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Manganese 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:

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 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 Manganese atom.
In total 4 binding sites of Manganese 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 Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7omb

Go back to Manganese Binding Sites List in 7omb
Manganese binding site 1 out of 4 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 Manganese with other atoms in the Mn 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:Mn804

b:34.9
occ:1.00
 OD2 A:ASP542 2.1 35.6 1.0
OD2 A:ASP404 2.1 35.5 1.0
O A:PHE405 2.2 33.3 1.0
O1B A:DTP801 2.2 35.0 1.0
O1G A:DTP801 2.2 28.4 1.0
O1A A:DTP801 2.3 34.8 1.0
CG A:ASP404 3.0 38.5 1.0
CG A:ASP542 3.1 32.6 1.0
H5'2 A:DTP801 3.2 40.1 1.0
PB A:DTP801 3.3 35.0 1.0
C A:PHE405 3.3 30.2 1.0
PA A:DTP801 3.4 33.2 1.0
OD1 A:ASP542 3.5 37.0 1.0
OD1 A:ASP404 3.5 39.9 1.0
MG A:MG803 3.5 30.0 1.0
MN A:MN806 3.5 36.6 0.6
O3A A:DTP801 3.5 30.4 1.0
PG A:DTP801 3.6 33.7 1.0
O3B A:DTP801 3.7 33.6 1.0
H A:PHE405 3.8 42.0 1.0
H A:LEU408 3.8 39.5 1.0
N A:PHE405 3.9 34.9 1.0
HB2 A:PHE405 4.0 40.2 1.0
O A:HOH931 4.0 34.3 1.0
CA A:PHE405 4.0 33.2 1.0
O A:HOH951 4.1 36.4 1.0
H A:SER407 4.1 43.1 1.0
C5' A:DTP801 4.2 33.3 1.0
HB2 A:LEU408 4.2 36.0 1.0
HA A:ARG406 4.3 44.0 1.0
O2G A:DTP801 4.3 30.3 1.0
O5' A:DTP801 4.3 31.6 1.0
CB A:ASP404 4.4 34.3 1.0
C A:ASP404 4.4 35.6 1.0
N A:ARG406 4.4 36.0 1.0
CB A:PHE405 4.4 33.5 1.0
N A:SER407 4.4 35.9 1.0
CB A:ASP542 4.4 32.2 1.0
HB2 A:ASP542 4.5 38.8 1.0
HB3 A:ASP404 4.5 41.3 1.0
O A:HOH1074 4.5 43.3 1.0
HB3 A:PHE405 4.6 40.2 1.0
H5'1 A:DTP801 4.6 40.1 1.0
O2A A:DTP801 4.6 30.4 1.0
N A:LEU408 4.6 32.8 1.0
O2B A:DTP801 4.6 32.8 1.0
CA A:ARG406 4.7 36.6 1.0
C A:ARG406 4.7 34.1 1.0
O A:ASP542 4.7 30.6 1.0
O3G A:DTP801 4.8 35.8 1.0
HA A:SER407 4.8 44.1 1.0
CA A:ASP404 4.9 37.2 1.0
HB3 A:ASP542 4.9 38.8 1.0
HA A:PHE405 4.9 39.9 1.0
O A:ASP404 4.9 32.3 1.0
HB3 A:LEU408 4.9 36.0 1.0
HA A:ASP404 4.9 44.7 1.0
CB A:LEU408 5.0 29.9 1.0

Manganese binding site 2 out of 4 in 7omb

Go back to Manganese Binding Sites List in 7omb
Manganese binding site 2 out of 4 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 Manganese with other atoms in the Mn 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:Mn805

b:74.1
occ:1.00
 O A:HOH1123 2.2 65.5 1.0
O T:HOH220 2.4 61.2 1.0
O T:HOH212 2.4 55.7 1.0
O A:HOH1121 2.5 55.5 1.0
O P:HOH202 2.6 50.0 1.0
O A:HOH1030 2.8 56.4 1.0
OE2 A:GLU664 3.2 57.1 1.0
H5' T:DT17 3.7 67.4 1.0
H21 P:DG7 3.9 51.1 1.0
CD A:GLU664 4.0 50.7 1.0
O T:HOH209 4.1 52.4 1.0
O T:HOH222 4.2 56.8 1.0
OE1 A:GLU664 4.2 55.8 1.0
H1' T:DG16 4.3 64.6 1.0
O A:HOH1003 4.5 50.8 1.0
C5' T:DT17 4.6 56.1 1.0
H21 T:DG16 4.6 62.9 1.0
O A:HOH909 4.6 51.4 1.0
O4' T:DG16 4.7 49.4 1.0
N3 T:DG16 4.7 47.8 1.0
N2 P:DG7 4.7 42.5 1.0
O3' T:DG16 4.8 58.1 1.0
H5'' T:DT17 4.8 67.4 1.0
H4' T:DG16 4.8 63.0 1.0
C1' T:DG16 4.9 53.7 1.0
OD2 A:ASP614 5.0 46.0 1.0

Manganese binding site 3 out of 4 in 7omb

Go back to Manganese Binding Sites List in 7omb
Manganese binding site 3 out of 4 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 Manganese with other atoms in the Mn binding site number 3 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:Mn806

b:36.6
occ:0.60
 O A:HOH931 2.0 34.3 1.0
OD2 A:ASP404 2.2 35.5 1.0
O1G A:DTP801 2.3 28.4 1.0
O A:HOH928 2.3 43.5 1.0
O A:HOH951 2.4 36.4 1.0
OE1 A:GLU580 2.4 68.4 1.0
HB3 A:ASP404 2.9 41.3 1.0
OE2 A:GLU580 2.9 58.3 1.0
CD A:GLU580 3.0 66.6 1.0
CG A:ASP404 3.0 38.5 1.0
PG A:DTP801 3.4 33.7 1.0
CB A:ASP404 3.5 34.3 1.0
MN A:MN804 3.5 34.9 1.0
O3G A:DTP801 3.6 35.8 1.0
O A:PHE405 3.8 33.3 1.0
O2G A:DTP801 3.9 30.3 1.0
HB2 A:ASP404 4.0 41.3 1.0
OD1 A:ASP404 4.0 39.9 1.0
OE1 A:GLU578 4.2 42.2 1.0
O1A A:DTP801 4.3 34.8 1.0
O A:HOH1041 4.4 53.4 1.0
O A:ASP404 4.5 32.3 1.0
O A:HOH1074 4.5 43.3 1.0
HA A:ARG406 4.5 44.0 1.0
C A:ASP404 4.5 35.6 1.0
HB2 A:GLU580 4.5 54.1 1.0
CG A:GLU580 4.5 56.7 1.0
CA A:ASP404 4.6 37.2 1.0
C A:PHE405 4.7 30.2 1.0
O3B A:DTP801 4.7 33.6 1.0
HZ2 A:LYS487 4.7 52.5 1.0
HB2 A:GLU578 4.8 46.1 1.0
O A:HOH964 4.8 36.0 1.0
HH22 A:ARG460 4.9 46.0 1.0
HG3 A:GLU580 4.9 68.1 1.0
MG A:MG803 5.0 30.0 1.0
HG2 A:GLU580 5.0 68.1 1.0

Manganese binding site 4 out of 4 in 7omb

Go back to Manganese Binding Sites List in 7omb
Manganese binding site 4 out of 4 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 Manganese with other atoms in the Mn binding site number 4 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
P:Mn101

b:80.3
occ:1.00
 N7 P:DG7 2.7 43.8 1.0
H8 P:DG7 3.5 48.5 1.0
C8 P:DG7 3.5 40.3 1.0
C5 P:DG7 3.8 44.9 1.0
O6 P:DG7 4.1 42.7 1.0
H2' P:DC6 4.3 58.4 1.0
C6 P:DG7 4.4 42.0 1.0
H5 P:DC6 4.5 57.1 1.0
O6 P:DG8 4.5 40.0 1.0
H6 P:DC6 4.5 55.1 1.0
C5 P:DC6 4.6 47.6 1.0
C6 P:DC6 4.7 45.9 1.0
N9 P:DG7 4.8 47.7 1.0
C4 P:DG7 5.0 44.6 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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