Calcium in PDB 7omg: 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;

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

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

Chlorine	(Cl)	1 atom
Manganese	(Mn)	1 atom
Magnesium	(Mg)	2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template, PDB code: 7omg:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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:Ca807 b:88.9 occ:1.00 NH2 A:ARG32 3.2 75.5 1.0 OE2 A:GLU10 3.5 79.2 1.0 CD A:GLU10 4.2 76.5 1.0 CE1 A:TYR30 4.2 59.2 1.0 OE1 A:GLU10 4.3 77.8 1.0 CZ A:TYR30 4.3 63.7 1.0 CD1 A:TYR30 4.5 62.3 1.0 CZ A:ARG32 4.5 78.1 1.0 CE2 A:TYR30 4.6 62.1 1.0 OH A:TYR30 4.7 60.2 1.0 CG A:TYR30 4.8 61.8 1.0 CD2 A:TYR30 4.8 63.1 1.0

Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca binding site number 2 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:Ca808 b:79.7 occ:1.00 O A:ASN568 2.4 71.2 1.0 O A:HOH902 2.5 68.1 1.0 O A:HOH979 2.5 69.9 1.0 O A:HOH973 2.5 69.0 1.0 O A:LEU571 2.5 67.2 1.0 O A:HOH930 2.9 63.6 1.0 C A:ASN568 3.7 68.0 1.0 C A:LEU571 3.7 66.5 1.0 O A:LEU575 4.3 66.5 1.0 CA A:LEU571 4.4 65.4 1.0 O A:GLY573 4.4 66.8 1.0 CB A:LEU571 4.4 64.1 1.0 N A:LEU571 4.5 66.3 1.0 CA A:ALA569 4.5 68.0 1.0 N A:ALA569 4.5 68.9 1.0 CA A:ASN568 4.6 68.4 1.0 N A:PRO572 4.7 60.8 1.0 C A:PRO572 4.7 62.9 1.0 C A:ALA569 4.8 69.5 1.0 CA A:PRO572 4.8 59.9 1.0 O A:PRO572 4.8 59.7 1.0 O A:ALA569 4.9 74.6 1.0

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