Iron in PDB 7lxd: Structure of Yeast Dna Polymerase Zeta (Apo)

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

The binding sites of Iron atom in the Structure of Yeast Dna Polymerase Zeta (Apo) (pdb code 7lxd). 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 Yeast Dna Polymerase Zeta (Apo), PDB code: 7lxd:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Yeast 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 Yeast Dna Polymerase Zeta (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1601 b:94.0 occ:1.00 FE1 A:SF41601 0.0 94.0 1.0 S3 A:SF41601 2.3 94.0 1.0 SG A:CYS1473 2.3 123.1 1.0 S2 A:SF41601 2.3 94.0 1.0 S4 A:SF41601 2.3 94.0 1.0 FE4 A:SF41601 2.7 94.0 1.0 FE3 A:SF41601 2.7 94.0 1.0 FE2 A:SF41601 2.7 94.0 1.0 CG2 A:VAL1475 3.3 113.3 1.0 S1 A:SF41601 3.9 94.0 1.0 CB A:CYS1473 3.9 123.1 1.0 SG A:CYS1449 4.4 111.9 1.0 SG A:CYS1446 4.5 106.5 1.0 CG A:ARG852 4.7 104.3 1.0 CB A:VAL1475 4.8 113.3 1.0 N A:PHE1476 4.8 114.2 1.0 SG A:CYS1468 4.8 115.5 1.0 CB A:PHE1476 4.9 114.2 1.0 CB A:CYS1449 4.9 111.9 1.0 CD A:ARG852 5.0 104.3 1.0

Iron binding site 2 out of 4 in the Structure of Yeast 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 Yeast Dna Polymerase Zeta (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1601 b:94.0 occ:1.00 FE2 A:SF41601 0.0 94.0 1.0 SG A:CYS1449 2.3 111.9 1.0 S4 A:SF41601 2.3 94.0 1.0 S3 A:SF41601 2.3 94.0 1.0 S1 A:SF41601 2.3 94.0 1.0 CB A:CYS1449 2.6 111.9 1.0 FE3 A:SF41601 2.7 94.0 1.0 FE4 A:SF41601 2.7 94.0 1.0 FE1 A:SF41601 2.7 94.0 1.0 CG A:PRO854 3.5 96.2 1.0 S2 A:SF41601 3.9 94.0 1.0 CA A:CYS1449 4.1 111.9 1.0 CB A:PRO854 4.2 96.2 1.0 CD A:PRO854 4.2 96.2 1.0 O A:CYS1446 4.3 106.5 1.0 C A:CYS1449 4.4 111.9 1.0 CA A:PRO854 4.4 96.2 1.0 CG A:ARG852 4.4 104.3 1.0 N A:PRO854 4.5 96.2 1.0 CA A:CYS1446 4.6 106.5 1.0 SG A:CYS1468 4.6 115.5 1.0 SG A:CYS1473 4.7 123.1 1.0 N A:SER1450 4.8 110.8 1.0 CA F:GLY128 4.8 132.1 1.0 O A:CYS1449 4.9 111.9 1.0 O A:VAL1445 4.9 116.0 1.0 C A:CYS1446 4.9 106.5 1.0 N A:CYS1449 5.0 111.9 1.0 SG A:CYS1446 5.0 106.5 1.0

Iron binding site 3 out of 4 in the Structure of Yeast 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 Yeast Dna Polymerase Zeta (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1601 b:94.0 occ:1.00 FE3 A:SF41601 0.0 94.0 1.0 SG A:CYS1446 2.3 106.5 1.0 S1 A:SF41601 2.3 94.0 1.0 S4 A:SF41601 2.3 94.0 1.0 S2 A:SF41601 2.3 94.0 1.0 FE4 A:SF41601 2.7 94.0 1.0 FE2 A:SF41601 2.7 94.0 1.0 FE1 A:SF41601 2.7 94.0 1.0 CA A:CYS1446 2.9 106.5 1.0 CB A:CYS1446 2.9 106.5 1.0 N A:CYS1446 3.9 106.5 1.0 S3 A:SF41601 3.9 94.0 1.0 C A:CYS1446 3.9 106.5 1.0 O A:CYS1446 3.9 106.5 1.0 CB A:CYS1449 4.2 111.9 1.0 NH1 A:ARG1479 4.2 122.5 1.0 CG2 A:VAL1475 4.3 113.3 1.0 C A:VAL1445 4.5 116.0 1.0 O A:VAL1445 4.5 116.0 1.0 SG A:CYS1449 4.7 111.9 1.0 SG A:CYS1468 4.8 115.5 1.0 CZ A:ARG1479 4.9 122.5 1.0 SG A:CYS1473 4.9 123.1 1.0

Iron binding site 4 out of 4 in the Structure of Yeast 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 Yeast Dna Polymerase Zeta (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1601 b:94.0 occ:1.00 FE4 A:SF41601 0.0 94.0 1.0 SG A:CYS1468 2.3 115.5 1.0 S2 A:SF41601 2.3 94.0 1.0 S3 A:SF41601 2.3 94.0 1.0 S1 A:SF41601 2.3 94.0 1.0 FE1 A:SF41601 2.7 94.0 1.0 FE3 A:SF41601 2.7 94.0 1.0 FE2 A:SF41601 2.7 94.0 1.0 CB A:CYS1468 3.2 115.5 1.0 S4 A:SF41601 3.9 94.0 1.0 CB A:PRO854 4.1 96.2 1.0 SG A:CYS1473 4.2 123.1 1.0 CA A:PRO854 4.3 96.2 1.0 CG A:PRO854 4.4 96.2 1.0 SG A:CYS1446 4.4 106.5 1.0 CA A:CYS1468 4.6 115.5 1.0 NH2 A:ARG1479 4.7 122.5 1.0 C A:CYS1468 4.9 115.5 1.0 SG A:CYS1449 4.9 111.9 1.0

C.D.Truong, T.A.Craig, G.Cui, M.V.Botuyan, R.A.Serkasevich, K.-Y.Chan, G.Mer, P.-L.Chiu, R.Kumar. Cryo-Em Reveals Conformational Variability in Apo Dna Polymerase Zeta J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X