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Manganese in PDB 7ktb: Dna Polymerase Mu, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN)

Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN), PDB code: 7ktb 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) 35.04 / 1.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.278, 62.319, 119.13, 90, 90, 90
R / Rfree (%) 15.8 / 17.7

Other elements in 7ktb:

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Mu, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN) (pdb code 7ktb). 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, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN), PDB code: 7ktb:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 7ktb

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Manganese binding site 1 out of 9 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN)


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, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:21.1
occ:1.00
 OD2 A:ASP330 1.7 29.8 1.0
OP1 P:8OG5 1.8 15.0 0.6
OD2 A:ASP418 2.1 17.9 1.0
OD1 A:ASP332 2.1 17.4 1.0
O A:HOH603 2.3 26.8 1.0
O3' P:DA4 2.7 21.1 0.4
O2A A:8DG501 2.7 15.7 0.4
O3' P:DA4 2.8 25.1 0.6
CG A:ASP330 2.8 26.1 1.0
P P:8OG5 2.9 14.8 0.6
CG A:ASP418 3.1 16.9 1.0
CG A:ASP332 3.2 16.9 1.0
OD1 A:ASP330 3.2 16.9 1.0
MN A:MN504 3.5 17.6 1.0
OD2 A:ASP332 3.5 17.0 1.0
PA A:8DG501 3.7 20.4 0.4
CB A:ASP418 3.8 16.5 1.0
C3' P:DA4 3.8 25.9 0.4
OP2 P:8OG5 3.9 15.5 0.6
C3' P:DA4 3.9 26.0 0.6
OD1 A:ASP418 4.0 18.4 1.0
C5' P:DA4 4.0 22.9 0.4
C5' P:DA4 4.1 26.5 0.6
O5' P:8OG5 4.1 22.5 0.6
C4' P:DA4 4.1 24.0 0.4
O5' A:8DG501 4.1 19.9 0.4
C4' P:DA4 4.1 25.0 0.6
O1A A:8DG501 4.1 20.7 0.4
O A:HOH721 4.2 22.9 0.5
CB A:ASP330 4.2 19.2 1.0
CE1 A:HIS329 4.3 17.1 0.6
C5' A:8DG501 4.3 21.8 0.4
C5' P:8OG5 4.3 18.9 0.6
CB A:ASP332 4.4 15.4 1.0
NH2 A:ARG416 4.5 19.6 1.0
OP1 P:DA4 4.5 22.8 0.4
O32 A:PPV515 4.6 26.8 0.5
OP1 P:DA4 4.7 24.2 0.6
CZ3 A:TRP434 4.8 22.1 1.0
O5' P:DA4 4.8 20.9 0.4
O5' P:DA4 4.8 25.8 0.6
NE2 A:HIS329 4.8 31.1 0.6
O A:VAL331 4.9 17.2 1.0
N A:ASP418 5.0 16.1 1.0
CA A:ASP332 5.0 15.7 1.0
CA A:ASP418 5.0 16.4 1.0

Manganese binding site 2 out of 9 in 7ktb

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Manganese binding site 2 out of 9 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN)


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, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:17.6
occ:1.00
 O2A A:8DG501 1.7 15.7 0.4
O21 A:PPV515 2.1 18.4 0.5
O1B A:8DG501 2.1 15.3 0.4
OD2 A:ASP332 2.1 17.0 1.0
OD1 A:ASP330 2.1 16.9 1.0
O32 A:PPV515 2.2 26.8 0.5
O A:HOH732 2.2 20.6 1.0
O1G A:8DG501 2.3 27.4 0.4
OP1 P:8OG5 2.6 15.0 0.6
PA A:8DG501 3.0 20.4 0.4
CG A:ASP332 3.1 16.9 1.0
P1 A:PPV515 3.2 22.0 0.5
CG A:ASP330 3.2 26.1 1.0
PB A:8DG501 3.2 16.3 0.4
O31 A:PPV515 3.4 23.0 0.5
P2 A:PPV515 3.4 32.6 0.5
OD1 A:ASP332 3.4 17.4 1.0
O3A A:8DG501 3.5 21.3 0.4
MN A:MN503 3.5 21.1 1.0
OD2 A:ASP330 3.5 29.8 1.0
PG A:8DG501 3.5 25.2 0.4
OPP A:PPV515 3.7 26.2 0.5
O3B A:8DG501 3.7 22.0 0.4
P P:8OG5 3.7 14.8 0.6
O5' P:8OG5 3.9 22.5 0.6
O A:HOH721 4.0 22.9 0.5
O5' A:8DG501 4.0 19.9 0.4
CE1 A:HIS329 4.1 17.1 0.6
O12 A:PPV515 4.1 33.0 0.5
C5' A:8DG501 4.1 21.8 0.4
ND1 A:HIS329 4.1 29.3 0.6
O1A A:8DG501 4.1 20.7 0.4
O A:ASP330 4.1 18.0 1.0
C5' P:8OG5 4.3 18.9 0.6
O A:HOH672 4.3 17.4 1.0
O A:HOH610 4.3 27.3 1.0
N A:GLY320 4.4 16.3 1.0
O2G A:8DG501 4.4 30.9 0.4
C A:ASP330 4.4 17.0 1.0
O A:HOH603 4.4 26.8 1.0
O11 A:PPV515 4.5 18.3 0.5
CB A:ASP332 4.5 15.4 1.0
OP2 P:8OG5 4.5 15.5 0.6
CA A:GLY319 4.5 16.0 1.0
CB A:ASP330 4.5 19.2 1.0
O2B A:8DG501 4.5 17.6 0.4
O3G A:8DG501 4.6 31.8 0.4
O22 A:PPV515 4.6 31.2 0.5
O3' P:DA4 4.8 21.1 0.4
O3' P:DA4 4.8 25.1 0.6
CA A:ASP330 4.8 17.0 1.0
N A:ASP330 4.8 17.7 1.0
N A:ASP332 4.9 16.0 1.0
N A:VAL331 4.9 17.3 1.0

Manganese binding site 3 out of 9 in 7ktb

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Manganese binding site 3 out of 9 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN)


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, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:24.9
occ:0.47
 O A:HOH823 2.0 48.7 1.0
O T:HOH203 2.1 36.8 1.0
OE2 A:GLU386 2.1 35.8 1.0
O A:HOH801 2.3 36.5 1.0
NE2 A:HIS459 2.3 42.4 1.0
CD A:GLU386 2.8 38.5 1.0
OE1 A:GLU386 2.8 45.9 1.0
CD2 A:HIS459 3.2 49.1 1.0
CE1 A:HIS459 3.4 42.3 1.0
OP1 T:DC8 4.2 28.3 1.0
O A:HOH646 4.3 39.0 1.0
CG A:GLU386 4.3 41.9 1.0
O A:HOH735 4.3 28.2 1.0
CG A:HIS459 4.4 31.1 1.0
ND1 A:HIS459 4.4 46.0 1.0
C5' T:DC8 4.5 22.5 1.0
OE1 A:GLN426 4.6 29.1 1.0

Manganese binding site 4 out of 9 in 7ktb

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Manganese binding site 4 out of 9 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN)


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, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:53.1
occ:0.54
 O D:HOH217 2.2 42.5 0.7
OP3 D:DG1 2.2 29.8 1.0
O D:HOH208 2.5 33.5 0.7
ND1 A:HIS208 2.5 32.3 1.0
CE1 A:HIS208 3.3 34.5 1.0
P D:DG1 3.4 26.7 1.0
CG A:HIS208 3.4 32.2 1.0
OP1 D:DG1 3.6 30.2 1.0
CB A:HIS208 3.8 25.7 1.0
O D:HOH203 3.9 41.6 1.0
OP2 D:DG1 4.0 28.4 1.0
O D:HOH209 4.2 47.1 1.0
NE2 A:HIS208 4.4 32.0 1.0
CD2 A:HIS208 4.4 30.2 1.0
NH1 A:ARG211 4.5 62.7 1.0
O5' D:DG1 4.6 23.8 1.0
CA A:HIS208 4.7 23.9 1.0
NH2 A:ARG211 4.8 64.0 1.0
C5' D:DG1 5.0 24.7 1.0

Manganese binding site 5 out of 9 in 7ktb

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Manganese binding site 5 out of 9 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN)


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, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn507

b:63.4
occ:0.63
 O A:HOH832 2.1 56.7 1.0
NE2 A:HIS219 2.1 51.9 1.0
CE1 A:HIS219 3.0 48.4 1.0
CD2 A:HIS219 3.1 46.6 1.0
CD A:GLU218 3.9 51.7 1.0
ND1 A:HIS219 4.1 46.5 1.0
CG A:HIS219 4.2 44.5 1.0
CB A:GLU218 4.6 45.1 1.0
CG A:GLU218 4.9 58.6 1.0

Manganese binding site 6 out of 9 in 7ktb

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Manganese binding site 6 out of 9 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN)


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, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn508

b:52.1
occ:0.60
 O A:HOH825 2.0 32.3 0.6
NE2 A:HIS152 2.4 49.5 1.0
O A:HOH864 2.8 31.6 0.5
CE1 A:HIS152 3.3 50.3 1.0
CD2 A:HIS152 3.3 45.0 1.0
O A:HOH689 3.9 43.9 1.0
O A:HOH664 4.4 32.9 1.0
ND1 A:HIS152 4.4 49.5 1.0
CG A:HIS152 4.5 43.5 1.0
O A:PRO190 4.5 33.4 1.0
O A:HOH864 4.5 30.8 0.6
O A:THR150 4.6 27.4 1.0
CG A:PRO148 5.0 28.0 1.0

Manganese binding site 7 out of 9 in 7ktb

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Manganese binding site 7 out of 9 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN)


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, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:53.5
occ:0.52
 N7 T:DG2 2.2 28.6 0.6
N7 T:DG2 2.2 27.7 0.5
O T:HOH208 2.4 49.4 1.0
O T:HOH207 2.7 51.2 1.0
C8 T:DG2 3.0 26.1 0.5
C8 T:DG2 3.0 26.6 0.6
C5 T:DG2 3.2 24.9 0.6
C5 T:DG2 3.3 23.3 0.5
O6 T:DG2 3.7 24.4 0.6
O6 T:DG2 3.7 24.3 0.5
C6 T:DG2 3.8 22.7 0.6
C6 T:DG2 3.9 22.6 0.5
N9 T:DG2 4.2 23.0 0.6
N9 T:DG2 4.2 22.9 0.5
O T:HOH213 4.2 39.9 1.0
O D:HOH212 4.3 39.7 0.6
C4 T:DG2 4.3 22.5 0.6
C4 T:DG2 4.3 22.7 0.5
O6 T:DG3 4.5 23.3 1.0
OP2 T:DG2 4.6 29.1 0.5
C6 T:DC1 4.8 25.6 0.6
C2' T:DC1 4.9 30.5 0.4
C5 T:DC1 4.9 27.7 0.6
C6 T:DC1 4.9 25.6 0.4
C2' T:DC1 5.0 27.6 0.6

Manganese binding site 8 out of 9 in 7ktb

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Manganese binding site 8 out of 9 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN)


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, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:27.1
occ:0.57
 O1A A:8DG501 1.8 20.7 0.4
O3A A:8DG501 2.1 21.3 0.4
O P:HOH209 2.1 22.4 0.6
O A:HOH634 2.2 25.5 0.6
O A:HOH844 2.2 26.1 0.6
O31 A:PPV515 2.2 23.0 0.5
OP2 P:8OG5 2.3 15.5 0.6
PA A:8DG501 2.4 20.4 0.4
O8 A:8DG501 2.4 45.9 0.4
O8 P:8OG5 2.4 45.6 0.6
O5' A:8DG501 2.9 19.9 0.4
O5' P:8OG5 3.1 22.5 0.6
P P:8OG5 3.2 14.8 0.6
C8 A:8DG501 3.5 31.7 0.4
C8 P:8OG5 3.5 30.9 0.6
PB A:8DG501 3.6 16.3 0.4
P1 A:PPV515 3.7 22.0 0.5
O A:HOH721 3.8 22.9 0.5
O2A A:8DG501 3.8 15.7 0.4
O A:HOH682 3.9 22.2 1.0
O2B A:8DG501 4.1 17.6 0.4
O A:HOH605 4.1 47.6 1.0
O22 A:PPV515 4.2 31.2 0.5
O3B A:8DG501 4.2 22.0 0.4
O11 A:PPV515 4.2 18.3 0.5
N7 A:8DG501 4.2 30.2 0.4
N7 P:8OG5 4.2 30.9 0.6
OP1 P:8OG5 4.2 15.0 0.6
C3' P:8OG5 4.2 28.5 0.6
C3' A:8DG501 4.2 28.1 0.4
C5' A:8DG501 4.3 21.8 0.4
O32 A:PPV515 4.3 26.8 0.5
OPP A:PPV515 4.4 26.2 0.5
C5' P:8OG5 4.5 18.9 0.6
O3' P:DA4 4.5 25.1 0.6
O1B A:8DG501 4.5 15.3 0.4
P2 A:PPV515 4.6 32.6 0.5
O3G A:8DG501 4.6 31.8 0.4
O21 A:PPV515 4.6 18.4 0.5
C4' A:8DG501 4.7 23.3 0.4
N9 A:8DG501 4.7 27.6 0.4
N9 P:8OG5 4.8 26.5 0.6
O3' P:DA4 4.8 21.1 0.4
C4' P:8OG5 4.8 23.2 0.6
CB A:LYS438 4.9 17.7 1.0
CE1 A:HIS329 4.9 17.1 0.6
C3' P:DA4 4.9 26.0 0.6
PG A:8DG501 4.9 25.2 0.4
O4' A:8DG501 4.9 20.3 0.4
O3' P:8OG5 4.9 24.2 0.6
C3' P:DA4 4.9 25.9 0.4
O A:HOH653 5.0 35.8 1.0
O4' P:8OG5 5.0 20.3 0.6

Manganese binding site 9 out of 9 in 7ktb

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Manganese binding site 9 out of 9 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN)


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, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn101

b:70.8
occ:0.66
 O D:HOH212 2.2 39.7 0.6
N7 D:DG1 2.3 21.0 1.0
O D:HOH206 2.9 47.0 1.0
C8 D:DG1 3.2 22.0 1.0
O D:HOH220 3.2 47.6 1.0
C5 D:DG1 3.4 20.4 1.0
O6 D:DG1 3.7 21.4 1.0
C6 D:DG1 3.9 20.1 1.0
O A:HOH806 4.0 50.5 1.0
N4 D:DC2 4.1 22.7 1.0
N9 D:DG1 4.4 21.3 1.0
O T:HOH208 4.5 49.4 1.0
C4 D:DG1 4.5 20.1 1.0
O D:HOH213 4.5 41.4 1.0
OP2 D:DG1 4.8 28.4 1.0
C4 D:DC2 4.9 22.9 1.0
O A:HOH829 5.0 29.6 0.4

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 09:28:26 2024

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