Iron in PDB 6v93: Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex

All present enzymatic activity of Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex:
2.7.7.7;

The structure of Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Iron atom in the Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex (pdb code 6v93). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex, PDB code: 6v93:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1601 b:52.0 occ:1.00 FE1 A:SF41601 0.0 52.0 1.0 S4 A:SF41601 2.1 52.0 1.0 S2 A:SF41601 2.1 52.0 1.0 S3 A:SF41601 2.1 52.0 1.0 SG A:CYS1473 2.3 43.0 1.0 FE3 A:SF41601 3.0 52.0 1.0 FE2 A:SF41601 3.0 52.0 1.0 FE4 A:SF41601 3.0 52.0 1.0 CB A:CYS1473 3.1 43.0 1.0 S1 A:SF41601 3.7 52.0 1.0 CB A:VAL1475 4.2 43.0 1.0 CG A:ARG852 4.4 41.8 1.0 CD A:ARG852 4.4 41.8 1.0 CG2 A:VAL1475 4.6 43.0 1.0 CA A:CYS1473 4.6 43.0 1.0 N A:PHE1476 4.7 42.0 1.0 SG A:CYS1468 4.8 41.8 1.0 SG A:CYS1449 4.9 44.2 1.0 N A:VAL1475 5.0 43.0 1.0 CA A:VAL1475 5.0 43.0 1.0

Iron binding site 2 out of 4 in the Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1601 b:52.0 occ:1.00 FE2 A:SF41601 0.0 52.0 1.0 S3 A:SF41601 2.1 52.0 1.0 S4 A:SF41601 2.1 52.0 1.0 S1 A:SF41601 2.1 52.0 1.0 SG A:CYS1449 2.3 44.2 1.0 FE4 A:SF41601 3.0 52.0 1.0 FE3 A:SF41601 3.0 52.0 1.0 FE1 A:SF41601 3.0 52.0 1.0 CB A:CYS1449 3.1 44.2 1.0 S2 A:SF41601 3.7 52.0 1.0 CG A:PRO854 4.0 38.2 1.0 CG A:ARG852 4.3 41.8 1.0 CB A:PRO854 4.4 38.2 1.0 CA A:PRO854 4.4 38.2 1.0 CA A:CYS1449 4.5 44.2 1.0 N A:PRO854 4.5 38.2 1.0 SG A:CYS1468 4.5 41.8 1.0 CD A:PRO854 4.6 38.2 1.0 C A:CYS1449 4.6 44.2 1.0 O A:CYS1446 4.9 45.7 1.0 O A:CYS1449 5.0 44.2 1.0 N A:SER1450 5.0 42.3 1.0

Iron binding site 3 out of 4 in the Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1601 b:52.0 occ:1.00 FE3 A:SF41601 0.0 52.0 1.0 S4 A:SF41601 2.1 52.0 1.0 S1 A:SF41601 2.1 52.0 1.0 S2 A:SF41601 2.1 52.0 1.0 SG A:CYS1468 2.2 41.8 1.0 FE2 A:SF41601 3.0 52.0 1.0 FE1 A:SF41601 3.0 52.0 1.0 FE4 A:SF41601 3.0 52.0 1.0 CB A:CYS1468 3.1 41.8 1.0 S3 A:SF41601 3.7 52.0 1.0 NH2 A:ARG1479 3.7 47.9 1.0 SG A:CYS1446 4.4 45.7 1.0 CA A:CYS1468 4.5 41.8 1.0 O A:CYS1468 4.5 41.8 1.0 C A:CYS1468 4.6 41.8 1.0 CB A:PRO854 4.7 38.2 1.0 CA A:PRO854 4.7 38.2 1.0 CB A:SER1470 4.7 39.3 1.0 CZ A:ARG1479 4.9 47.9 1.0

Iron binding site 4 out of 4 in the Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1601 b:52.0 occ:1.00 FE4 A:SF41601 0.0 52.0 1.0 S1 A:SF41601 2.1 52.0 1.0 S2 A:SF41601 2.1 52.0 1.0 S3 A:SF41601 2.1 52.0 1.0 SG A:CYS1446 2.3 45.7 1.0 FE2 A:SF41601 3.0 52.0 1.0 FE3 A:SF41601 3.0 52.0 1.0 FE1 A:SF41601 3.0 52.0 1.0 CB A:CYS1446 3.2 45.7 1.0 CA A:CYS1446 3.3 45.7 1.0 S4 A:SF41601 3.7 52.0 1.0 N A:CYS1446 4.0 45.7 1.0 CG1 A:VAL1475 4.2 43.0 1.0 CB A:VAL1475 4.3 43.0 1.0 CB A:CYS1449 4.4 44.2 1.0 C A:CYS1446 4.4 45.7 1.0 O A:CYS1446 4.5 45.7 1.0 C A:VAL1445 4.6 47.1 1.0 O A:VAL1445 4.7 47.1 1.0 NH2 A:ARG1479 4.7 47.9 1.0 SG A:CYS1449 4.7 44.2 1.0 SG A:CYS1473 4.8 43.0 1.0 CG1 A:VAL1445 5.0 47.1 1.0

R.Malik, M.Kopylov, Y.Gomez-Llorente, R.Jain, R.E.Johnson, L.Prakash, S.Prakash, I.Ubarretxena-Belandia, A.K.Aggarwal. Structure and Mechanism of B-Family Dna Polymerase Zeta Specialized For Translesion Dna Synthesis. Nat.Struct.Mol.Biol. V. 27 913 2020.
ISSN: ESSN 1545-9985
PubMed: 32807989
DOI: 10.1038/S41594-020-0476-7