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Manganese in PDB 7ktm: Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (30MIN)

Enzymatic activity of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (30MIN)

All present enzymatic activity of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (30MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (30MIN), PDB code: 7ktm 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) 34.98 / 1.53
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.241, 62.223, 118.797, 90, 90, 90
R / Rfree (%) 16 / 18.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (30MIN) (pdb code 7ktm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 10 binding sites of Manganese where determined in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (30MIN), PDB code: 7ktm:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 7ktm

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Manganese binding site 1 out of 10 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (30MIN)


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 Reaction State Ternary Complex, 50 Mm MN2+ (30MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:15.8
occ:1.00
 O12 A:PPV508 2.0 23.4 0.6
O2A A:8DG507 2.1 10.2 0.4
O21 A:PPV508 2.1 15.2 0.6
O2B A:8DG507 2.1 13.1 0.4
OD1 A:ASP330 2.1 16.9 1.0
OD2 A:ASP332 2.1 15.8 1.0
O A:HOH711 2.3 16.3 1.0
O2G A:8DG507 2.3 25.9 0.4
OP1 P:8OG5 2.8 16.4 0.6
PA A:8DG507 3.1 17.3 0.4
CG A:ASP332 3.1 14.8 1.0
CG A:ASP330 3.2 22.5 1.0
PB A:8DG507 3.2 17.2 0.4
P1 A:PPV508 3.2 16.4 0.6
P2 A:PPV508 3.3 25.4 0.6
PG A:8DG507 3.4 27.3 0.4
O31 A:PPV508 3.5 18.4 0.6
OD1 A:ASP332 3.5 17.0 1.0
MN P:MN102 3.6 17.4 1.0
O3A A:8DG507 3.6 17.3 0.4
O3B A:8DG507 3.6 20.8 0.4
OD2 A:ASP330 3.6 25.7 1.0
OPP A:PPV508 3.7 22.8 0.6
P P:8OG5 3.7 16.1 0.6
O A:HOH796 3.9 17.7 0.5
O5' A:8DG507 4.1 13.0 0.4
O5' P:8OG5 4.1 25.2 0.6
O A:ASP330 4.1 16.6 1.0
C5' A:8DG507 4.2 13.9 0.4
ND1 A:HIS329 4.2 23.9 0.5
CE1 A:HIS329 4.2 22.4 0.5
O3G A:8DG507 4.2 27.3 0.4
O32 A:PPV508 4.2 28.6 0.6
C5' P:8OG5 4.3 24.7 0.6
O A:HOH651 4.3 21.8 1.0
O1A A:8DG507 4.3 15.3 0.4
O A:HOH685 4.3 17.0 1.0
N A:GLY320 4.4 14.3 1.0
C A:ASP330 4.4 16.5 1.0
O22 A:PPV508 4.4 26.2 0.6
OP2 P:8OG5 4.5 22.0 0.6
O A:HOH713 4.5 17.1 0.6
CB A:ASP330 4.5 16.5 1.0
CB A:ASP332 4.5 13.0 1.0
CA A:GLY319 4.5 14.5 1.0
O1B A:8DG507 4.5 17.9 0.4
O11 A:PPV508 4.6 17.0 0.6
O1G A:8DG507 4.6 26.6 0.4
O A:HOH715 4.7 13.4 0.4
N A:ASP330 4.7 17.4 1.0
O A:HOH713 4.7 14.3 0.4
CA A:ASP330 4.8 16.6 1.0
O3' P:DA4 4.8 17.9 0.6
N A:ASP332 4.8 13.9 1.0
N A:VAL331 4.9 15.9 1.0

Manganese binding site 2 out of 10 in 7ktm

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Manganese binding site 2 out of 10 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (30MIN)


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 Reaction State Ternary Complex, 50 Mm MN2+ (30MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:25.1
occ:0.50
 O A:HOH820 2.0 33.5 0.7
O T:HOH201 2.1 33.0 0.8
OE2 A:GLU386 2.2 31.1 1.0
NE2 A:HIS459 2.3 38.8 1.0
O A:HOH772 2.3 26.5 0.6
OE1 A:GLU386 2.9 44.2 1.0
CD A:GLU386 2.9 32.0 1.0
CD2 A:HIS459 3.2 38.6 1.0
CE1 A:HIS459 3.3 39.2 1.0
OP1 T:DC8 4.2 27.7 1.0
O A:HOH703 4.2 31.2 1.0
O A:HOH673 4.3 26.8 1.0
CG A:HIS459 4.4 29.9 1.0
ND1 A:HIS459 4.4 37.9 1.0
CG A:GLU386 4.4 32.2 1.0
C5' T:DC8 4.4 24.8 1.0
OE1 A:GLN426 4.6 27.2 1.0

Manganese binding site 3 out of 10 in 7ktm

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Manganese binding site 3 out of 10 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (30MIN)


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 Reaction State Ternary Complex, 50 Mm MN2+ (30MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:61.7
occ:0.75
 O A:HOH824 2.1 53.8 0.8
NE2 A:HIS219 2.2 64.1 1.0
O A:HOH846 2.5 39.0 0.7
CE1 A:HIS219 3.1 59.1 1.0
CD2 A:HIS219 3.2 56.9 1.0
O A:HOH875 3.5 57.8 1.0
ND1 A:HIS219 4.3 57.3 1.0
CG A:HIS219 4.3 54.1 1.0
CB A:GLU218 4.8 36.9 1.0

Manganese binding site 4 out of 10 in 7ktm

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Manganese binding site 4 out of 10 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (30MIN)


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 Reaction State Ternary Complex, 50 Mm MN2+ (30MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:31.0
occ:0.49
 O A:HOH877 2.0 35.4 0.6
O A:HOH827 2.1 36.1 0.6
NE2 A:HIS152 2.3 43.6 1.0
O A:HOH662 2.6 29.5 0.4
CE1 A:HIS152 3.3 45.7 1.0
CD2 A:HIS152 3.3 43.3 1.0
O A:HOH662 4.4 31.3 0.6
ND1 A:HIS152 4.4 44.0 1.0
O A:HOH698 4.4 31.8 1.0
CG A:HIS152 4.5 42.0 1.0
O A:PRO190 4.5 30.8 1.0
O A:THR150 4.6 27.1 1.0

Manganese binding site 5 out of 10 in 7ktm

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Manganese binding site 5 out of 10 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (30MIN)


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 Reaction State Ternary Complex, 50 Mm MN2+ (30MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:29.3
occ:0.35
 O A:HOH633 2.1 37.6 0.6
OP3 D:DG1 2.2 30.0 1.0
ND1 A:HIS208 2.5 29.8 1.0
O D:HOH212 2.5 33.5 0.8
CE1 A:HIS208 3.3 32.0 1.0
P D:DG1 3.4 25.2 1.0
CG A:HIS208 3.4 27.9 1.0
CB A:HIS208 3.7 23.3 1.0
OP1 D:DG1 3.7 26.4 1.0
O D:HOH205 3.9 36.7 1.0
O D:HOH209 4.0 45.8 1.0
OP2 D:DG1 4.1 27.1 1.0
NH2 A:ARG211 4.1 74.4 1.0
NE2 A:HIS208 4.4 29.5 1.0
CD2 A:HIS208 4.4 31.1 1.0
NH1 A:ARG211 4.6 68.3 1.0
O5' D:DG1 4.6 23.3 1.0
CA A:HIS208 4.7 22.6 1.0
CZ A:ARG211 4.9 72.5 1.0
C5' D:DG1 4.9 23.7 1.0

Manganese binding site 6 out of 10 in 7ktm

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Manganese binding site 6 out of 10 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (30MIN)


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 Reaction State Ternary Complex, 50 Mm MN2+ (30MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:18.1
occ:0.57
 O P:HOH201 2.3 25.5 1.0
O A:VAL246 2.3 17.4 1.0
O A:THR241 2.3 19.2 1.0
O P:HOH218 2.4 23.3 1.0
OP1 P:DT3 2.5 17.9 0.4
O A:ILE243 2.5 19.1 1.0
OP1 P:DT3 2.7 18.0 0.6
C A:VAL246 3.4 15.9 1.0
C A:THR241 3.4 18.4 1.0
C A:ILE243 3.5 20.1 1.0
P P:DT3 3.7 17.1 0.4
P P:DT3 3.7 16.0 0.6
N A:VAL246 3.8 17.4 1.0
O P:HOH211 3.8 24.2 0.6
OP2 P:DT3 3.9 16.3 0.6
OP2 P:DT3 4.0 17.6 0.4
O A:HOH804 4.0 46.3 1.0
CA A:VAL246 4.1 16.6 1.0
N A:ILE243 4.1 17.8 1.0
CA A:THR241 4.2 18.1 1.0
C A:GLN242 4.2 21.3 1.0
N A:GLY245 4.3 16.9 1.0
N A:PHE244 4.3 18.7 1.0
CA A:PHE244 4.4 18.8 1.0
N A:GLY247 4.4 16.9 1.0
N A:GLN242 4.4 20.8 1.0
O3' P:DA4 4.4 32.2 0.4
CA A:ILE243 4.5 19.4 1.0
O P:HOH220 4.5 38.9 1.0
CA A:GLN242 4.5 21.9 1.0
CB A:VAL246 4.5 18.4 1.0
C3' P:DA4 4.6 28.6 0.4
O A:GLN242 4.6 24.6 1.0
O3' P:DG2 4.7 17.6 1.0
CA A:GLY247 4.7 17.5 1.0
C A:PHE244 4.7 17.7 1.0
O5' P:DT3 4.7 18.2 0.4
OP2 P:DA4 4.7 24.2 0.4
CB A:THR241 4.8 17.8 1.0
C A:GLY245 4.8 16.1 1.0
O A:PHE240 4.8 19.2 1.0
O5' P:DT3 4.9 18.5 0.6

Manganese binding site 7 out of 10 in 7ktm

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Manganese binding site 7 out of 10 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (30MIN)


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 Reaction State Ternary Complex, 50 Mm MN2+ (30MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:75.8
occ:0.63
 N7 T:DG2 2.3 24.2 0.5
N7 T:DG2 2.3 23.9 0.5
O T:HOH205 2.4 34.2 0.7
O T:HOH204 2.7 35.9 0.7
C8 T:DG2 3.1 23.9 0.5
C8 T:DG2 3.2 23.9 0.5
C5 T:DG2 3.3 23.0 0.5
C5 T:DG2 3.4 23.6 0.5
O6 T:DG2 3.7 22.4 0.5
O6 T:DG2 3.8 23.1 0.5
C6 T:DG2 3.9 21.8 0.5
C6 T:DG2 3.9 21.8 0.5
O T:HOH218 4.1 36.8 1.0
O D:HOH216 4.2 56.7 0.8
N9 T:DG2 4.3 24.1 0.5
N9 T:DG2 4.4 24.2 0.5
O6 T:DG3 4.4 21.4 1.0
C4 T:DG2 4.4 23.0 0.5
C4 T:DG2 4.5 22.8 0.5
OP2 T:DG2 4.5 26.5 0.5
C6 T:DC1 4.8 24.2 0.6
C6 T:DC1 4.9 23.4 0.4
C5 T:DC1 4.9 23.2 0.6
C2' T:DC1 5.0 29.6 0.4
C2' T:DC1 5.0 30.1 0.6

Manganese binding site 8 out of 10 in 7ktm

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Manganese binding site 8 out of 10 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (30MIN)


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 Reaction State Ternary Complex, 50 Mm MN2+ (30MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:19.1
occ:0.57
 O1A A:8DG507 1.7 15.3 0.4
O3A A:8DG507 2.1 17.3 0.4
O A:HOH830 2.1 20.1 0.6
O31 A:PPV508 2.2 18.4 0.6
O A:HOH601 2.2 18.4 0.6
O P:HOH217 2.2 22.7 0.6
O A:HOH601 2.3 17.9 0.4
OP2 P:8OG5 2.3 22.0 0.6
PA A:8DG507 2.3 17.3 0.4
O8 P:8OG5 2.3 33.8 0.6
O8 A:8DG507 2.4 24.2 0.4
O5' A:8DG507 3.0 13.0 0.4
P P:8OG5 3.2 16.1 0.6
O5' P:8OG5 3.2 25.2 0.6
C8 P:8OG5 3.4 34.5 0.6
C8 A:8DG507 3.5 20.5 0.4
P1 A:PPV508 3.6 16.4 0.6
PB A:8DG507 3.6 17.2 0.4
O2A A:8DG507 3.7 10.2 0.4
O A:HOH632 3.9 19.0 1.0
O A:HOH635 4.0 66.2 1.0
N7 P:8OG5 4.0 34.2 0.6
O3B A:8DG507 4.0 20.8 0.4
N7 A:8DG507 4.0 20.1 0.4
O11 A:PPV508 4.1 17.0 0.6
O22 A:PPV508 4.1 26.2 0.6
O A:HOH796 4.2 17.7 0.5
O P:HOH216 4.2 21.8 0.6
C3' P:8OG5 4.2 28.5 0.6
O1B A:8DG507 4.3 17.9 0.4
C5' A:8DG507 4.3 13.9 0.4
C3' A:8DG507 4.3 14.9 0.4
OP1 P:8OG5 4.4 16.4 0.6
O A:HOH713 4.4 14.3 0.4
OPP A:PPV508 4.4 22.8 0.6
O2B A:8DG507 4.5 13.1 0.4
O1G A:8DG507 4.5 26.6 0.4
O3' P:DA4 4.5 17.9 0.6
C5' P:8OG5 4.6 24.7 0.6
O21 A:PPV508 4.6 15.2 0.6
O12 A:PPV508 4.6 23.4 0.6
PG A:8DG507 4.7 27.3 0.4
N9 P:8OG5 4.7 31.9 0.6
P2 A:PPV508 4.7 25.4 0.6
N9 A:8DG507 4.7 18.0 0.4
O2G A:8DG507 4.7 25.9 0.4
CB A:ASP438 4.8 18.0 1.0
C3' P:DA4 4.8 18.0 0.6
CE1 A:HIS329 4.8 22.4 0.5
C4' A:8DG507 4.9 13.8 0.4
C4' P:8OG5 4.9 27.6 0.6
C5' P:DA4 4.9 24.2 0.4
O3' P:8OG5 4.9 28.5 0.6
O4' P:8OG5 4.9 28.1 0.6
OD2 A:ASP438 4.9 44.2 1.0

Manganese binding site 9 out of 10 in 7ktm

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Manganese binding site 9 out of 10 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (30MIN)


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 Reaction State Ternary Complex, 50 Mm MN2+ (30MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn102

b:17.4
occ:1.00
 OP1 P:8OG5 1.5 16.4 0.6
OD2 A:ASP330 1.9 25.7 1.0
OD2 A:ASP418 2.0 17.5 1.0
OD1 A:ASP332 2.1 17.0 1.0
O A:HOH713 2.2 17.1 0.6
O A:HOH713 2.5 14.3 0.4
O A:HOH715 2.5 13.4 0.4
O2A A:8DG507 2.5 10.2 0.4
O3' P:DA4 2.6 17.9 0.6
P P:8OG5 2.8 16.1 0.6
CG A:ASP330 2.9 22.5 1.0
CG A:ASP418 3.1 17.2 1.0
CG A:ASP332 3.2 14.8 1.0
OD1 A:ASP330 3.2 16.9 1.0
OD2 A:ASP332 3.6 15.8 1.0
MN A:MN501 3.6 15.8 1.0
CB A:ASP418 3.7 16.0 1.0
C3' P:DA4 3.8 18.0 0.6
OP2 P:8OG5 3.8 22.0 0.6
PA A:8DG507 3.8 17.3 0.4
O5' P:8OG5 4.0 25.2 0.6
OD1 A:ASP418 4.0 18.2 1.0
C5' P:DA4 4.0 13.0 0.6
C4' P:DA4 4.1 13.4 0.6
O A:HOH796 4.1 17.7 0.5
O5' A:8DG507 4.1 13.0 0.4
CE1 A:HIS329 4.2 22.4 0.5
O1A A:8DG507 4.2 15.3 0.4
C5' A:8DG507 4.3 13.9 0.4
CB A:ASP330 4.3 16.5 1.0
C5' P:8OG5 4.3 24.7 0.6
NH2 A:ARG416 4.4 20.1 1.0
CB A:ASP332 4.4 13.0 1.0
OP1 P:DA4 4.5 17.5 0.4
OP1 P:DA4 4.7 16.6 0.6
CZ3 A:TRP434 4.7 22.4 1.0
O12 A:PPV508 4.7 23.4 0.6
O5' P:DA4 4.8 12.8 0.6
NE2 A:HIS329 4.8 25.3 0.5
N A:ASP418 4.9 14.1 1.0
O2G A:8DG507 5.0 25.9 0.4
O2B A:8DG507 5.0 13.1 0.4
CA A:ASP418 5.0 14.9 1.0
C2' P:DA4 5.0 14.2 0.6
O A:VAL331 5.0 15.5 1.0
CA A:ASP332 5.0 13.7 1.0

Manganese binding site 10 out of 10 in 7ktm

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Manganese binding site 10 out of 10 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (30MIN)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (30MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn101

b:54.5
occ:0.50
 O A:HOH763 2.1 46.7 0.5
O D:HOH216 2.2 56.7 0.8
N7 D:DG1 2.3 20.2 1.0
O D:HOH202 2.9 50.6 1.0
C8 D:DG1 3.2 20.9 1.0
C5 D:DG1 3.4 18.1 1.0
O6 D:DG1 3.7 21.2 1.0
O D:HOH218 3.7 48.0 1.0
C6 D:DG1 3.9 19.0 1.0
O A:HOH763 4.0 43.4 0.5
N4 D:DC2 4.2 21.8 1.0
O D:HOH210 4.4 41.0 1.0
N9 D:DG1 4.4 19.7 1.0
O T:HOH205 4.5 34.2 0.7
C4 D:DG1 4.5 18.5 1.0
OP2 D:DG1 4.7 27.1 1.0
O D:HOH220 4.8 30.5 0.5
CG A:ARG175 4.9 21.8 1.0
C4 D:DC2 5.0 20.2 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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