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Iron in PDB 6ppu: Cryo-Em Structure of Adnab-Amppnp-Dna Complex

Enzymatic activity of Cryo-Em Structure of Adnab-Amppnp-Dna Complex

All present enzymatic activity of Cryo-Em Structure of Adnab-Amppnp-Dna Complex:
3.6.4.12;

Other elements in 6ppu:

The structure of Cryo-Em Structure of Adnab-Amppnp-Dna Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of Adnab-Amppnp-Dna Complex (pdb code 6ppu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cryo-Em Structure of Adnab-Amppnp-Dna Complex, PDB code: 6ppu:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6ppu

Go back to Iron Binding Sites List in 6ppu
Iron binding site 1 out of 4 in the Cryo-Em Structure of Adnab-Amppnp-Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Adnab-Amppnp-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1102

b:18.0
occ:1.00
FE1 A:SF41102 0.0 18.0 1.0
S3 A:SF41102 2.3 18.0 1.0
S2 A:SF41102 2.3 18.0 1.0
S4 A:SF41102 2.3 18.0 1.0
FE4 A:SF41102 2.7 18.0 1.0
FE3 A:SF41102 2.7 18.0 1.0
FE2 A:SF41102 2.7 18.0 1.0
SG A:CYS1030 3.1 13.2 1.0
CB A:CYS1030 3.5 13.2 1.0
S1 A:SF41102 3.9 18.0 1.0
SG A:CYS1027 4.1 16.5 1.0
CA A:CYS1027 4.2 16.5 1.0
O A:GLY1026 4.4 18.5 1.0
CB A:CYS1027 4.5 16.5 1.0
NH1 A:ARG810 4.7 13.5 1.0
O A:VAL1032 4.8 15.0 1.0
CD A:ARG810 4.9 13.5 1.0
N A:CYS1027 5.0 16.5 1.0
CA A:CYS1030 5.0 13.2 1.0

Iron binding site 2 out of 4 in 6ppu

Go back to Iron Binding Sites List in 6ppu
Iron binding site 2 out of 4 in the Cryo-Em Structure of Adnab-Amppnp-Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Adnab-Amppnp-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1102

b:18.0
occ:1.00
FE2 A:SF41102 0.0 18.0 1.0
S1 A:SF41102 2.3 18.0 1.0
S4 A:SF41102 2.3 18.0 1.0
S3 A:SF41102 2.3 18.0 1.0
FE1 A:SF41102 2.7 18.0 1.0
FE4 A:SF41102 2.7 18.0 1.0
FE3 A:SF41102 2.7 18.0 1.0
SG A:CYS1036 3.1 9.6 1.0
CB A:CYS1036 3.5 9.6 1.0
O A:VAL1032 3.8 15.0 1.0
S2 A:SF41102 3.9 18.0 1.0
SG A:CYS1030 4.4 13.2 1.0
CA A:CYS1036 4.7 9.6 1.0
CD2 A:LEU809 4.7 15.5 1.0

Iron binding site 3 out of 4 in 6ppu

Go back to Iron Binding Sites List in 6ppu
Iron binding site 3 out of 4 in the Cryo-Em Structure of Adnab-Amppnp-Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Adnab-Amppnp-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1102

b:18.0
occ:1.00
FE3 A:SF41102 0.0 18.0 1.0
S1 A:SF41102 2.3 18.0 1.0
S4 A:SF41102 2.3 18.0 1.0
S2 A:SF41102 2.3 18.0 1.0
FE1 A:SF41102 2.7 18.0 1.0
FE2 A:SF41102 2.7 18.0 1.0
FE4 A:SF41102 2.7 18.0 1.0
O A:ARG1022 2.9 15.7 1.0
SG A:CYS1027 3.6 16.5 1.0
S3 A:SF41102 3.9 18.0 1.0
C A:ARG1022 4.0 15.7 1.0
SG A:CYS1036 4.2 9.6 1.0
CA A:VAL1023 4.2 13.2 1.0
N A:VAL1023 4.6 13.2 1.0
N A:ASN1024 4.7 16.8 1.0
SG A:CYS807 4.8 13.4 1.0
CG2 A:VAL1023 4.9 13.2 1.0
CB A:CYS1027 4.9 16.5 1.0

Iron binding site 4 out of 4 in 6ppu

Go back to Iron Binding Sites List in 6ppu
Iron binding site 4 out of 4 in the Cryo-Em Structure of Adnab-Amppnp-Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Adnab-Amppnp-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1102

b:18.0
occ:1.00
FE4 A:SF41102 0.0 18.0 1.0
S2 A:SF41102 2.3 18.0 1.0
S1 A:SF41102 2.3 18.0 1.0
S3 A:SF41102 2.3 18.0 1.0
FE1 A:SF41102 2.7 18.0 1.0
FE2 A:SF41102 2.7 18.0 1.0
FE3 A:SF41102 2.7 18.0 1.0
SG A:CYS807 3.0 13.4 1.0
CB A:CYS807 3.6 13.4 1.0
S4 A:SF41102 3.9 18.0 1.0
CB A:ARG810 4.0 13.5 1.0
N A:ARG810 4.3 13.5 1.0
O A:ARG1022 4.3 15.7 1.0
CA A:ARG810 4.5 13.5 1.0
CD A:ARG810 4.7 13.5 1.0
ND2 A:ASN1024 4.8 16.8 1.0
CG A:ARG810 4.8 13.5 1.0

Reference:

N.Jia, M.C.Unciuleac, C.Xue, E.C.Greene, D.J.Patel, S.Shuman. Structures and Single-Molecule Analysis of Bacterial Motor Nuclease Adnab Illuminate the Mechanism of Dna Double-Strand Break Resection. Proc.Natl.Acad.Sci.Usa 2019.
ISSN: ESSN 1091-6490
PubMed: 31740608
DOI: 10.1073/PNAS.1913546116
Page generated: Wed Aug 7 06:43:02 2024

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