Atomistry » Manganese » PDB 7ksu-7lrd » 7ktm
Atomistry »
  Manganese »
    PDB 7ksu-7lrd »
      7ktm »

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

Go back to Manganese Binding Sites List in 7ktm
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

Go back to Manganese Binding Sites List in 7ktm
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

Go back to Manganese Binding Sites List in 7ktm
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

Go back to Manganese Binding Sites List in 7ktm
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

Go back to Manganese Binding Sites List in 7ktm
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

Go back to Manganese Binding Sites List in 7ktm
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

Go back to Manganese Binding Sites List in 7ktm
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

Go back to Manganese Binding Sites List in 7ktm
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

Go back to Manganese Binding Sites List in 7ktm
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

Go back to Manganese Binding Sites List in 7ktm
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy