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Manganese in PDB 7ktl: Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN)

Enzymatic activity of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN)

All present enzymatic activity of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN), PDB code: 7ktl was solved by J.A.Jamsen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.96 / 1.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.271, 62.099, 118.774, 90, 90, 90
R / Rfree (%) 15.8 / 17.4

Other elements in 7ktl:

The structure of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN) (pdb code 7ktl). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 9 binding sites of Manganese where determined in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN), PDB code: 7ktl:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 7ktl

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Manganese binding site 1 out of 9 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:14.6
occ:1.00
 O21 A:PPV513 2.1 15.3 1.0
O12 A:PPV513 2.1 19.4 1.0
OD1 A:ASP330 2.1 15.6 1.0
OD2 A:ASP332 2.1 14.4 1.0
O A:HOH727 2.3 16.3 1.0
OP1 P:8OG5 2.3 17.1 1.0
CG A:ASP332 3.2 14.2 1.0
P1 A:PPV513 3.2 16.4 1.0
CG A:ASP330 3.3 17.6 1.0
P2 A:PPV513 3.4 16.5 0.7
OD1 A:ASP332 3.5 16.0 1.0
MN A:MN503 3.6 17.0 1.0
O31 A:PPV513 3.6 18.4 1.0
OPP A:PPV513 3.6 18.3 0.8
P P:8OG5 3.6 16.2 1.0
OD2 A:ASP330 3.8 21.0 1.0
O A:HOH708 3.9 20.5 0.7
O5' P:8OG5 4.0 15.5 1.0
CE1 A:HIS329 4.0 19.9 0.3
ND1 A:HIS329 4.1 21.2 0.3
O32 A:PPV513 4.2 22.3 0.9
C5' P:8OG5 4.2 15.2 1.0
O A:ASP330 4.2 16.1 1.0
O A:HOH718 4.3 21.4 1.0
O A:HOH627 4.4 15.7 1.0
OP2 P:8OG5 4.4 15.7 1.0
N A:GLY320 4.4 14.4 1.0
O P:HOH210 4.4 18.7 1.0
C A:ASP330 4.5 16.4 1.0
CB A:ASP332 4.5 13.3 1.0
CA A:GLY319 4.5 15.1 1.0
CB A:ASP330 4.5 15.6 1.0
O22 A:PPV513 4.5 21.0 1.0
O11 A:PPV513 4.5 18.9 1.0
O3' P:DA4 4.7 15.6 1.0
N A:ASP330 4.8 17.7 1.0
CA A:ASP330 4.8 16.2 1.0
N A:ASP332 4.8 14.1 1.0
N A:VAL331 5.0 15.2 1.0

Manganese binding site 2 out of 9 in 7ktl

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Manganese binding site 2 out of 9 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:17.0
occ:1.00
 OD2 A:ASP330 2.0 21.0 1.0
OD2 A:ASP418 2.0 15.6 1.0
OD1 A:ASP332 2.1 16.0 1.0
OP1 P:8OG5 2.1 17.1 1.0
O P:HOH210 2.2 18.7 1.0
O3' P:DA4 2.7 15.6 1.0
CG A:ASP330 2.9 17.6 1.0
CG A:ASP418 3.0 15.3 1.0
P P:8OG5 3.0 16.2 1.0
CG A:ASP332 3.1 14.2 1.0
OD1 A:ASP330 3.2 15.6 1.0
OD2 A:ASP332 3.5 14.4 1.0
MN A:MN502 3.6 14.6 1.0
CB A:ASP418 3.7 14.3 1.0
C3' P:DA4 3.9 16.8 1.0
OD1 A:ASP418 4.0 16.9 1.0
C5' P:DA4 4.1 16.8 1.0
OP2 P:8OG5 4.1 15.7 1.0
C4' P:DA4 4.1 16.3 1.0
O5' P:8OG5 4.2 15.5 1.0
O A:HOH708 4.2 20.5 0.7
CB A:ASP330 4.2 15.6 1.0
CE1 A:HIS329 4.3 19.9 0.3
C5' P:8OG5 4.4 15.2 1.0
CB A:ASP332 4.4 13.3 1.0
NH2 A:ARG416 4.4 17.6 1.0
OP1 P:DA4 4.7 18.2 1.0
CZ3 A:TRP434 4.7 17.2 1.0
O12 A:PPV513 4.8 19.4 1.0
N A:ASP418 4.8 13.9 1.0
CA A:ASP418 4.9 14.5 1.0
NE2 A:HIS329 4.9 21.4 0.3
O A:VAL331 4.9 16.5 1.0
O5' P:DA4 4.9 17.4 1.0
CA A:ASP332 4.9 13.4 1.0

Manganese binding site 3 out of 9 in 7ktl

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Manganese binding site 3 out of 9 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:20.6
occ:0.55
 O A:HOH849 2.1 29.2 0.8
O T:HOH205 2.2 30.0 0.9
OE2 A:GLU386 2.3 26.8 1.0
O A:HOH768 2.3 22.2 0.6
NE2 A:HIS459 2.3 34.1 1.0
OE1 A:GLU386 2.5 33.1 1.0
CD A:GLU386 2.8 28.2 1.0
CD2 A:HIS459 3.2 33.0 1.0
CE1 A:HIS459 3.4 34.2 1.0
O A:HOH848 4.2 46.0 1.0
O T:HOH234 4.2 51.5 1.0
O A:HOH695 4.2 29.6 1.0
OP1 T:DC8 4.2 22.8 1.0
CG A:GLU386 4.3 30.6 1.0
O A:HOH623 4.3 22.8 1.0
CG A:HIS459 4.4 27.4 1.0
ND1 A:HIS459 4.4 33.0 1.0
OE1 A:GLN426 4.6 24.9 1.0
C5' T:DC8 4.6 20.1 1.0

Manganese binding site 4 out of 9 in 7ktl

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Manganese binding site 4 out of 9 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:57.6
occ:0.67
 O A:HOH840 2.0 53.5 0.8
O A:HOH624 2.1 55.4 1.0
NE2 A:HIS219 2.3 42.0 1.0
OE1 A:GLU218 3.0 58.8 1.0
CE1 A:HIS219 3.3 42.1 1.0
CD2 A:HIS219 3.3 40.1 1.0
CD A:GLU218 4.0 54.5 1.0
ND1 A:HIS219 4.4 42.1 1.0
CG A:HIS219 4.4 40.5 1.0
OE2 A:GLU218 4.5 56.5 1.0
CB A:GLU218 4.8 36.9 1.0

Manganese binding site 5 out of 9 in 7ktl

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Manganese binding site 5 out of 9 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:30.4
occ:0.49
 O A:HOH845 2.0 34.7 0.8
O A:HOH888 2.1 37.2 0.7
NE2 A:HIS152 2.3 40.6 1.0
O A:HOH647 2.5 39.0 0.9
CD2 A:HIS152 3.3 40.4 1.0
CE1 A:HIS152 3.3 43.0 1.0
ND1 A:HIS152 4.4 41.5 1.0
CG A:HIS152 4.4 38.2 1.0
O A:HOH726 4.4 32.4 1.0
O A:PRO190 4.5 30.0 1.0
O A:HOH880 4.5 37.7 1.0
O A:THR150 4.6 26.2 1.0

Manganese binding site 6 out of 9 in 7ktl

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Manganese binding site 6 out of 9 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn507

b:32.0
occ:0.41
 OP3 D:DG1 2.1 27.6 1.0
ND1 A:HIS208 2.5 28.2 1.0
O D:HOH211 2.5 35.3 0.9
CE1 A:HIS208 3.3 28.9 1.0
CG A:HIS208 3.3 26.5 1.0
P D:DG1 3.3 24.7 1.0
CB A:HIS208 3.6 23.2 1.0
OP1 D:DG1 3.7 26.3 1.0
O D:HOH202 3.9 38.7 1.0
OP2 D:DG1 4.1 27.3 1.0
O D:HOH213 4.1 41.9 1.0
NE2 A:HIS208 4.3 28.3 1.0
CD2 A:HIS208 4.3 28.3 1.0
NH2 A:ARG211 4.4 66.6 1.0
NH1 A:ARG211 4.5 55.5 1.0
O5' D:DG1 4.6 23.5 1.0
CA A:HIS208 4.6 23.3 1.0
C5' D:DG1 4.9 21.6 1.0
CZ A:ARG211 5.0 61.8 1.0

Manganese binding site 7 out of 9 in 7ktl

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Manganese binding site 7 out of 9 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:37.3
occ:0.36
 N7 T:DG2 2.1 25.6 0.6
O T:HOH213 2.3 43.9 1.0
N7 T:DG2 2.5 23.1 0.5
C8 T:DG2 2.9 23.4 0.6
C5 T:DG2 3.1 21.2 0.6
C8 T:DG2 3.3 23.2 0.5
C5 T:DG2 3.6 22.7 0.5
O6 T:DG2 3.7 20.6 0.6
C6 T:DG2 3.7 19.4 0.6
O6 T:DG2 3.9 20.0 0.5
N9 T:DG2 4.0 23.2 0.6
O T:HOH208 4.1 39.6 1.0
C4 T:DG2 4.1 22.1 0.6
C6 T:DG2 4.1 19.9 0.5
O T:HOH229 4.2 37.3 0.8
O D:HOH210 4.3 50.3 0.8
O6 T:DG3 4.4 21.9 1.0
N9 T:DG2 4.5 24.4 0.5
C2' T:DC1 4.7 26.7 0.5
C4 T:DG2 4.7 20.8 0.5
C6 T:DC1 5.0 23.0 0.6
C6 T:DC1 5.0 22.1 0.5
C5 T:DC1 5.0 21.7 0.6

Manganese binding site 8 out of 9 in 7ktl

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Manganese binding site 8 out of 9 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:15.4
occ:0.65
 OP2 P:8OG5 2.1 15.7 1.0
O31 A:PPV513 2.1 18.4 1.0
O A:HOH829 2.2 16.7 0.7
O P:HOH217 2.2 20.9 0.7
O P:HOH201 2.2 17.2 0.7
O8 P:8OG5 2.3 21.1 1.0
O P:HOH201 2.3 15.5 0.3
O5' P:8OG5 3.2 15.5 1.0
P P:8OG5 3.2 16.2 1.0
C8 P:8OG5 3.3 20.2 1.0
P1 A:PPV513 3.6 16.4 1.0
O A:HOH681 4.0 17.6 1.0
N7 P:8OG5 4.0 19.4 1.0
OP1 P:8OG5 4.1 17.1 1.0
O A:HOH708 4.2 20.5 0.7
O P:HOH216 4.2 34.2 1.0
O22 A:PPV513 4.2 21.0 1.0
O11 A:PPV513 4.2 18.9 1.0
C3' P:8OG5 4.3 18.2 1.0
OPP A:PPV513 4.3 18.3 0.8
O21 A:PPV513 4.5 15.3 1.0
O12 A:PPV513 4.5 19.4 1.0
O3' P:DA4 4.5 15.6 1.0
C5' P:8OG5 4.5 15.2 1.0
N9 P:8OG5 4.6 17.3 1.0
P2 A:PPV513 4.6 16.5 0.7
O A:HOH656 4.7 46.7 1.0
CB A:ASP438 4.8 17.2 1.0
C3' P:DA4 4.8 16.8 1.0
CE1 A:HIS329 4.8 19.9 0.3
C4' P:8OG5 4.9 16.0 1.0

Manganese binding site 9 out of 9 in 7ktl

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Manganese binding site 9 out of 9 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn101

b:53.1
occ:0.49
 O D:HOH210 2.1 50.3 0.8
O D:HOH218 2.1 48.2 1.0
N7 D:DG1 2.4 19.9 1.0
O D:HOH205 2.9 41.0 0.8
O D:HOH219 3.2 44.8 1.0
C8 D:DG1 3.3 19.8 1.0
C5 D:DG1 3.4 18.4 1.0
O6 D:DG1 3.7 21.0 1.0
C6 D:DG1 4.0 18.7 1.0
N4 D:DC2 4.2 22.1 1.0
O T:HOH213 4.4 43.9 1.0
O D:HOH204 4.4 42.9 1.0
N9 D:DG1 4.5 18.9 1.0
C4 D:DG1 4.6 18.1 1.0
OP2 D:DG1 4.7 27.3 1.0
C4 D:DC2 5.0 19.4 1.0
CG A:ARG175 5.0 21.7 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Watching A Double Strand Break Repair Polymerase Insert A Pro-Mutagenic Oxidized Nucleotide. Nat Commun V. 12 2059 2021.
ISSN: ESSN 2041-1723
PubMed: 33824325
DOI: 10.1038/S41467-021-21354-6
Page generated: Sun Oct 6 09:48:45 2024

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