Manganese in PDB 7kt4: Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN)

Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN), PDB code: 7kt4 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) 21.43 / 1.92
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.119, 68.819, 110.296, 90, 90, 90
R / Rfree (%) 16.6 / 20.4

Other elements in 7kt4:

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN) also contains other interesting chemical elements:

Sodium (Na) 1 atom
Chlorine (Cl) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN) (pdb code 7kt4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN), PDB code: 7kt4:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7kt4

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Manganese binding site 1 out of 4 in the Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 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, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:20.4
occ:1.00
 OD2 A:ASP330 1.7 15.9 0.5
OP1 P:8OG5 1.9 10.5 0.6
OD1 A:ASP332 2.1 17.1 1.0
OD2 A:ASP418 2.1 13.0 1.0
O P:HOH202 2.4 21.4 1.0
OD1 A:ASP330 2.5 20.6 0.5
O A:HOH705 2.5 25.1 0.5
CG A:ASP330 2.7 20.2 0.5
O2A A:8DG512 2.8 10.4 0.4
P P:8OG5 3.0 13.8 0.6
O3' P:DA4 3.0 18.9 0.4
O3' P:DA4 3.1 18.6 0.6
CG A:ASP418 3.1 14.7 1.0
OD1 A:ASP330 3.1 12.9 0.5
CG A:ASP332 3.1 16.4 1.0
CG A:ASP330 3.3 33.6 0.5
MN A:MN503 3.4 16.3 1.0
OD2 A:ASP332 3.5 14.0 1.0
PA A:8DG512 3.7 16.2 0.4
CB A:ASP418 3.8 16.6 1.0
OD2 A:ASP330 3.8 28.8 0.5
OP2 P:8OG5 3.8 18.0 0.6
O1A A:8DG512 3.9 15.6 0.4
CB A:ASP330 4.0 16.2 0.5
OD1 A:ASP418 4.0 14.5 1.0
C3' P:DA4 4.1 15.5 0.4
C5' P:DA4 4.1 15.7 0.4
C5' P:DA4 4.1 16.3 0.6
C3' P:DA4 4.1 11.0 0.6
CB A:ASP330 4.2 19.6 0.5
O5' A:8DG512 4.2 10.2 0.4
C4' P:DA4 4.2 14.4 0.4
O5' P:8OG5 4.3 14.0 0.6
C4' P:DA4 4.3 11.9 0.6
CB A:ASP332 4.5 10.6 1.0
NH2 A:ARG416 4.5 15.2 1.0
O P:HOH205 4.6 22.3 0.5
OP1 P:DA4 4.6 13.6 0.6
C5' A:8DG512 4.6 10.0 0.4
OP1 P:DA4 4.6 15.5 0.4
O1G A:8DG512 4.6 21.5 0.4
C5' P:8OG5 4.7 15.4 0.6
O A:VAL331 4.7 13.7 1.0
CZ3 A:TRP434 4.7 16.1 1.0
O32 A:PPV511 4.8 29.3 0.2
NE2 A:HIS329 4.9 29.5 0.5
O5' P:DA4 4.9 21.0 0.4
O5' P:DA4 4.9 17.7 0.6
N A:ASP418 4.9 12.6 1.0
O A:HOH617 5.0 13.2 1.0
C A:VAL331 5.0 13.7 1.0
CA A:ASP418 5.0 12.5 1.0

Manganese binding site 2 out of 4 in 7kt4

Go back to Manganese Binding Sites List in 7kt4
Manganese binding site 2 out of 4 in the Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 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, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:16.3
occ:1.00
 O2A A:8DG512 1.6 10.4 0.4
O A:HOH617 1.9 13.2 1.0
OD1 A:ASP330 2.1 12.9 0.5
OD2 A:ASP332 2.1 14.0 1.0
O1B A:8DG512 2.1 16.6 0.4
O1G A:8DG512 2.1 21.5 0.4
O11 A:PPV511 2.2 17.2 0.6
OD1 A:ASP330 2.3 20.6 0.5
O32 A:PPV511 2.3 29.3 0.2
OP1 P:8OG5 2.4 10.5 0.6
PA A:8DG512 2.9 16.2 0.4
CG A:ASP330 3.1 33.6 0.5
CG A:ASP332 3.1 16.4 1.0
P1 A:PPV511 3.1 27.7 0.6
CG A:ASP330 3.1 20.2 0.5
PB A:8DG512 3.1 23.5 0.4
O31 A:PPV511 3.2 29.9 0.6
OD2 A:ASP330 3.2 28.8 0.5
O3A A:8DG512 3.3 32.9 0.4
OD1 A:ASP332 3.4 17.1 1.0
PG A:8DG512 3.4 36.3 0.4
MN A:MN502 3.4 20.4 1.0
OD2 A:ASP330 3.5 15.9 0.5
P2 A:PPV511 3.6 29.2 0.2
OPP A:PPV511 3.7 28.8 0.2
O3B A:8DG512 3.7 25.0 0.4
P P:8OG5 3.7 13.8 0.6
O5' P:8OG5 3.9 14.0 0.6
O5' A:8DG512 3.9 10.2 0.4
O1A A:8DG512 4.0 15.6 0.4
O A:ASP330 4.0 15.5 0.5
C5' A:8DG512 4.0 10.0 0.4
O2G A:8DG512 4.0 25.9 0.4
O A:HOH722 4.1 11.3 0.6
C5' P:8OG5 4.3 15.4 0.6
O12 A:PPV511 4.3 33.9 0.2
O A:ASP330 4.3 11.6 0.5
OP2 P:8OG5 4.3 18.0 0.6
N A:GLY320 4.3 12.0 1.0
C A:ASP330 4.3 15.5 0.5
O A:HOH629 4.4 15.6 1.0
CB A:ASP330 4.4 16.2 0.5
CB A:ASP332 4.4 10.6 1.0
CB A:ASP330 4.5 19.6 0.5
CA A:GLY319 4.5 13.2 1.0
O21 A:PPV511 4.5 24.4 0.6
O P:HOH202 4.5 21.4 1.0
C A:ASP330 4.5 15.9 0.5
O2B A:8DG512 4.5 17.4 0.4
O3G A:8DG512 4.6 36.5 0.4
CD2 A:HIS329 4.6 35.9 0.5
O P:HOH205 4.7 22.3 0.5
NE2 A:HIS329 4.7 29.5 0.5
O22 A:PPV511 4.8 41.8 0.2
O A:HOH705 4.8 25.1 0.5
O3' P:DA4 4.8 18.9 0.4
CA A:ASP330 4.8 18.6 0.5
O3' P:DA4 4.8 18.6 0.6
N A:ASP330 4.9 14.7 0.5
N A:ASP332 4.9 11.2 1.0
N A:VAL331 4.9 14.1 1.0
CA A:ASP330 5.0 12.2 0.5
C A:GLY319 5.0 11.0 1.0

Manganese binding site 3 out of 4 in 7kt4

Go back to Manganese Binding Sites List in 7kt4
Manganese binding site 3 out of 4 in the Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 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, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:31.4
occ:0.65
 O A:HOH777 2.3 33.0 1.0
OE2 A:GLU386 2.3 33.2 1.0
O T:HOH101 2.4 28.1 1.0
O A:HOH826 2.5 34.8 1.0
OE1 A:GLU386 2.5 41.4 1.0
NE2 A:HIS459 2.7 37.4 1.0
CD A:GLU386 2.8 32.6 1.0
CD2 A:HIS459 3.2 53.2 1.0
CE1 A:HIS459 3.8 47.9 1.0
O A:HOH683 4.1 31.5 1.0
CG A:GLU386 4.3 29.6 1.0
OP1 T:DC8 4.3 21.4 1.0
CG A:HIS459 4.4 29.9 1.0
O A:HOH610 4.5 21.8 1.0
OE1 A:GLN426 4.6 25.1 1.0
C5' T:DC8 4.6 17.7 1.0
ND1 A:HIS459 4.7 46.2 1.0

Manganese binding site 4 out of 4 in 7kt4

Go back to Manganese Binding Sites List in 7kt4
Manganese binding site 4 out of 4 in the Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 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, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:81.8
occ:1.00
 NE2 A:HIS219 2.3 56.1 1.0
CE1 A:HIS219 3.2 47.4 1.0
CD2 A:HIS219 3.4 54.0 1.0
CD A:GLU218 3.7 52.1 1.0
ND1 A:HIS219 4.4 51.0 1.0
CB A:GLU218 4.4 41.6 1.0
CG A:HIS219 4.5 44.2 1.0
CG A:GLU218 4.7 53.0 1.0
CD A:GLN214 5.0 40.0 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN) To Be Published.
Page generated: Fri Dec 17 11:05:29 2021

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