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Magnesium 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:

Iron (Fe) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total only one binding site of Magnesium was determined in the The Crystal Structure of POL2CORE in Complex with Dna and An Incoming Nucleotide, Carrying An Fe-S Cluster, PDB code: 6h1v:

Magnesium binding site 1 out of 1 in 6h1v

Go back to Magnesium Binding Sites List in 6h1v
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1203

b:44.2
occ:1.00
 OD1 A:ASP640 1.9 58.8 1.0
OD2 A:ASP877 2.1 51.3 1.0
O1A A:DTP1202 2.1 36.5 1.0
O3G A:DTP1202 2.2 35.3 1.0
O2B A:DTP1202 2.4 44.0 1.0
OD2 A:ASP640 2.4 44.1 1.0
CG A:ASP640 2.5 51.1 1.0
O A:VAL641 2.7 49.4 1.0
CG A:ASP877 3.0 43.8 1.0
OD1 A:ASP877 3.2 45.9 1.0
PA A:DTP1202 3.3 29.5 1.0
PB A:DTP1202 3.4 35.4 1.0
O3A A:DTP1202 3.5 38.5 1.0
PG A:DTP1202 3.6 44.5 1.0
C A:VAL641 3.9 52.3 1.0
O3B A:DTP1202 4.0 31.4 1.0
CB A:ASP640 4.0 42.9 1.0
N A:VAL641 4.2 44.5 1.0
C5' A:DTP1202 4.2 31.0 1.0
O2A A:DTP1202 4.3 41.5 1.0
CB A:ASP877 4.3 35.0 1.0
O5' A:DTP1202 4.4 25.6 1.0
C A:ASP640 4.4 49.2 1.0
O2G A:DTP1202 4.5 47.1 1.0
O1G A:DTP1202 4.5 49.3 1.0
CA A:VAL641 4.6 49.0 1.0
N A:SER643 4.6 43.1 1.0
CA A:ASP640 4.7 52.0 1.0
O1B A:DTP1202 4.7 32.9 1.0
CG2 A:VAL641 4.8 45.3 1.0
N A:ALA642 4.9 50.1 1.0
N A:MET644 4.9 46.0 1.0
O A:ASP640 5.0 47.4 1.0
CA A:ALA642 5.0 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: Wed Aug 13 06:48:42 2025

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