Iron in PDB 6v8p: Structure of Dna Polymerase Zeta (Apo)

All present enzymatic activity of Structure of Dna Polymerase Zeta (Apo):
2.7.7.7;

The binding sites of Iron atom in the Structure of Dna Polymerase Zeta (Apo) (pdb code 6v8p). 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 (Apo), PDB code: 6v8p:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Dna Polymerase Zeta (Apo)


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 (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1601 b:0.4 occ:1.00 FE1 A:SF41601 0.0 0.4 1.0 S3 A:SF41601 2.1 0.4 1.0 S4 A:SF41601 2.1 0.4 1.0 S2 A:SF41601 2.1 0.4 1.0 SG A:CYS1473 2.3 0.1 1.0 FE4 A:SF41601 3.0 0.4 1.0 FE2 A:SF41601 3.0 0.4 1.0 FE3 A:SF41601 3.0 0.4 1.0 CB A:CYS1473 3.4 0.1 1.0 S1 A:SF41601 3.7 0.4 1.0 CD A:ARG852 4.0 0.1 1.0 CB A:VAL1475 4.3 0.8 1.0 CG A:ARG852 4.3 0.1 1.0 SG A:CYS1449 4.4 0.8 1.0 CG2 A:VAL1475 4.6 0.8 1.0 CA A:CYS1473 4.9 0.1 1.0 SG A:CYS1468 4.9 0.6 1.0

Iron binding site 2 out of 4 in the Structure of Dna Polymerase Zeta (Apo)


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 (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1601 b:0.4 occ:1.00 FE2 A:SF41601 0.0 0.4 1.0 S3 A:SF41601 2.1 0.4 1.0 S1 A:SF41601 2.1 0.4 1.0 S4 A:SF41601 2.1 0.4 1.0 SG A:CYS1449 2.4 0.8 1.0 FE4 A:SF41601 3.0 0.4 1.0 FE3 A:SF41601 3.0 0.4 1.0 FE1 A:SF41601 3.0 0.4 1.0 CB A:CYS1449 3.1 0.8 1.0 CG A:PRO854 3.5 0.8 1.0 S2 A:SF41601 3.7 0.4 1.0 CB A:PRO854 4.0 0.8 1.0 SG A:CYS1468 4.3 0.6 1.0 CA A:CYS1449 4.4 0.8 1.0 CD A:PRO854 4.4 0.8 1.0 C A:CYS1449 4.5 0.8 1.0 CA A:PRO854 4.5 0.8 1.0 O A:CYS1446 4.5 0.8 1.0 N A:SER1450 4.6 0.2 1.0 N A:PRO854 4.7 0.8 1.0 CA A:CYS1446 4.9 0.8 1.0 O A:CYS1449 4.9 0.8 1.0

Iron binding site 3 out of 4 in the Structure of Dna Polymerase Zeta (Apo)


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 (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1601 b:0.4 occ:1.00 FE3 A:SF41601 0.0 0.4 1.0 S1 A:SF41601 2.1 0.4 1.0 S4 A:SF41601 2.1 0.4 1.0 S2 A:SF41601 2.1 0.4 1.0 SG A:CYS1468 2.3 0.6 1.0 FE2 A:SF41601 3.0 0.4 1.0 FE1 A:SF41601 3.0 0.4 1.0 FE4 A:SF41601 3.0 0.4 1.0 CB A:CYS1468 3.2 0.6 1.0 S3 A:SF41601 3.7 0.4 1.0 NH2 A:ARG1479 3.7 0.6 1.0 O A:CYS1468 4.4 0.6 1.0 CA A:CYS1468 4.5 0.6 1.0 SG A:CYS1446 4.6 0.8 1.0 SG A:CYS1473 4.6 0.1 1.0 C A:CYS1468 4.7 0.6 1.0 CB A:PRO854 4.7 0.8 1.0 CB A:PHE1476 4.9 0.2 1.0 CA A:PRO854 5.0 0.8 1.0

Iron binding site 4 out of 4 in the Structure of Dna Polymerase Zeta (Apo)


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 (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1601 b:0.4 occ:1.00 FE4 A:SF41601 0.0 0.4 1.0 S1 A:SF41601 2.1 0.4 1.0 S3 A:SF41601 2.1 0.4 1.0 S2 A:SF41601 2.1 0.4 1.0 SG A:CYS1446 2.4 0.8 1.0 FE2 A:SF41601 3.0 0.4 1.0 FE1 A:SF41601 3.0 0.4 1.0 FE3 A:SF41601 3.0 0.4 1.0 CB A:CYS1446 3.2 0.8 1.0 CA A:CYS1446 3.2 0.8 1.0 S4 A:SF41601 3.7 0.4 1.0 N A:CYS1446 4.0 0.8 1.0 NH2 A:ARG1479 4.1 0.6 1.0 CG1 A:VAL1475 4.1 0.8 1.0 CB A:CYS1449 4.3 0.8 1.0 C A:CYS1446 4.3 0.8 1.0 CB A:VAL1475 4.3 0.8 1.0 O A:CYS1446 4.4 0.8 1.0 SG A:CYS1449 4.5 0.8 1.0 O A:VAL1445 4.6 0.0 1.0 C A:VAL1445 4.7 0.0 1.0 SG A:CYS1473 4.8 0.1 1.0 NE A:ARG1479 5.0 0.6 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