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Manganese in PDB 7ktc: Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN)

Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN), PDB code: 7ktc 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) 35.02 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.272, 62.354, 118.901, 90, 90, 90
R / Rfree (%) 15.6 / 17.6

Other elements in 7ktc:

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN) 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 Product State Ternary Complex, 10 Mm MN2+ (120MIN) (pdb code 7ktc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN), PDB code: 7ktc:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 7ktc

Go back to Manganese Binding Sites List in 7ktc
Manganese binding site 1 out of 7 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN)


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 Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:9.2
occ:1.00
 OD2 A:ASP330 1.6 16.0 1.0
OP1 P:8OG5 1.8 8.2 1.0
OD2 A:ASP418 2.0 6.4 1.0
OD1 A:ASP332 2.1 7.7 1.0
O A:HOH601 2.2 13.3 1.0
CG A:ASP330 2.7 13.2 1.0
O3' P:DA4 2.8 11.8 1.0
P P:8OG5 3.0 11.8 1.0
OD1 A:ASP330 3.0 8.0 1.0
CG A:ASP418 3.0 8.0 1.0
CG A:ASP332 3.1 6.8 1.0
MN A:MN503 3.5 6.7 1.0
OD2 A:ASP332 3.5 5.2 1.0
CB A:ASP418 3.8 6.3 1.0
OD1 A:ASP418 3.9 7.8 1.0
OP2 P:8OG5 4.0 11.7 1.0
C3' P:DA4 4.0 10.2 1.0
C5' P:DA4 4.1 8.2 1.0
CB A:ASP330 4.1 8.7 1.0
C4' P:DA4 4.2 8.7 1.0
O A:HOH732 4.2 16.4 0.5
O5' P:8OG5 4.2 10.1 1.0
CE1 A:HIS329 4.2 15.5 0.5
C5' P:8OG5 4.4 8.4 1.0
CB A:ASP332 4.4 3.5 1.0
NH2 A:ARG416 4.5 8.9 1.0
OP1 P:DA4 4.6 11.4 1.0
O32 A:PPV508 4.7 15.2 1.0
CZ3 A:TRP434 4.8 10.1 1.0
O5' P:DA4 4.8 8.9 1.0
NE2 A:HIS329 4.8 18.0 0.5
O A:VAL331 4.8 8.1 1.0
N A:ASP418 4.9 3.5 1.0
CA A:ASP332 4.9 3.9 1.0
CA A:ASP418 5.0 4.1 1.0

Manganese binding site 2 out of 7 in 7ktc

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Manganese binding site 2 out of 7 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN)


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 Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:6.7
occ:1.00
 O21 A:PPV508 2.1 5.5 1.0
O32 A:PPV508 2.1 15.2 1.0
OD1 A:ASP330 2.1 8.0 1.0
OD2 A:ASP332 2.1 5.2 1.0
O A:HOH724 2.3 9.6 1.0
OP1 P:8OG5 2.4 8.2 1.0
CG A:ASP332 3.1 6.8 1.0
P1 A:PPV508 3.2 12.9 1.0
CG A:ASP330 3.2 13.2 1.0
P2 A:PPV508 3.4 15.1 0.6
OD1 A:ASP332 3.5 7.7 1.0
MN A:MN502 3.5 9.2 1.0
O31 A:PPV508 3.5 17.1 1.0
OD2 A:ASP330 3.6 16.0 1.0
P P:8OG5 3.6 11.8 1.0
OPP A:PPV508 3.7 12.4 0.7
O5' P:8OG5 3.9 10.1 1.0
O A:HOH732 3.9 16.4 0.5
O12 A:PPV508 4.1 23.5 1.0
C5' P:8OG5 4.1 8.4 1.0
ND1 A:HIS329 4.2 17.3 0.5
CE1 A:HIS329 4.2 15.5 0.5
O A:ASP330 4.2 7.3 1.0
O A:HOH605 4.3 17.5 1.0
O A:HOH645 4.3 7.1 1.0
O A:HOH601 4.3 13.3 1.0
N A:GLY320 4.4 5.9 1.0
OP2 P:8OG5 4.4 11.7 1.0
CB A:ASP332 4.5 3.5 1.0
C A:ASP330 4.5 5.9 1.0
O11 A:PPV508 4.5 10.5 1.0
CA A:GLY319 4.5 5.1 1.0
CB A:ASP330 4.5 8.7 1.0
O22 A:PPV508 4.6 17.9 0.8
O3' P:DA4 4.7 11.8 1.0
CA A:ASP330 4.9 6.9 1.0
N A:ASP332 4.9 4.6 1.0
N A:ASP330 4.9 8.8 1.0
N A:VAL331 5.0 5.5 1.0

Manganese binding site 3 out of 7 in 7ktc

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Manganese binding site 3 out of 7 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN)


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 Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:48.8
occ:0.53
 O A:HOH783 1.8 53.3 1.0
O A:HOH880 2.1 51.9 0.7
NE2 A:HIS219 2.2 43.5 1.0
CE1 A:HIS219 3.2 44.2 1.0
CD2 A:HIS219 3.2 40.1 1.0
ND1 A:HIS219 4.3 43.1 1.0
CG A:HIS219 4.3 39.7 1.0
CB A:GLU218 4.9 33.9 1.0

Manganese binding site 4 out of 7 in 7ktc

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Manganese binding site 4 out of 7 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN)


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 Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:27.2
occ:0.49
 O T:HOH207 2.2 25.7 0.5
O A:HOH838 2.2 32.1 0.5
OE2 A:GLU386 2.3 27.9 1.0
NE2 A:HIS459 2.4 16.5 0.5
O A:HOH817 2.4 20.1 0.5
OE1 A:GLU386 2.9 32.9 1.0
CD A:GLU386 2.9 30.1 1.0
CD2 A:HIS459 3.2 17.3 0.5
NE2 A:HIS459 3.3 16.5 0.5
CE1 A:HIS459 3.5 16.4 0.5
CE1 A:HIS459 3.6 16.7 0.5
CD2 A:HIS459 3.9 15.7 0.5
OP1 T:DC8 4.1 16.8 1.0
O A:HOH679 4.4 16.2 1.0
ND1 A:HIS459 4.4 16.3 0.5
CG A:HIS459 4.4 15.2 0.5
CG A:GLU386 4.4 24.5 1.0
O A:HOH725 4.4 28.0 1.0
C5' T:DC8 4.5 12.5 1.0
ND1 A:HIS459 4.5 16.4 0.5
CG A:HIS459 4.5 15.6 0.5
OE1 A:GLN426 4.8 15.7 1.0

Manganese binding site 5 out of 7 in 7ktc

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Manganese binding site 5 out of 7 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN)


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 Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:51.7
occ:0.60
 N7 T:DG2 2.2 15.3 0.5
N7 T:DG2 2.5 15.9 0.5
O T:HOH206 2.6 29.6 1.0
O T:HOH203 2.6 22.4 0.7
C8 T:DG2 3.1 16.2 0.5
C5 T:DG2 3.2 15.2 0.5
C8 T:DG2 3.3 14.3 0.5
O6 T:DG2 3.6 14.3 0.5
C5 T:DG2 3.6 13.3 0.5
C6 T:DG2 3.8 13.2 0.5
O6 T:DG2 4.0 13.2 0.5
O T:HOH234 4.2 19.3 0.5
O D:HOH216 4.2 49.2 0.8
C6 T:DG2 4.2 12.9 0.5
N9 T:DG2 4.3 15.4 0.5
O T:HOH215 4.3 33.1 1.0
C4 T:DG2 4.3 13.2 0.5
C2' T:DC1 4.5 18.3 0.5
N9 T:DG2 4.5 16.1 0.5
O6 T:DG3 4.6 12.9 1.0
OP2 T:DG2 4.7 20.2 0.5
C4 T:DG2 4.7 13.3 0.5
C6 T:DC1 4.8 18.4 0.5
C6 T:DC1 4.9 18.3 0.5
C5 T:DC1 4.9 17.8 0.5
O D:HOH217 4.9 36.8 1.0

Manganese binding site 6 out of 7 in 7ktc

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Manganese binding site 6 out of 7 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN)


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 Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:9.5
occ:0.43
 O P:HOH209 2.1 12.4 0.6
O A:HOH749 2.2 13.0 0.6
O31 A:PPV508 2.2 17.1 1.0
O A:HOH836 2.2 19.6 0.6
OP2 P:8OG5 2.2 11.7 1.0
O8 P:8OG5 2.4 22.7 1.0
O5' P:8OG5 3.1 10.1 1.0
P P:8OG5 3.2 11.8 1.0
C8 P:8OG5 3.5 17.1 1.0
P1 A:PPV508 3.6 12.9 1.0
O P:HOH210 3.7 31.3 1.0
O A:HOH861 3.9 43.7 1.0
O A:HOH730 3.9 10.8 1.0
O A:HOH732 4.0 16.4 0.5
O A:HOH636 4.1 35.8 1.0
O11 A:PPV508 4.2 10.5 1.0
N7 P:8OG5 4.2 16.3 1.0
C3' P:8OG5 4.2 12.6 1.0
O22 A:PPV508 4.3 17.9 0.8
OP1 P:8OG5 4.3 8.2 1.0
O32 A:PPV508 4.4 15.2 1.0
OPP A:PPV508 4.4 12.4 0.7
C5' P:8OG5 4.5 8.4 1.0
O21 A:PPV508 4.6 5.5 1.0
O3' P:DA4 4.6 11.8 1.0
P2 A:PPV508 4.7 15.1 0.6
N9 P:8OG5 4.7 13.0 1.0
CB A:LYS438 4.8 8.0 1.0
O P:HOH213 4.8 21.8 1.0
C4' P:8OG5 4.9 9.7 1.0
C3' P:DA4 4.9 10.2 1.0
CE1 A:HIS329 4.9 15.5 0.5
O4' P:8OG5 5.0 9.5 1.0

Manganese binding site 7 out of 7 in 7ktc

Go back to Manganese Binding Sites List in 7ktc
Manganese binding site 7 out of 7 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN)


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 Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn101

b:49.9
occ:0.49
 O D:HOH216 2.2 49.2 0.8
N7 D:DG1 2.4 10.8 1.0
O D:HOH205 2.8 24.3 0.6
C8 D:DG1 3.3 11.1 1.0
C5 D:DG1 3.5 9.7 1.0
O D:HOH217 3.6 36.8 1.0
O6 D:DG1 3.8 11.8 1.0
C6 D:DG1 4.0 11.4 1.0
N4 D:DC2 4.3 14.8 1.0
O A:HOH703 4.3 42.9 1.0
O D:HOH215 4.5 32.8 1.0
N9 D:DG1 4.5 9.4 1.0
O T:HOH206 4.6 29.6 1.0
C4 D:DG1 4.6 9.3 1.0
OP2 D:DG1 4.9 18.5 1.0
CG A:ARG175 5.0 13.3 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 09:31:22 2024

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