ap Site Analogue:8-Oxog (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:48.4
occ:1.00
 FE4 A:SF4501 0.0 48.4 1.0
S2 A:SF4501 2.2 42.0 1.0
S1 A:SF4501 2.3 40.0 1.0
SG A:CYS268 2.3 52.7 1.0
S3 A:SF4501 2.3 44.1 1.0
FE3 A:SF4501 2.7 43.6 1.0
FE1 A:SF4501 2.7 41.4 1.0
FE2 A:SF4501 2.8 40.7 1.0
CB A:CYS268 3.3 62.2 1.0
CA A:CYS268 3.6 56.9 1.0
S4 A:SF4501 3.9 42.1 1.0
N A:CYS268 4.2 56.1 1.0
CG2 A:VAL323 4.5 47.0 1.0
CB A:PRO266 4.6 51.9 1.0
CD1 A:TYR280 4.7 59.5 1.0
CB A:CYS271 4.7 46.2 1.0
CG1 A:VAL323 4.7 54.2 1.0
CG A:PRO266 4.7 47.9 1.0
SG A:CYS277 4.8 48.1 1.0
SG A:CYS271 4.8 46.4 1.0
SG A:CYS261 4.9 41.5 1.0
CB A:VAL323 4.9 54.7 1.0
C A:CYS268 4.9 60.3 1.0
CB A:TYR280 5.0 55.2 1.0

Reference:

T.Nakamura, K.Okabe, S.Hirayama, M.Chirifu, S.Ikemizu, H.Morioka, Y.Nakabeppu, Y.Yamagata. Structure of the Mammalian Adenine Dna Glycosylase Mutyh: Insights Into the Base Excision Repair Pathway and Cancer. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
DOI: 10.1093/NAR/GKAB492
Page generated: Thu Aug 8 05:05:27 2024

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