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Manganese in PDB 7kst: Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN)

Enzymatic activity of Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN)

All present enzymatic activity of Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN), PDB code: 7kst 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) 41.79 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.865, 68.831, 110.059, 90, 90, 90
R / Rfree (%) 16.4 / 18.5

Other elements in 7kst:

The structure of Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN) (pdb code 7kst). 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, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN), PDB code: 7kst:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 7kst

Go back to Manganese Binding Sites List in 7kst
Manganese binding site 1 out of 6 in the Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN)


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, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn510

b:16.3
occ:1.00
 OD2 A:ASP330 2.0 30.6 1.0
OP1 P:DG5 2.1 11.6 0.4
OD2 A:ASP418 2.1 16.4 1.0
OD1 A:ASP332 2.2 13.8 1.0
O P:HOH203 2.3 23.4 1.0
O3' P:DA4 2.5 15.4 0.6
O3' P:DA4 2.6 16.2 0.4
O1A A:DGT501 2.7 11.5 0.6
P P:DG5 2.9 17.0 0.4
CG A:ASP330 2.9 15.8 1.0
OD1 A:ASP330 3.0 17.2 1.0
CG A:ASP332 3.2 13.9 1.0
CG A:ASP418 3.3 15.7 1.0
PA A:DGT501 3.6 13.3 0.6
OD2 A:ASP332 3.6 13.2 1.0
C3' P:DA4 3.6 14.9 0.6
MN A:MN511 3.7 18.5 1.0
C3' P:DA4 3.7 18.6 0.4
OP2 P:DG5 3.9 13.4 0.4
O5' A:DGT501 3.9 15.2 0.6
C4' P:DA4 3.9 15.6 0.4
CB A:ASP418 4.0 15.1 1.0
C5' P:DA4 4.0 15.0 0.4
O5' P:DG5 4.1 12.4 0.4
C5' P:DA4 4.1 15.7 0.6
C5' A:DGT501 4.1 17.1 0.6
C4' P:DA4 4.1 15.1 0.6
O2A A:DGT501 4.1 19.4 0.6
OD1 A:ASP418 4.2 16.1 1.0
C5' P:DG5 4.2 14.8 0.4
CE1 A:HIS329 4.3 23.4 0.5
CB A:ASP330 4.3 13.2 1.0
O32 A:PPV502 4.5 11.9 0.4
CB A:ASP332 4.5 11.7 1.0
OP1 P:DA4 4.6 20.7 0.6
NH2 A:ARG416 4.6 17.3 1.0
OP1 P:DA4 4.6 19.6 0.4
O5' P:DA4 4.7 15.7 0.4
O5' P:DA4 4.7 21.8 0.6
CZ3 A:TRP434 4.7 20.3 1.0
C2' P:DA4 5.0 16.7 0.4
C2' P:DA4 5.0 20.2 0.6
NE2 A:HIS329 5.0 26.8 0.5
O A:VAL331 5.0 13.9 1.0

Manganese binding site 2 out of 6 in 7kst

Go back to Manganese Binding Sites List in 7kst
Manganese binding site 2 out of 6 in the Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN)


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, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn511

b:18.5
occ:1.00
 O1A A:DGT501 1.9 11.5 0.6
OD1 A:ASP330 2.1 17.2 1.0
O2B A:DGT501 2.2 11.3 0.6
O A:HOH662 2.2 23.3 1.0
OD2 A:ASP332 2.2 13.2 1.0
O2G A:DGT501 2.3 15.0 0.6
O11 A:PPV502 2.4 17.8 0.4
O32 A:PPV502 2.5 11.9 0.4
OP1 P:DG5 2.8 11.6 0.4
PB A:DGT501 3.2 13.5 0.6
CG A:ASP332 3.2 13.9 1.0
CG A:ASP330 3.3 15.8 1.0
PA A:DGT501 3.3 13.3 0.6
PG A:DGT501 3.5 16.2 0.6
O3A A:DGT501 3.5 14.9 0.6
P1 A:PPV502 3.6 15.7 0.4
OD1 A:ASP332 3.6 13.8 1.0
O A:ASP330 3.7 19.9 1.0
O3B A:DGT501 3.7 14.8 0.6
MN A:MN510 3.7 16.3 1.0
OD2 A:ASP330 3.8 30.6 1.0
P2 A:PPV502 3.8 21.0 0.4
O A:HOH675 3.8 18.4 0.4
OPP A:PPV502 4.0 16.8 0.4
C A:ASP330 4.1 17.6 1.0
P P:DG5 4.2 17.0 0.4
C5' A:DGT501 4.2 17.1 0.6
O A:HOH628 4.2 15.2 1.0
ND1 A:HIS329 4.2 24.8 0.5
O3G A:DGT501 4.2 18.6 0.6
O5' A:DGT501 4.3 15.2 0.6
O21 A:PPV502 4.3 16.8 0.4
C5' P:DG5 4.3 14.8 0.4
CE1 A:HIS329 4.4 23.4 0.5
O2A A:DGT501 4.4 19.4 0.6
N A:GLY320 4.4 11.8 1.0
CB A:ASP330 4.4 13.2 1.0
N A:ASP330 4.5 14.5 1.0
O5' P:DG5 4.5 12.4 0.4
O A:HOH675 4.5 14.6 0.6
CA A:ASP330 4.6 16.1 1.0
CB A:ASP332 4.6 11.7 1.0
O1B A:DGT501 4.6 16.7 0.6
O1G A:DGT501 4.6 21.2 0.6
CA A:GLY319 4.7 12.3 1.0
O12 A:PPV502 4.7 19.1 0.4
N A:VAL331 4.7 12.9 1.0
N A:ASP332 4.8 12.5 1.0
O31 A:PPV502 4.8 11.1 0.4
O P:HOH203 4.8 23.4 1.0
O22 A:PPV502 4.9 20.9 0.4
C A:VAL331 5.0 12.5 1.0

Manganese binding site 3 out of 6 in 7kst

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Manganese binding site 3 out of 6 in the Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN)


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, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn512

b:70.7
occ:0.66
 NE2 A:HIS219 2.1 52.9 1.0
O A:HOH848 2.2 60.6 0.7
O A:HOH640 2.5 49.8 0.6
CE1 A:HIS219 3.0 49.6 1.0
CD2 A:HIS219 3.2 43.6 1.0
O A:HOH844 3.7 55.8 1.0
ND1 A:HIS219 4.1 48.1 1.0
CG A:HIS219 4.3 44.0 1.0
CB A:GLU218 4.7 34.4 1.0

Manganese binding site 4 out of 6 in 7kst

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Manganese binding site 4 out of 6 in the Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN)


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, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn513

b:35.0
occ:0.41
 O A:HOH843 2.2 48.1 0.8
OE2 A:GLU386 2.2 35.4 1.0
O T:HOH101 2.4 35.0 0.8
O A:HOH788 2.5 35.5 0.8
NE2 A:HIS459 2.6 18.9 0.3
OE1 A:GLU386 2.8 48.5 1.0
CD A:GLU386 2.9 35.4 1.0
CD2 A:HIS459 3.1 25.5 0.3
CE1 A:HIS459 3.2 21.2 0.7
NE2 A:HIS459 3.4 24.1 0.7
CE1 A:HIS459 3.9 20.8 0.3
ND1 A:HIS459 3.9 19.9 0.7
O A:HOH716 4.1 38.4 1.0
OP1 T:DC8 4.1 31.4 1.0
CD2 A:HIS459 4.2 17.3 0.7
O A:HOH612 4.3 23.6 1.0
CG A:GLU386 4.4 23.4 1.0
CG A:HIS459 4.4 19.7 0.3
CG A:HIS459 4.5 19.7 0.7
C5' T:DC8 4.5 20.0 1.0
ND1 A:HIS459 4.8 21.6 0.3
OE1 A:GLN426 4.8 22.8 1.0

Manganese binding site 5 out of 6 in 7kst

Go back to Manganese Binding Sites List in 7kst
Manganese binding site 5 out of 6 in the Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN)


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, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn514

b:39.5
occ:0.36
 O A:PHE205 2.2 34.0 1.0
O A:HOH639 2.2 41.1 1.0
O D:HOH107 2.8 45.4 1.0
C A:PHE205 3.4 35.9 1.0
O A:LEU202 4.2 25.3 1.0
O A:HOH758 4.2 42.2 1.0
N A:GLY206 4.2 21.1 1.0
CA A:GLY206 4.3 23.4 1.0
CA A:PHE205 4.4 21.7 1.0
CB A:PHE205 4.6 19.5 1.0
N A:PHE205 4.6 20.1 1.0
OP1 D:DC3 4.7 22.0 1.0
OP2 D:DC3 4.8 22.6 1.0

Manganese binding site 6 out of 6 in 7kst

Go back to Manganese Binding Sites List in 7kst
Manganese binding site 6 out of 6 in the Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN)


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, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn102

b:27.2
occ:0.36
 O2A A:DGT501 2.0 19.4 0.6
O P:HOH216 2.1 20.5 0.4
O P:HOH212 2.1 19.1 0.4
OP2 P:DG5 2.2 13.4 0.4
O A:HOH839 2.3 19.7 0.4
O22 A:PPV502 2.3 20.9 0.4
PA A:DGT501 3.5 13.3 0.6
P P:DG5 3.6 17.0 0.4
O P:HOH203 3.7 23.4 1.0
P2 A:PPV502 3.7 21.0 0.4
O A:HOH692 3.8 25.7 1.0
CE1 A:HIS329 3.8 23.4 0.5
O A:HOH816 4.0 36.4 1.0
O3A A:DGT501 4.1 14.9 0.6
OP1 P:DG5 4.2 11.6 0.4
O32 A:PPV502 4.3 11.9 0.4
O5' A:DGT501 4.3 15.2 0.6
O5' P:DG5 4.4 12.4 0.4
NE2 A:HIS329 4.4 26.8 0.5
OP2 P:DA4 4.4 18.9 0.6
OPP A:PPV502 4.4 16.8 0.4
OP2 P:DA4 4.4 17.9 0.4
ND1 A:HIS329 4.5 24.8 0.5
O1A A:DGT501 4.6 11.5 0.6
O12 A:PPV502 4.7 19.1 0.4
OP1 P:DA4 4.7 20.7 0.6
O3' P:DA4 4.7 16.2 0.4
OP1 P:DA4 4.8 19.6 0.4
O5' P:DA4 4.8 15.7 0.4
P P:DA4 4.9 25.5 0.4
C3' P:DA4 4.9 18.6 0.4
P P:DA4 4.9 16.1 0.6
O5' P:DA4 5.0 21.8 0.6

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN) To Be Published.
Page generated: Sun Oct 6 09:23:00 2024

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