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Manganese in PDB 7ktd: Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN)

Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN), PDB code: 7ktd 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) 43.38 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.316, 62.42, 119.135, 90, 90, 90
R / Rfree (%) 16 / 17.8

Other elements in 7ktd:

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN) 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+ (960MIN) (pdb code 7ktd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN), PDB code: 7ktd:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 7ktd

Go back to Manganese Binding Sites List in 7ktd
Manganese binding site 1 out of 6 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN)


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+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:21.4
occ:0.93
 OD2 A:ASP330 1.7 35.4 1.0
OP1 P:8OG5 2.0 20.4 1.0
OD2 A:ASP418 2.0 19.3 1.0
OD1 A:ASP332 2.1 20.7 1.0
O A:HOH608 2.2 25.5 1.0
CG A:ASP330 2.7 32.6 1.0
O3' P:DA4 3.0 20.5 1.0
OD1 A:ASP330 3.0 19.7 1.0
CG A:ASP418 3.0 18.5 1.0
P P:8OG5 3.0 20.3 1.0
CG A:ASP332 3.1 18.6 1.0
MN A:MN507 3.5 18.7 1.0
OD2 A:ASP332 3.5 17.2 1.0
CB A:ASP418 3.8 18.1 1.0
OD1 A:ASP418 3.9 19.8 1.0
OP2 P:8OG5 4.0 22.4 1.0
CB A:ASP330 4.1 22.4 1.0
C3' P:DA4 4.1 21.3 1.0
C5' P:DA4 4.1 20.0 1.0
O A:HOH692 4.1 37.8 1.0
C4' P:DA4 4.2 21.3 1.0
O5' P:8OG5 4.3 21.0 1.0
CB A:ASP332 4.4 16.5 1.0
NH2 A:ARG416 4.5 20.9 1.0
C5' P:8OG5 4.5 20.6 1.0
OP1 P:DA4 4.6 21.6 1.0
O32 A:PPV511 4.7 30.9 0.8
O A:VAL331 4.7 20.3 1.0
N A:ASP418 4.8 17.2 1.0
CZ3 A:TRP434 4.8 21.4 1.0
CA A:ASP418 4.9 17.6 1.0
O5' P:DA4 4.9 20.6 1.0
CA A:ASP332 4.9 16.6 1.0
C A:VAL331 4.9 19.1 1.0

Manganese binding site 2 out of 6 in 7ktd

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Manganese binding site 2 out of 6 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN)


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+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn507

b:18.7
occ:1.00
 O21 A:PPV511 2.1 16.0 0.9
O32 A:PPV511 2.1 30.9 0.8
OD2 A:ASP332 2.1 17.2 1.0
OD1 A:ASP330 2.2 19.7 1.0
O A:HOH709 2.3 20.7 1.0
OP1 P:8OG5 2.3 20.4 1.0
CG A:ASP332 3.1 18.6 1.0
P1 A:PPV511 3.2 23.3 0.8
CG A:ASP330 3.3 32.6 1.0
P2 A:PPV511 3.4 65.1 0.9
OD1 A:ASP332 3.4 20.7 1.0
MN A:MN506 3.5 21.4 0.9
O31 A:PPV511 3.5 27.3 0.9
P P:8OG5 3.6 20.3 1.0
OPP A:PPV511 3.6 34.9 0.9
OD2 A:ASP330 3.7 35.4 1.0
O5' P:8OG5 3.9 21.0 1.0
O A:HOH692 3.9 37.8 1.0
C5' P:8OG5 4.1 20.6 1.0
O12 A:PPV511 4.1 51.9 1.0
O A:HOH607 4.2 33.5 1.0
O A:ASP330 4.2 19.3 1.0
OP2 P:8OG5 4.3 22.4 1.0
O A:HOH613 4.4 20.9 1.0
O A:HOH608 4.4 25.5 1.0
N A:GLY320 4.4 17.9 1.0
O11 A:PPV511 4.5 20.2 0.8
C A:ASP330 4.5 18.0 1.0
CA A:GLY319 4.5 17.0 1.0
CB A:ASP332 4.5 16.5 1.0
CB A:ASP330 4.6 22.4 1.0
O22 A:PPV511 4.6 43.5 0.9
O3' P:DA4 4.7 20.5 1.0
CA A:ASP330 4.9 18.3 1.0
N A:ASP332 4.9 16.8 1.0
N A:ASP330 4.9 20.6 1.0
N A:VAL331 5.0 18.9 1.0

Manganese binding site 3 out of 6 in 7ktd

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Manganese binding site 3 out of 6 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN)


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+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn508

b:72.8
occ:0.80
 O A:HOH780 2.0 54.3 0.9
NE2 A:HIS219 2.3 50.4 1.0
O A:HOH854 2.5 59.5 0.8
CD2 A:HIS219 3.2 49.6 1.0
OE2 A:GLU218 3.2 64.6 1.0
CE1 A:HIS219 3.3 52.2 1.0
ND1 A:HIS219 4.4 50.8 1.0
CG A:HIS219 4.4 49.0 1.0
CD A:GLU218 4.4 66.3 1.0
CB A:GLU218 4.7 43.6 1.0

Manganese binding site 4 out of 6 in 7ktd

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Manganese binding site 4 out of 6 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN)


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+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn509

b:37.0
occ:0.45
 OE2 A:GLU386 2.2 35.1 1.0
O T:HOH204 2.2 30.6 0.5
NE2 A:HIS459 2.4 27.5 0.5
O A:HOH769 2.5 28.1 0.5
OE1 A:GLU386 2.9 57.2 1.0
CD A:GLU386 2.9 37.5 1.0
CD2 A:HIS459 3.1 30.1 0.5
NE2 A:HIS459 3.3 34.5 0.6
CE1 A:HIS459 3.6 33.0 0.5
CE1 A:HIS459 3.6 29.8 0.6
CD2 A:HIS459 3.9 24.1 0.6
OP1 T:DC8 4.1 30.1 1.0
ND1 A:HIS459 4.3 27.5 0.6
O A:HOH672 4.3 40.1 1.0
O A:HOH679 4.3 28.8 1.0
CG A:GLU386 4.3 34.3 1.0
CG A:HIS459 4.4 28.2 0.5
C5' T:DC8 4.5 23.8 1.0
CG A:HIS459 4.5 25.2 0.6
ND1 A:HIS459 4.5 33.3 0.5
OE1 A:GLN426 4.8 28.0 1.0

Manganese binding site 5 out of 6 in 7ktd

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Manganese binding site 5 out of 6 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN)


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+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:48.6
occ:0.46
 N7 T:DG2 2.1 27.0 0.6
O T:HOH212 2.4 41.9 0.8
N7 T:DG2 2.5 24.9 0.4
O T:HOH201 2.6 40.7 0.7
C8 T:DG2 2.9 25.2 0.6
C5 T:DG2 3.1 28.0 0.6
C8 T:DG2 3.3 24.9 0.4
C5 T:DG2 3.6 24.3 0.4
O6 T:DG2 3.6 24.6 0.6
C6 T:DG2 3.7 24.3 0.6
O6 T:DG2 4.0 24.3 0.4
N9 T:DG2 4.1 24.6 0.6
C6 T:DG2 4.2 24.0 0.4
O T:HOH230 4.2 31.9 0.6
C4 T:DG2 4.2 24.2 0.6
O T:HOH216 4.2 43.8 1.0
O D:HOH102 4.4 34.0 0.4
N9 T:DG2 4.5 24.4 0.4
C2' T:DC1 4.5 31.1 0.4
O6 T:DG3 4.5 24.9 1.0
C4 T:DG2 4.7 24.0 0.4
C6 T:DC1 4.8 27.7 0.4
OP2 T:DG2 4.9 27.7 0.4
O D:HOH115 4.9 45.2 1.0
C5 T:DC1 4.9 27.4 0.6
C6 T:DC1 5.0 27.7 0.6

Manganese binding site 6 out of 6 in 7ktd

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Manganese binding site 6 out of 6 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN)


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+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:25.3
occ:0.46
 O P:HOH207 2.0 24.6 0.5
O A:HOH810 2.1 23.4 0.5
O A:HOH713 2.2 21.3 0.5
O31 A:PPV511 2.2 27.3 0.9
O A:HOH713 2.3 21.6 0.5
OP2 P:8OG5 2.3 22.4 1.0
O8 P:8OG5 2.4 33.8 1.0
O5' P:8OG5 3.1 21.0 1.0
P P:8OG5 3.3 20.3 1.0
O P:HOH210 3.6 24.5 0.5
C8 P:8OG5 3.6 30.7 1.0
P1 A:PPV511 3.6 23.3 0.8
O A:HOH708 3.9 22.8 1.0
O A:HOH824 4.1 50.6 1.0
O A:HOH692 4.1 37.8 1.0
O11 A:PPV511 4.1 20.2 0.8
O22 A:PPV511 4.2 43.5 0.9
OP1 P:8OG5 4.2 20.4 1.0
C3' P:8OG5 4.2 24.1 1.0
N7 P:8OG5 4.3 28.0 1.0
O32 A:PPV511 4.3 30.9 0.8
OPP A:PPV511 4.4 34.9 0.9
C5' P:8OG5 4.5 20.6 1.0
O21 A:PPV511 4.5 16.0 0.9
O3' P:DA4 4.6 20.5 1.0
P2 A:PPV511 4.6 65.1 0.9
N9 P:8OG5 4.8 21.2 1.0
O P:HOH213 4.8 31.5 1.0
C4' P:8OG5 4.8 19.4 1.0
CB A:LYS438 4.8 19.5 1.0
C3' P:DA4 4.9 21.3 1.0
O4' P:8OG5 5.0 19.6 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 09:31:59 2024

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