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Magnesium in PDB 8s84: Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate

Enzymatic activity of Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate

All present enzymatic activity of Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate:
2.7.7.7;

Protein crystallography data

The structure of Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate, PDB code: 8s84 was solved by C.Gutfreund, K.Betz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.58 / 2.35
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.97, 152.462, 70.125, 90, 90, 90
R / Rfree (%) 23.7 / 27.6

Other elements in 8s84:

The structure of Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate (pdb code 8s84). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate, PDB code: 8s84:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 8s84

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Magnesium binding site 1 out of 5 in the Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:83.1
occ:1.00
 O1B A:XG4804 2.2 96.9 1.0
NZ A:LYS487 2.7 117.9 1.0
O1G A:XG4804 2.8 109.6 1.0
O2B A:XG4804 3.2 82.3 1.0
PB A:XG4804 3.2 89.0 1.0
NH2 A:ARG460 3.5 99.7 1.0
PG A:XG4804 3.9 104.7 1.0
CE A:LYS487 4.0 91.8 1.0
CD A:LYS487 4.1 79.8 1.0
O3B A:XG4804 4.1 97.2 1.0
O3G A:XG4804 4.3 87.9 1.0
CZ A:ARG460 4.3 97.7 1.0
NH1 A:ARG460 4.4 88.5 1.0
N3A A:XG4804 4.6 68.0 1.0

Magnesium binding site 2 out of 5 in 8s84

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Magnesium binding site 2 out of 5 in the Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:60.9
occ:1.00
 OD2 A:ASP542 1.9 72.3 1.0
O3B A:XG4804 2.5 97.2 1.0
O A:PHE405 2.6 76.0 1.0
OD2 A:ASP404 2.7 81.6 1.0
CG A:ASP542 2.9 72.6 1.0
N3A A:XG4804 3.0 68.0 1.0
CB A:ASP542 3.2 55.4 1.0
O1A A:XG4804 3.2 88.9 1.0
PB A:XG4804 3.3 89.0 1.0
MG A:MG803 3.4 73.5 1.0
PA A:XG4804 3.5 94.2 1.0
C5' A:XG4804 3.6 65.0 1.0
C A:PHE405 3.6 76.6 1.0
PG A:XG4804 3.8 104.7 1.0
CG A:ASP404 3.9 76.7 1.0
O5' A:XG4804 4.0 70.7 1.0
N A:LEU408 4.0 62.2 1.0
OD1 A:ASP542 4.0 68.2 1.0
N A:SER407 4.1 73.1 1.0
O3G A:XG4804 4.2 87.9 1.0
N A:PHE405 4.2 61.4 1.0
O2B A:XG4804 4.2 82.3 1.0
O2G A:XG4804 4.2 79.3 1.0
CA A:PHE405 4.3 71.0 1.0
O A:HOH901 4.3 66.7 1.0
CB A:LEU408 4.3 62.7 1.0
CB A:PHE405 4.4 75.8 1.0
O1B A:XG4804 4.4 96.9 1.0
OD1 A:ASP404 4.5 86.6 1.0
CA A:SER407 4.6 69.6 1.0
CA A:ASP542 4.6 57.7 1.0
N A:ARG406 4.6 72.1 1.0
C4' A:XG4804 4.7 57.0 1.0
O A:ASP542 4.7 66.1 1.0
C A:ARG406 4.7 75.3 1.0
CA A:LEU408 4.8 64.3 1.0
C A:SER407 4.8 68.7 1.0
CA A:ARG406 4.9 71.1 1.0
C A:ASP542 4.9 58.7 1.0
CB A:ASP404 5.0 67.7 1.0
O2A A:XG4804 5.0 75.8 1.0

Magnesium binding site 3 out of 5 in 8s84

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Magnesium binding site 3 out of 5 in the Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:73.5
occ:1.00
 O1A A:XG4804 2.2 88.9 1.0
OD2 A:ASP542 2.3 72.3 1.0
OD2 A:ASP404 2.5 81.6 1.0
O A:HOH904 2.6 88.5 1.0
O3G A:XG4804 2.8 87.9 1.0
O3' P:DA13 3.0 92.5 1.0
CG A:ASP542 3.0 72.6 1.0
CG A:ASP404 3.0 76.7 1.0
OD1 A:ASP542 3.1 68.2 1.0
OD1 A:ASP404 3.1 86.6 1.0
MG A:MG802 3.4 60.9 1.0
O3B A:XG4804 3.5 97.2 1.0
PA A:XG4804 3.6 94.2 1.0
PG A:XG4804 3.8 104.7 1.0
OH A:TYR402 3.9 91.9 1.0
N3A A:XG4804 4.3 68.0 1.0
O1B A:XG4804 4.3 96.9 1.0
PB A:XG4804 4.3 89.0 1.0
C3' P:DA13 4.3 73.0 1.0
CB A:ASP404 4.4 67.7 1.0
CB A:ASP542 4.4 55.4 1.0
O2A A:XG4804 4.4 75.8 1.0
C5' A:XG4804 4.5 65.0 1.0
O2G A:XG4804 4.5 79.3 1.0
OE1 A:GLU580 4.6 86.3 1.0
O5' A:XG4804 4.6 70.7 1.0
CE2 A:TYR402 4.8 82.3 1.0
CZ A:TYR402 4.9 77.7 1.0
C2' P:DA13 4.9 69.7 1.0

Magnesium binding site 4 out of 5 in 8s84

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Magnesium binding site 4 out of 5 in the Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg805

b:70.8
occ:1.00
 OD2 A:ASP343 2.7 64.5 1.0
OD1 A:ASP4 2.8 60.9 1.0
OE2 A:GLU251 3.0 72.5 1.0
CG A:ASP4 3.5 73.0 1.0
OD2 A:ASP4 3.6 90.2 1.0
OG A:SER340 3.6 63.9 1.0
CG A:ASP343 3.7 58.0 1.0
OD1 A:ASP343 4.1 59.2 1.0
CD A:GLU251 4.2 81.7 1.0
CE3 A:TRP342 4.3 50.4 1.0
O A:THR5 4.3 71.6 1.0
CB A:SER340 4.4 53.8 1.0
CB A:TRP342 4.9 70.6 1.0
CD2 A:TRP342 4.9 55.8 1.0
CZ3 A:TRP342 4.9 55.6 1.0
OE1 A:GLU251 4.9 65.0 1.0
CB A:ASP4 5.0 60.2 1.0
CB A:ASP343 5.0 63.7 1.0

Magnesium binding site 5 out of 5 in 8s84

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Magnesium binding site 5 out of 5 in the Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg806

b:72.3
occ:1.00
 NH2 A:ARG503 2.7 77.2 1.0
OD1 A:ASN370 2.9 69.2 1.0
N A:GLU111 3.1 61.6 1.0
O A:ALA368 3.1 71.6 1.0
O A:PRO369 3.4 70.5 1.0
C A:PRO369 3.5 68.4 1.0
N A:ASN370 3.6 72.9 1.0
CA A:ASN370 3.7 68.5 1.0
C A:ALA368 3.7 63.5 1.0
CA A:GLU111 3.8 68.2 1.0
CZ A:ARG503 3.8 65.7 1.0
CG A:GLU111 3.9 72.5 1.0
CG A:ASN370 4.0 65.8 1.0
CA A:TYR110 4.0 63.4 1.0
C A:TYR110 4.0 60.3 1.0
CB A:ALA368 4.0 55.4 1.0
NE A:ARG503 4.0 75.8 1.0
CB A:TYR110 4.1 68.9 1.0
CA A:PRO369 4.3 67.9 1.0
N A:PRO369 4.3 71.2 1.0
CB A:ASN370 4.4 63.6 1.0
CB A:GLU111 4.5 59.6 1.0
CA A:ALA368 4.5 61.4 1.0
CD1 A:TYR110 4.6 70.0 1.0
C A:ASN370 4.9 72.3 1.0
CG A:TYR110 4.9 66.9 1.0
NH1 A:ARG503 5.0 78.0 1.0

Reference:

C.Gutfreund, K.Betz. Structural Insights Into A Dna Polymerase Reading the Xeno Nucleic Acid Hna Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
Page generated: Wed Nov 27 18:50:07 2024

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