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Calcium 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:

Iron (Fe) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total only one binding site of Calcium was determined in the The Crystal Structure of POL2CORE in Complex with Dna and An Incoming Nucleotide, Carrying An Fe-S Cluster, PDB code: 6qib:

Calcium binding site 1 out of 1 in 6qib

Go back to Calcium Binding Sites List in 6qib
Calcium binding site 1 out of 1 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 Calcium with other atoms in the Ca 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:Ca1203

b:46.4
occ:1.00
 OD2 A:ASP877 2.1 48.4 1.0
O1B A:DTP1202 2.1 49.8 1.0
O3G A:DTP1202 2.1 45.5 1.0
O1A A:DTP1202 2.1 45.5 1.0
O A:VAL641 2.2 54.8 1.0
OD2 A:ASP640 2.8 58.1 1.0
CG A:ASP877 3.0 53.6 1.0
OD1 A:ASP640 3.1 60.1 1.0
CG A:ASP640 3.1 59.5 1.0
PG A:DTP1202 3.3 48.9 1.0
PB A:DTP1202 3.3 48.8 1.0
C A:VAL641 3.3 49.9 1.0
PA A:DTP1202 3.5 45.1 1.0
OD1 A:ASP877 3.5 51.0 1.0
O3B A:DTP1202 3.6 42.2 1.0
O1G A:DTP1202 3.8 44.2 1.0
O3A A:DTP1202 3.9 46.3 1.0
N A:VAL641 4.0 49.7 1.0
C5' A:DTP1202 4.1 40.6 1.0
N A:SER643 4.1 49.0 1.0
CB A:ASP877 4.1 51.0 1.0
N A:ALA642 4.1 49.1 1.0
CA A:ALA642 4.1 48.3 1.0
O5' A:DTP1202 4.2 41.4 1.0
C A:ASP640 4.2 54.2 1.0
CA A:VAL641 4.3 50.0 1.0
CB A:ASP640 4.4 56.7 1.0
C A:ALA642 4.5 48.3 1.0
O A:ASP640 4.5 53.5 1.0
O2G A:DTP1202 4.5 40.3 1.0
O2B A:DTP1202 4.6 50.0 1.0
N A:MET644 4.6 48.7 1.0
O2A A:DTP1202 4.7 38.3 1.0
CA A:ASP640 4.8 57.2 1.0
CG2 A:VAL641 4.9 54.5 1.0
CB A:MET644 5.0 55.4 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 Jul 16 13:51:49 2024

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