Magnesium in PDB 7omb: Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang

Enzymatic activity of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang

All present enzymatic activity of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang, PDB code: 7omb 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) 46.28 / 2.01
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 108.081, 147.153, 71.332, 90, 90, 90
R / Rfree (%) 20 / 23.6

Other elements in 7omb:

The structure of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang (pdb code 7omb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang, PDB code: 7omb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7omb

Go back to Magnesium Binding Sites List in 7omb
Magnesium binding site 1 out of 2 in the Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:33.0
occ:1.00
 O A:HOH970 1.9 53.3 1.0
O A:HOH999 2.0 38.4 1.0
O A:HOH1052 2.1 47.4 1.0
OE2 A:GLU251 2.2 53.5 1.0
O A:HOH907 2.3 43.8 1.0
O A:HOH1100 2.3 43.3 1.0
CD A:GLU251 3.4 55.8 1.0
OE1 A:GLU251 3.9 48.3 1.0
OD2 A:ASP343 3.9 49.8 1.0
HZ3 A:LYS253 3.9 58.6 1.0
OD2 A:ASP4 4.0 49.9 1.0
O A:HOH1020 4.1 54.2 1.0
OD1 A:ASP4 4.1 43.7 1.0
O A:THR5 4.2 34.9 1.0
HE3 A:TRP342 4.4 43.4 1.0
OD1 A:ASP343 4.5 46.3 1.0
CG A:ASP4 4.5 45.8 1.0
HB3 A:ASP6 4.5 40.6 1.0
HZ1 A:LYS253 4.5 58.6 1.0
CE3 A:TRP342 4.6 36.1 1.0
O A:HOH1061 4.6 51.3 1.0
HG2 A:GLU251 4.6 62.1 1.0
CG A:GLU251 4.6 51.7 1.0
CG A:ASP343 4.6 38.7 1.0
HZ2 A:LYS118 4.6 58.8 1.0
O A:HOH993 4.6 41.4 1.0
NZ A:LYS253 4.6 48.8 1.0
O T:HOH202 4.7 54.3 1.0
CZ3 A:TRP342 4.8 38.6 1.0
HZ3 A:TRP342 4.9 46.3 1.0
HB3 A:TRP342 4.9 43.9 1.0
HE22 A:GLN242 4.9 75.7 1.0
HG3 A:GLU251 4.9 62.1 1.0

Magnesium binding site 2 out of 2 in 7omb

Go back to Magnesium Binding Sites List in 7omb
Magnesium binding site 2 out of 2 in the Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:30.0
occ:1.00
 OD1 A:ASP404 2.1 39.9 1.0
OD1 A:ASP542 2.1 37.0 1.0
O1A A:DTP801 2.3 34.8 1.0
O A:HOH1043 2.3 33.5 1.0
O A:HOH1074 2.4 43.3 1.0
H3'2 P:DOC12 3.0 40.1 1.0
CG A:ASP404 3.0 38.5 1.0
CG A:ASP542 3.1 32.6 1.0
OD2 A:ASP404 3.3 35.5 1.0
PA A:DTP801 3.4 33.2 1.0
OD2 A:ASP542 3.4 35.6 1.0
MN A:MN804 3.5 34.9 1.0
HH A:TYR402 3.7 68.7 1.0
H5'1 A:DTP801 3.7 40.1 1.0
OH A:TYR402 3.8 57.2 1.0
H5'2 A:DTP801 3.8 40.1 1.0
H5'' P:DOC12 3.8 42.0 1.0
C3' P:DOC12 3.9 33.4 1.0
HA3 A:GLY543 3.9 48.7 1.0
O5' A:DTP801 3.9 31.6 1.0
O2A A:DTP801 4.0 30.4 1.0
H A:ASP542 4.0 45.6 1.0
H3'1 P:DOC12 4.0 40.1 1.0
C5' A:DTP801 4.1 33.3 1.0
N A:GLY543 4.1 34.0 1.0
O A:HOH951 4.1 36.4 1.0
H A:GLY543 4.1 40.9 1.0
C A:ASP542 4.3 30.6 1.0
O A:ASP540 4.3 36.0 1.0
CB A:ASP404 4.4 34.3 1.0
CB A:ASP542 4.5 32.2 1.0
CA A:GLY543 4.5 40.5 1.0
H4' P:DOC12 4.5 41.2 1.0
HB2 A:ASP404 4.5 41.3 1.0
C4' P:DOC12 4.5 34.3 1.0
C5' P:DOC12 4.6 35.0 1.0
O A:ASP542 4.6 30.6 1.0
N A:ASP542 4.6 38.0 1.0
CA A:ASP542 4.7 31.3 1.0
O P:HOH203 4.7 38.4 1.0
HB A:THR541 4.7 39.6 1.0
O1G A:DTP801 4.8 28.4 1.0
O3A A:DTP801 4.8 30.4 1.0
HA A:ASP404 4.9 44.7 1.0
HB3 A:ASP542 4.9 38.8 1.0
CZ A:TYR402 4.9 54.8 1.0
H A:PHE405 5.0 42.0 1.0
MN A:MN806 5.0 36.6 0.6
H5' P:DOC12 5.0 42.0 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: Fri Nov 5 15:31:17 2021

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