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Iron in PDB 6h1v: 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: 6h1v 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) 19.99 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 148.210, 70.040, 149.930, 90.00, 109.43, 90.00
R / Rfree (%) 23.9 / 26.6

Other elements in 6h1v:

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:

Magnesium (Mg) 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 6h1v). 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: 6h1v:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6h1v

Go back to Iron Binding Sites List in 6h1v
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:83.7
occ:0.70
 FE1 A:SF41201 0.0 83.7 0.7
SG A:CYS665 2.3 1.0 1.0
S3 A:SF41201 2.3 73.6 0.7
S2 A:SF41201 2.3 57.0 0.7
S4 A:SF41201 2.3 87.9 0.7
FE2 A:SF41201 2.7 81.0 0.7
FE4 A:SF41201 2.7 53.9 0.7
FE3 A:SF41201 2.7 85.0 0.7
CB A:CYS665 3.4 95.9 1.0
CA A:CYS665 3.8 93.8 1.0
S1 A:SF41201 3.9 66.1 0.7
N A:CYS665 4.6 0.1 1.0
SG A:CYS677 4.8 0.0 1.0
C A:CYS665 4.9 0.7 1.0
O A:ASP664 4.9 96.0 1.0
SG A:CYS763 4.9 52.8 1.0
O A:CYS665 4.9 99.9 1.0
CB A:ALA678 4.9 48.1 1.0

Iron binding site 2 out of 4 in 6h1v

Go back to Iron Binding Sites List in 6h1v
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:81.0
occ:0.70
 FE2 A:SF41201 0.0 81.0 0.7
S4 A:SF41201 2.3 87.9 0.7
S1 A:SF41201 2.3 66.1 0.7
S3 A:SF41201 2.3 73.6 0.7
FE1 A:SF41201 2.7 83.7 0.7
FE3 A:SF41201 2.7 85.0 0.7
FE4 A:SF41201 2.7 53.9 0.7
S2 A:SF41201 3.9 57.0 0.7
O A:CYS665 4.3 99.9 1.0
CA A:CYS665 4.3 93.8 1.0
SG A:CYS665 4.5 1.0 1.0
CB A:CYS665 4.6 95.9 1.0
SG A:CYS763 4.7 52.8 1.0
C A:CYS665 4.7 0.7 1.0
SG A:CYS677 4.9 0.0 1.0

Iron binding site 3 out of 4 in 6h1v

Go back to Iron Binding Sites List in 6h1v
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:85.0
occ:0.70
 FE3 A:SF41201 0.0 85.0 0.7
SG A:CYS677 2.3 0.0 1.0
S1 A:SF41201 2.3 66.1 0.7
S2 A:SF41201 2.3 57.0 0.7
S4 A:SF41201 2.3 87.9 0.7
FE4 A:SF41201 2.7 53.9 0.7
FE2 A:SF41201 2.7 81.0 0.7
FE1 A:SF41201 2.7 83.7 0.7
CB A:CYS677 3.5 59.7 1.0
S3 A:SF41201 3.9 73.6 0.7
N A:ALA678 4.4 53.7 1.0
SG A:CYS763 4.6 52.8 1.0
CA A:CYS677 4.6 71.7 1.0
C A:CYS677 4.7 62.2 1.0
SG A:CYS665 4.7 1.0 1.0

Iron binding site 4 out of 4 in 6h1v

Go back to Iron Binding Sites List in 6h1v
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:53.9
occ:0.70
 FE4 A:SF41201 0.0 53.9 0.7
SG A:CYS763 2.3 52.8 1.0
S2 A:SF41201 2.3 57.0 0.7
S1 A:SF41201 2.3 66.1 0.7
S3 A:SF41201 2.3 73.6 0.7
FE3 A:SF41201 2.7 85.0 0.7
FE1 A:SF41201 2.7 83.7 0.7
FE2 A:SF41201 2.7 81.0 0.7
CB A:CYS763 3.1 45.8 1.0
S4 A:SF41201 3.9 87.9 0.7
CA A:CYS763 3.9 39.0 1.0
SG A:CYS677 4.5 0.0 1.0
CB A:CYS677 4.7 59.7 1.0
C A:CYS763 4.9 35.9 1.0
SG A:CYS665 4.9 1.0 1.0
N A:CYS763 4.9 40.9 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: Tue Aug 6 20:33:21 2024

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