Iron in PDB 9ekb: Cryo-Em Structure of Apo-Form Human Dna Polymerase Delta

All present enzymatic activity of Cryo-Em Structure of Apo-Form Human Dna Polymerase Delta:
2.7.7.7;

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

Zinc

(Zn)

1 atom

The binding sites of Iron atom in the Cryo-Em Structure of Apo-Form Human Dna Polymerase Delta (pdb code 9ekb). 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 Apo-Form Human Dna Polymerase Delta, PDB code: 9ekb:
Jump to Iron binding site number: 1; 2; 3; 4;

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


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 Apo-Form Human Dna Polymerase Delta within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1202 b:140.6 occ:1.00 FE1 A:SF41202 0.0 140.6 1.0 SG A:CYS1071 2.3 122.7 1.0 S3 A:SF41202 2.3 140.6 1.0 S2 A:SF41202 2.3 140.6 1.0 S4 A:SF41202 2.3 140.6 1.0 FE3 A:SF41202 2.7 140.6 1.0 FE2 A:SF41202 2.7 140.6 1.0 FE4 A:SF41202 2.7 140.6 1.0 CB A:CYS1071 3.3 122.7 1.0 S1 A:SF41202 3.9 140.6 1.0 SG A:CYS1058 4.1 128.8 1.0 O A:CYS1071 4.4 122.7 1.0 SG A:CYS1076 4.4 148.7 1.0 C A:CYS1071 4.5 122.7 1.0 CA A:CYS1071 4.5 122.7 1.0 CB A:SER1073 4.5 138.2 1.0 CB A:CYS1076 4.5 148.7 1.0 NH1 A:ARG1082 4.6 130.8 1.0 N A:SER1073 4.8 138.2 1.0

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


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 Apo-Form Human Dna Polymerase Delta within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1202 b:140.6 occ:1.00 FE2 A:SF41202 0.0 140.6 1.0 S4 A:SF41202 2.3 140.6 1.0 S3 A:SF41202 2.3 140.6 1.0 S1 A:SF41202 2.3 140.6 1.0 SG A:CYS1076 2.6 148.7 1.0 FE1 A:SF41202 2.7 140.6 1.0 FE3 A:SF41202 2.7 140.6 1.0 FE4 A:SF41202 2.7 140.6 1.0 CB A:CYS1076 3.3 148.7 1.0 S2 A:SF41202 3.9 140.6 1.0 OE1 A:GLN485 3.9 140.2 1.0 SG A:CYS1061 4.0 132.4 1.0 CD A:GLN485 4.0 140.2 1.0 CG A:GLN485 4.4 140.2 1.0 NE2 A:GLN485 4.4 140.2 1.0 SG A:CYS1071 4.4 122.7 1.0 CA A:CYS1076 4.7 148.7 1.0 CB A:CYS1061 4.9 132.4 1.0 CB A:GLN485 4.9 140.2 1.0

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


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 Apo-Form Human Dna Polymerase Delta within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1202 b:140.6 occ:1.00 FE3 A:SF41202 0.0 140.6 1.0 S2 A:SF41202 2.3 140.6 1.0 S4 A:SF41202 2.3 140.6 1.0 S1 A:SF41202 2.3 140.6 1.0 SG A:CYS1058 2.6 128.8 1.0 FE1 A:SF41202 2.7 140.6 1.0 FE4 A:SF41202 2.7 140.6 1.0 FE2 A:SF41202 2.7 140.6 1.0 CB A:CYS1058 3.9 128.8 1.0 S3 A:SF41202 3.9 140.6 1.0 SG A:CYS1076 3.9 148.7 1.0 CA A:CYS1058 3.9 128.8 1.0 CG2 A:ILE1078 4.1 140.0 1.0 CB A:ILE1078 4.1 140.0 1.0 CD1 A:ILE1078 4.3 140.0 1.0 CB A:CYS1061 4.4 132.4 1.0 SG A:CYS1061 4.6 132.4 1.0 NH1 A:ARG1082 4.6 130.8 1.0 N A:CYS1058 4.6 128.8 1.0 CG1 A:ILE1078 4.8 140.0 1.0 SG A:CYS1071 4.8 122.7 1.0

Iron binding site 4 out of 4 in the Cryo-Em Structure of Apo-Form Human Dna Polymerase Delta


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 Apo-Form Human Dna Polymerase Delta within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1202 b:140.6 occ:1.00 FE4 A:SF41202 0.0 140.6 1.0 S1 A:SF41202 2.3 140.6 1.0 S3 A:SF41202 2.3 140.6 1.0 S2 A:SF41202 2.3 140.6 1.0 SG A:CYS1061 2.4 132.4 1.0 FE3 A:SF41202 2.7 140.6 1.0 FE2 A:SF41202 2.7 140.6 1.0 FE1 A:SF41202 2.7 140.6 1.0 CB A:CYS1061 2.8 132.4 1.0 SG A:CYS1071 3.7 122.7 1.0 S4 A:SF41202 3.9 140.6 1.0 CA A:CYS1061 4.2 132.4 1.0 CB A:CYS1071 4.4 122.7 1.0 O A:CYS1058 4.4 128.8 1.0 SG A:CYS1058 4.4 128.8 1.0 C A:CYS1061 4.5 132.4 1.0 CA A:CYS1058 4.6 128.8 1.0 O A:CYS1061 4.7 132.4 1.0 CB A:CYS1058 4.9 128.8 1.0 N A:GLN1062 4.9 127.5 1.0 O A:GLN485 4.9 140.2 1.0

K.S.Murakami, Y.Shin, M.Hedglin. Cryo-Em Structure of Apo-Form Human Dna Polymerase Delta Elucidates Its Minimal Dna Synthesis Activity Without Pcna To Be Published.