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Iron in PDB 7ef8: Crystal Structure of Mouse Mutyh in Complex with Dna Containing Ap Site Analogue:8-Oxog (Form I)

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

All present enzymatic activity of Crystal Structure of Mouse Mutyh in Complex with Dna Containing Ap Site Analogue:8-Oxog (Form I):
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 I), PDB code: 7ef8 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) 46.89 / 2.45
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 74.274, 107.236, 156.432, 90, 90, 90
R / Rfree (%) 19.8 / 22.1

Other elements in 7ef8:

The structure of Crystal Structure of Mouse Mutyh in Complex with Dna Containing Ap Site Analogue:8-Oxog (Form I) 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 I) (pdb code 7ef8). 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 I), PDB code: 7ef8:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7ef8

Go back to Iron Binding Sites List in 7ef8
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 I)


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 I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:70.7
occ:1.00
 FE1 A:SF4501 0.0 70.7 1.0
S4 A:SF4501 2.3 77.6 1.0
S3 A:SF4501 2.3 63.9 1.0
S2 A:SF4501 2.3 72.3 1.0
SG A:CYS271 2.3 81.6 1.0
FE3 A:SF4501 2.7 80.2 1.0
FE2 A:SF4501 2.7 71.7 1.0
FE4 A:SF4501 2.7 74.9 1.0
CB A:CYS271 3.2 81.2 1.0
S1 A:SF4501 3.9 71.2 1.0
CG2 A:VAL273 4.3 63.3 1.0
SG A:CYS268 4.4 94.0 1.0
CA A:CYS271 4.6 84.9 1.0
CA A:GLN274 4.7 94.1 1.0
SG A:CYS261 4.8 72.2 1.0
CG1 A:VAL260 4.8 63.1 1.0
N A:GLN274 4.8 89.0 1.0
CA A:CYS268 4.8 93.2 1.0
O A:VAL273 4.8 85.6 1.0
CB A:CYS261 4.8 65.2 1.0
C A:VAL273 4.8 83.8 1.0
CB A:CYS268 4.9 95.3 1.0
SG A:CYS277 4.9 96.5 1.0
CB A:GLN274 4.9 99.3 1.0

Iron binding site 2 out of 4 in 7ef8

Go back to Iron Binding Sites List in 7ef8
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 I)


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 I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:71.7
occ:1.00
 FE2 A:SF4501 0.0 71.7 1.0
S4 A:SF4501 2.3 77.6 1.0
S1 A:SF4501 2.3 71.2 1.0
S3 A:SF4501 2.3 63.9 1.0
SG A:CYS261 2.3 72.2 1.0
FE1 A:SF4501 2.7 70.7 1.0
FE4 A:SF4501 2.7 74.9 1.0
FE3 A:SF4501 2.7 80.2 1.0
CB A:CYS261 3.2 65.2 1.0
CA A:CYS261 3.8 63.0 1.0
S2 A:SF4501 3.9 72.3 1.0
CD A:ARG216 4.1 77.4 1.0
NH1 A:ARG216 4.3 73.1 1.0
CB A:ARG216 4.7 79.6 1.0
N A:CYS261 4.7 62.4 1.0
SG A:CYS277 4.8 96.5 1.0
CB A:PRO266 4.8 78.4 1.0
SG A:CYS268 4.9 94.0 1.0
SG A:CYS271 4.9 81.6 1.0
C A:CYS261 5.0 62.2 1.0

Iron binding site 3 out of 4 in 7ef8

Go back to Iron Binding Sites List in 7ef8
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 I)


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 I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:80.2
occ:1.00
 FE3 A:SF4501 0.0 80.2 1.0
S2 A:SF4501 2.3 72.3 1.0
S4 A:SF4501 2.3 77.6 1.0
S1 A:SF4501 2.3 71.2 1.0
SG A:CYS277 2.3 96.5 1.0
FE1 A:SF4501 2.7 70.7 1.0
FE4 A:SF4501 2.7 74.9 1.0
FE2 A:SF4501 2.7 71.7 1.0
CB A:CYS277 3.1 92.2 1.0
S3 A:SF4501 3.9 63.9 1.0
CG2 A:VAL217 4.6 64.7 1.0
CA A:CYS277 4.6 91.5 1.0
CB A:TYR280 4.6 102.6 1.0
SG A:CYS271 4.6 81.6 1.0
CB A:ARG216 4.6 79.6 1.0
SG A:CYS261 4.8 72.2 1.0
SG A:CYS268 4.9 94.0 1.0
O A:VAL273 4.9 85.6 1.0
N A:VAL217 5.0 79.5 1.0
N A:TYR280 5.0 102.7 1.0

Iron binding site 4 out of 4 in 7ef8

Go back to Iron Binding Sites List in 7ef8
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 I)


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 I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:74.9
occ:1.00
 FE4 A:SF4501 0.0 74.9 1.0
S2 A:SF4501 2.3 72.3 1.0
S1 A:SF4501 2.3 71.2 1.0
S3 A:SF4501 2.3 63.9 1.0
SG A:CYS268 2.3 94.0 1.0
FE3 A:SF4501 2.7 80.2 1.0
FE1 A:SF4501 2.7 70.7 1.0
FE2 A:SF4501 2.7 71.7 1.0
CB A:CYS268 3.7 95.3 1.0
S4 A:SF4501 3.9 77.6 1.0
CG2 A:VAL323 4.2 71.3 1.0
CA A:CYS268 4.3 93.2 1.0
CB A:PRO266 4.3 78.4 1.0
N A:CYS268 4.6 88.2 1.0
SG A:CYS271 4.7 81.6 1.0
CG1 A:VAL323 4.7 81.8 1.0
SG A:CYS277 4.8 96.5 1.0
CD1 A:TYR280 4.8 108.2 1.0
CB A:VAL323 4.8 76.9 1.0
CB A:CYS271 4.9 81.2 1.0
SG A:CYS261 4.9 72.2 1.0
CB A:TYR280 4.9 102.6 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 05:04:55 2024

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