Iron in PDB 7sjr: Cryo-Em Structure of Adna-Adnb(W325A) in Complex with Dna and Amppnp

All present enzymatic activity of Cryo-Em Structure of Adna-Adnb(W325A) in Complex with Dna and Amppnp:
3.6.4.12;

The structure of Cryo-Em Structure of Adna-Adnb(W325A) in Complex with Dna and Amppnp also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Iron atom in the Cryo-Em Structure of Adna-Adnb(W325A) in Complex with Dna and Amppnp (pdb code 7sjr). 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 Adna-Adnb(W325A) in Complex with Dna and Amppnp, PDB code: 7sjr:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cryo-Em Structure of Adna-Adnb(W325A) in Complex with Dna and Amppnp


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 Adna-Adnb(W325A) in Complex with Dna and Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:45.6 occ:1.00 FE1 A:SF41102 0.0 45.6 1.0 SG A:CYS1030 2.3 21.8 1.0 S4 A:SF41102 2.3 45.6 1.0 S2 A:SF41102 2.3 45.6 1.0 S3 A:SF41102 2.3 45.6 1.0 FE3 A:SF41102 2.7 45.6 1.0 FE4 A:SF41102 2.7 45.6 1.0 FE2 A:SF41102 2.7 45.6 1.0 O A:VAL1032 3.4 14.2 1.0 CB A:CYS1030 3.5 21.8 1.0 S1 A:SF41102 3.9 45.6 1.0 SG A:CYS1027 4.1 25.4 1.0 CB A:ARG810 4.5 17.1 1.0 C A:VAL1032 4.5 14.2 1.0 CD A:ARG810 4.5 17.1 1.0 SG A:CYS807 4.7 18.1 1.0 CA A:CYS1027 4.7 25.4 1.0 CG A:ARG810 4.8 17.1 1.0 SG A:CYS1036 4.8 19.9 1.0 CB A:CYS1027 4.8 25.4 1.0 CB A:CYS1036 4.9 19.9 1.0 CA A:CYS1030 4.9 21.8 1.0 CA A:ARG1033 5.0 15.6 1.0

Iron binding site 2 out of 4 in the Cryo-Em Structure of Adna-Adnb(W325A) in Complex with Dna and Amppnp


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 Adna-Adnb(W325A) in Complex with Dna and Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:45.6 occ:1.00 FE2 A:SF41102 0.0 45.6 1.0 S1 A:SF41102 2.3 45.6 1.0 SG A:CYS1036 2.3 19.9 1.0 S4 A:SF41102 2.3 45.6 1.0 S3 A:SF41102 2.3 45.6 1.0 CB A:CYS1036 2.6 19.9 1.0 FE4 A:SF41102 2.7 45.6 1.0 FE3 A:SF41102 2.7 45.6 1.0 FE1 A:SF41102 2.7 45.6 1.0 S2 A:SF41102 3.9 45.6 1.0 CA A:CYS1036 4.1 19.9 1.0 O A:VAL1032 4.2 14.2 1.0 SG A:CYS1027 4.2 25.4 1.0 SG A:CYS1030 4.5 21.8 1.0 N A:CYS1036 4.8 19.9 1.0 N A:GLN1039 4.8 20.0 1.0 C A:CYS1036 4.8 19.9 1.0 SG A:CYS807 4.9 18.1 1.0 CA A:ARG1033 4.9 15.6 1.0

Iron binding site 3 out of 4 in the Cryo-Em Structure of Adna-Adnb(W325A) in Complex with Dna and Amppnp


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 Adna-Adnb(W325A) in Complex with Dna and Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:45.6 occ:1.00 FE3 A:SF41102 0.0 45.6 1.0 SG A:CYS1027 2.3 25.4 1.0 S4 A:SF41102 2.3 45.6 1.0 S2 A:SF41102 2.3 45.6 1.0 S1 A:SF41102 2.3 45.6 1.0 FE1 A:SF41102 2.7 45.6 1.0 FE4 A:SF41102 2.7 45.6 1.0 FE2 A:SF41102 2.7 45.6 1.0 CB A:CYS1027 3.2 25.4 1.0 O A:ARG1022 3.6 24.7 1.0 S3 A:SF41102 3.9 45.6 1.0 CA A:CYS1027 4.0 25.4 1.0 CA A:VAL1023 4.3 23.2 1.0 SG A:CYS1030 4.5 21.8 1.0 SG A:CYS807 4.6 18.1 1.0 SG A:CYS1036 4.6 19.9 1.0 C A:ARG1022 4.6 24.7 1.0 O A:CYS1027 4.7 25.4 1.0 CG2 A:VAL1023 4.7 23.2 1.0 CB A:VAL1023 4.8 23.2 1.0 C A:CYS1027 4.9 25.4 1.0 N A:VAL1023 4.9 23.2 1.0 N A:ASN1024 5.0 24.9 1.0

Iron binding site 4 out of 4 in the Cryo-Em Structure of Adna-Adnb(W325A) in Complex with Dna and Amppnp


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 Adna-Adnb(W325A) in Complex with Dna and Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:45.6 occ:1.00 FE4 A:SF41102 0.0 45.6 1.0 SG A:CYS807 2.3 18.1 1.0 S2 A:SF41102 2.3 45.6 1.0 S1 A:SF41102 2.3 45.6 1.0 S3 A:SF41102 2.3 45.6 1.0 FE3 A:SF41102 2.7 45.6 1.0 FE1 A:SF41102 2.7 45.6 1.0 FE2 A:SF41102 2.7 45.6 1.0 CB A:CYS807 3.5 18.1 1.0 O A:ARG1022 3.6 24.7 1.0 S4 A:SF41102 3.9 45.6 1.0 CB A:ARG810 4.0 17.1 1.0 N A:ARG810 4.3 17.1 1.0 CA A:ARG810 4.6 17.1 1.0 CB A:CYS1036 4.6 19.9 1.0 CD2 A:LEU809 4.7 14.7 1.0 CB A:ALA1021 4.7 19.3 1.0 C A:ARG1022 4.8 24.7 1.0 CA A:ALA1021 4.8 19.3 1.0 C A:ALA1021 4.8 19.3 1.0 SG A:CYS1036 4.9 19.9 1.0 CA A:CYS807 4.9 18.1 1.0 N A:ARG1022 4.9 24.7 1.0 CB A:LEU809 4.9 14.7 1.0 SG A:CYS1030 5.0 21.8 1.0 SG A:CYS1027 5.0 25.4 1.0

G.M.Warren, A.Meir, J.Wang, D.J.Patel, E.C.Greene, S.Shuman. Structure-Activity Relationships at A Nucleobase-Stacking Tryptophan Required For Chemomechanical Coupling in the Dna Resecting Motor-Nuclease Adnab Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962