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Iron in PDB 6qib: The Crystal Structure of POL2CORE in Complex with Dna and An Incoming Nucleotide, Carrying An Fe-S Cluster

Enzymatic activity of The Crystal Structure of POL2CORE in Complex with Dna and An Incoming Nucleotide, Carrying An Fe-S Cluster

All present enzymatic activity of The Crystal Structure of POL2CORE in Complex with Dna and An Incoming Nucleotide, Carrying An Fe-S Cluster:
2.7.7.7;

Protein crystallography data

The structure of The Crystal Structure of POL2CORE in Complex with Dna and An Incoming Nucleotide, Carrying An Fe-S Cluster, PDB code: 6qib was solved by V.Parkash, E.Johansson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.48 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.360, 70.402, 154.240, 90.00, 112.99, 90.00
R / Rfree (%) 22.3 / 28.6

Other elements in 6qib:

The structure of The Crystal Structure of POL2CORE in Complex with Dna and An Incoming Nucleotide, Carrying An Fe-S Cluster also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the The Crystal Structure of POL2CORE in Complex with Dna and An Incoming Nucleotide, Carrying An Fe-S Cluster (pdb code 6qib). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The Crystal Structure of POL2CORE in Complex with Dna and An Incoming Nucleotide, Carrying An Fe-S Cluster, PDB code: 6qib:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6qib

Go back to Iron Binding Sites List in 6qib
Iron binding site 1 out of 4 in the The Crystal Structure of POL2CORE in Complex with Dna and An Incoming Nucleotide, Carrying An Fe-S Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of POL2CORE in Complex with Dna and An Incoming Nucleotide, Carrying An Fe-S Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1201

b:82.0
occ:0.80
 FE1 A:SF41201 0.0 82.0 0.8
S3 A:SF41201 2.3 77.6 0.8
S4 A:SF41201 2.3 85.5 0.8
S2 A:SF41201 2.3 76.8 0.8
SG A:CYS665 2.3 91.7 1.0
FE4 A:SF41201 2.7 68.2 0.8
FE2 A:SF41201 2.7 80.3 0.8
FE3 A:SF41201 2.8 85.2 0.8
CB A:CYS665 3.4 93.1 1.0
CA A:CYS665 3.5 94.9 1.0
O A:CYS665 3.7 99.3 1.0
S1 A:SF41201 3.9 73.9 0.8
C A:CYS665 4.1 99.1 1.0
CB A:CYS668 4.2 0.8 1.0
SG A:CYS668 4.5 0.9 1.0
CB A:CYS763 4.8 73.1 1.0
N A:CYS665 4.8 95.8 1.0
SG A:CYS677 4.9 89.3 1.0
SG A:CYS763 4.9 73.9 1.0
CB A:ALA678 5.0 73.6 1.0

Iron binding site 2 out of 4 in 6qib

Go back to Iron Binding Sites List in 6qib
Iron binding site 2 out of 4 in the The Crystal Structure of POL2CORE in Complex with Dna and An Incoming Nucleotide, Carrying An Fe-S Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of POL2CORE in Complex with Dna and An Incoming Nucleotide, Carrying An Fe-S Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1201

b:80.3
occ:0.80
 FE2 A:SF41201 0.0 80.3 0.8
S4 A:SF41201 2.3 85.5 0.8
S1 A:SF41201 2.3 73.9 0.8
S3 A:SF41201 2.3 77.6 0.8
SG A:CYS668 2.3 0.9 1.0
FE3 A:SF41201 2.7 85.2 0.8
FE1 A:SF41201 2.7 82.0 0.8
FE4 A:SF41201 2.7 68.2 0.8
CB A:CYS668 2.9 0.8 1.0
S2 A:SF41201 3.9 76.8 0.8
CB A:PHE670 4.0 0.9 1.0
CA A:CYS668 4.3 0.6 1.0
O A:CYS665 4.5 99.3 1.0
N A:PHE670 4.6 0.1 1.0
CA A:PHE670 4.7 0.7 1.0
SG A:CYS677 4.7 89.3 1.0
SG A:CYS763 4.7 73.9 1.0
CD1 A:LEU181 4.8 57.0 1.0
C A:CYS668 4.8 0.7 1.0
C A:PHE670 4.8 0.4 1.0
SG A:CYS665 4.9 91.7 1.0
O A:PHE670 5.0 0.9 1.0

Iron binding site 3 out of 4 in 6qib

Go back to Iron Binding Sites List in 6qib
Iron binding site 3 out of 4 in the The Crystal Structure of POL2CORE in Complex with Dna and An Incoming Nucleotide, Carrying An Fe-S Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Crystal Structure of POL2CORE in Complex with Dna and An Incoming Nucleotide, Carrying An Fe-S Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1201

b:85.2
occ:0.80
 FE3 A:SF41201 0.0 85.2 0.8
S1 A:SF41201 2.3 73.9 0.8
SG A:CYS677 2.3 89.3 1.0
S2 A:SF41201 2.3 76.8 0.8
S4 A:SF41201 2.3 85.5 0.8
FE4 A:SF41201 2.7 68.2 0.8
FE2 A:SF41201 2.7 80.3 0.8
FE1 A:SF41201 2.8 82.0 0.8
CB A:CYS677 3.3 79.7 1.0
S3 A:SF41201 3.9 77.6 0.8
C A:CYS677 3.9 79.2 1.0
O A:CYS677 3.9 77.3 1.0
CA A:CYS677 4.2 79.4 1.0
N A:ALA678 4.3 76.2 1.0
SG A:CYS665 4.4 91.7 1.0
CB A:PHE670 4.4 0.9 1.0
O A:PHE670 4.5 0.9 1.0
CG A:LYS675 4.5 0.5 1.0
SG A:CYS763 4.6 73.9 1.0
CB A:ALA678 4.7 73.6 1.0
CA A:ALA678 4.8 71.8 1.0
CD A:LYS675 4.9 0.6 1.0
CD A:ARG765 4.9 80.4 1.0
N A:CYS677 4.9 81.5 1.0
C A:PHE670 5.0 0.4 1.0

Iron binding site 4 out of 4 in 6qib

Go back to Iron Binding Sites List in 6qib
Iron binding site 4 out of 4 in the The Crystal Structure of POL2CORE in Complex with Dna and An Incoming Nucleotide, Carrying An Fe-S Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Crystal Structure of POL2CORE in Complex with Dna and An Incoming Nucleotide, Carrying An Fe-S Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1201

b:68.2
occ:0.80
 FE4 A:SF41201 0.0 68.2 0.8
SG A:CYS763 2.3 73.9 1.0
S2 A:SF41201 2.3 76.8 0.8
S1 A:SF41201 2.3 73.9 0.8
S3 A:SF41201 2.3 77.6 0.8
FE3 A:SF41201 2.7 85.2 0.8
FE1 A:SF41201 2.7 82.0 0.8
FE2 A:SF41201 2.7 80.3 0.8
CB A:CYS763 2.8 73.1 1.0
CA A:CYS763 3.7 69.6 1.0
S4 A:SF41201 3.9 85.5 0.8
O A:CYS677 4.3 77.3 1.0
C A:CYS763 4.5 69.7 1.0
SG A:CYS668 4.6 0.9 1.0
N A:GLN764 4.6 67.4 1.0
CB A:ARG765 4.7 68.1 1.0
SG A:CYS677 4.7 89.3 1.0
N A:ARG765 4.8 65.5 1.0
CB A:CYS677 4.9 79.7 1.0
N A:CYS763 4.9 67.3 1.0
SG A:CYS665 4.9 91.7 1.0
CD1 A:LEU181 5.0 57.0 1.0

Reference:

J.Ter Beek, V.Parkash, G.O.Bylund, P.Osterman, A.E.Sauer-Eriksson, E.Johansson. Structural Evidence For An Essential Fe-S Cluster in the Catalytic Core Domain of Dna Polymerase ε. Nucleic Acids Res. V. 47 5712 2019.
ISSN: ESSN 1362-4962
PubMed: 30968138
DOI: 10.1093/NAR/GKZ248
Page generated: Wed Aug 6 12:35:28 2025

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