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Manganese in PDB 7omg: Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template

Enzymatic activity of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template

All present enzymatic activity of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template, PDB code: 7omg was solved by K.Betz, H.M.Kropp, K.Diederichs, A.Marx, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.25 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 108.403, 147.138, 71.129, 90, 90, 90
R / Rfree (%) 21 / 24.8

Other elements in 7omg:

The structure of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 1 atom
Magnesium (Mg) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template (pdb code 7omg). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template, PDB code: 7omg:

Manganese binding site 1 out of 1 in 7omg

Go back to Manganese Binding Sites List in 7omg
Manganese binding site 1 out of 1 in the Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn804

b:51.6
occ:1.00
 OD2 A:ASP542 2.0 52.0 1.0
O A:PHE405 2.2 52.9 1.0
OD2 A:ASP404 2.2 58.4 1.0
O1B A:DTP801 2.3 51.8 1.0
O2G A:DTP801 2.3 50.7 1.0
O1A A:DTP801 2.5 54.0 1.0
CG A:ASP542 3.1 50.2 1.0
CG A:ASP404 3.1 57.3 1.0
PB A:DTP801 3.3 47.7 1.0
C A:PHE405 3.3 52.8 1.0
MG A:MG803 3.4 45.8 1.0
PG A:DTP801 3.5 49.8 1.0
OD1 A:ASP542 3.5 51.0 1.0
PA A:DTP801 3.5 50.8 1.0
OD1 A:ASP404 3.6 55.0 1.0
O3B A:DTP801 3.6 49.6 1.0
MG A:MG802 3.6 57.2 1.0
O3A A:DTP801 3.6 48.3 1.0
N A:PHE405 3.8 52.1 1.0
O A:HOH965 3.8 59.0 1.0
O A:HOH959 3.9 56.1 1.0
CA A:PHE405 4.0 54.2 1.0
O1G A:DTP801 4.2 51.0 1.0
C5' A:DTP801 4.2 49.1 1.0
CB A:ASP542 4.3 49.7 1.0
CB A:ASP404 4.3 60.0 1.0
N A:SER407 4.3 48.5 1.0
C A:ASP404 4.4 53.3 1.0
CB A:PHE405 4.4 54.2 1.0
N A:ARG406 4.4 53.6 1.0
O5' A:DTP801 4.4 46.9 1.0
N A:LEU408 4.6 45.7 1.0
O2B A:DTP801 4.7 49.8 1.0
O3G A:DTP801 4.7 53.4 1.0
CA A:ARG406 4.7 52.0 1.0
O A:HOH913 4.7 56.0 1.0
O A:ASP542 4.7 49.2 1.0
C A:ARG406 4.7 50.7 1.0
O2A A:DTP801 4.8 54.8 1.0
CA A:ASP404 4.8 55.2 1.0
O A:ASP404 5.0 57.5 1.0

Reference:

H.M.Kropp, S.Ludmann, K.Diederichs, K.Betz, A.Marx. Structural Basis For the Recognition of Deaminated Nucleobases By An Archaeal Dna Polymerase. Chembiochem 2021.
ISSN: ESSN 1439-7633
PubMed: 34486208
DOI: 10.1002/CBIC.202100306
Page generated: Sun Oct 6 10:22:58 2024

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