Iron in PDB 6p1h: Cryo-Em Structure of Dna Polymerase Delta Holoenzyme

All present enzymatic activity of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme:
2.7.7.7;

The structure of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme also contains other interesting chemical elements:

Calcium

(Ca)

5 atoms

The binding sites of Iron atom in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme (pdb code 6p1h). 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 Dna Polymerase Delta Holoenzyme, PDB code: 6p1h:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme


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 Dna Polymerase Delta Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:0.3 occ:1.00 FE1 A:SF41101 0.0 0.3 1.0 SG A:CYS1069 2.2 91.2 1.0 S2 A:SF41101 2.3 0.3 1.0 S3 A:SF41101 2.3 0.3 1.0 S4 A:SF41101 2.3 0.3 1.0 FE3 A:SF41101 2.7 0.3 1.0 FE4 A:SF41101 2.7 0.3 1.0 FE2 A:SF41101 2.7 0.3 1.0 CB A:CYS1069 2.9 91.2 1.0 S1 A:SF41101 3.9 0.3 1.0 NH2 A:ARG1080 4.1 88.0 1.0 CA A:CYS1069 4.3 91.2 1.0 SG A:CYS1056 4.5 96.7 1.0 CA A:GLU492 4.6 91.4 1.0 CB A:ASN1071 4.7 80.1 1.0 SG A:CYS1059 4.8 96.0 1.0 CG A:GLU492 4.9 91.4 1.0 SG A:CYS1074 5.0 84.9 1.0 CZ A:ARG1080 5.0 88.0 1.0 C A:CYS1069 5.0 91.2 1.0

Iron binding site 2 out of 4 in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme


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 Dna Polymerase Delta Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:0.3 occ:1.00 FE2 A:SF41101 0.0 0.3 1.0 S1 A:SF41101 2.3 0.3 1.0 S4 A:SF41101 2.3 0.3 1.0 S3 A:SF41101 2.3 0.3 1.0 SG A:CYS1074 2.3 84.9 1.0 FE3 A:SF41101 2.7 0.3 1.0 FE1 A:SF41101 2.7 0.3 1.0 FE4 A:SF41101 2.7 0.3 1.0 CB A:CYS1074 3.1 84.9 1.0 S2 A:SF41101 3.9 0.3 1.0 SG A:CYS1069 4.3 91.2 1.0 CA A:CYS1074 4.6 84.9 1.0 N A:PHE1077 4.6 79.6 1.0 CB A:ILE1076 4.6 86.1 1.0 CD1 B:LEU119 4.8 0.1 1.0 O A:ASN1071 4.8 80.1 1.0 SG A:CYS1056 4.9 96.7 1.0 CB A:ASN1071 5.0 80.1 1.0

Iron binding site 3 out of 4 in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme


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 Dna Polymerase Delta Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:0.3 occ:1.00 FE3 A:SF41101 0.0 0.3 1.0 S4 A:SF41101 2.3 0.3 1.0 S1 A:SF41101 2.3 0.3 1.0 S2 A:SF41101 2.3 0.3 1.0 SG A:CYS1056 2.4 96.7 1.0 FE1 A:SF41101 2.7 0.3 1.0 FE2 A:SF41101 2.7 0.3 1.0 FE4 A:SF41101 2.7 0.3 1.0 CB A:CYS1056 3.5 96.7 1.0 CA A:CYS1056 3.5 96.7 1.0 NH2 A:ARG1080 3.7 88.0 1.0 S3 A:SF41101 3.9 0.3 1.0 N A:CYS1056 4.3 96.7 1.0 CB A:CYS1059 4.5 96.0 1.0 SG A:CYS1059 4.6 96.0 1.0 C A:CYS1056 4.7 96.7 1.0 O A:CYS1056 4.7 96.7 1.0 SG A:CYS1074 4.8 84.9 1.0 SG A:CYS1069 4.8 91.2 1.0 O A:GLN1055 4.8 95.8 1.0 CZ A:ARG1080 4.9 88.0 1.0 C A:GLN1055 4.9 95.8 1.0 CB A:ILE1076 4.9 86.1 1.0 CG2 A:ILE1076 5.0 86.1 1.0 CB A:CYS1069 5.0 91.2 1.0

Iron binding site 4 out of 4 in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme


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 Dna Polymerase Delta Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:0.3 occ:1.00 FE4 A:SF41101 0.0 0.3 1.0 S2 A:SF41101 2.3 0.3 1.0 S3 A:SF41101 2.3 0.3 1.0 S1 A:SF41101 2.3 0.3 1.0 SG A:CYS1059 2.4 96.0 1.0 FE1 A:SF41101 2.7 0.3 1.0 FE3 A:SF41101 2.7 0.3 1.0 FE2 A:SF41101 2.7 0.3 1.0 CB A:CYS1059 3.2 96.0 1.0 S4 A:SF41101 3.9 0.3 1.0 SG A:CYS1074 4.3 84.9 1.0 N A:GLU492 4.6 91.4 1.0 SG A:CYS1069 4.6 91.2 1.0 C A:LYS491 4.7 87.8 1.0 O A:GLN490 4.7 89.8 1.0 CA A:CYS1059 4.7 96.0 1.0 CA A:GLU492 4.8 91.4 1.0 CD1 B:LEU119 5.0 0.1 1.0 O A:LYS491 5.0 87.8 1.0

R.Jain, W.J.Rice, R.Malik, R.E.Johnson, L.Prakash, S.Prakash, I.Ubarretxena-Belandia, A.K.Aggarwal. Cryo-Em Structure and Dynamics of Eukaryotic Dna Polymerase Delta Holoenzyme. Nat.Struct.Mol.Biol. V. 26 955 2019.
ISSN: ESSN 1545-9985
PubMed: 31582849
DOI: 10.1038/S41594-019-0305-Z