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Manganese in PDB 6vfb: Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)

Enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min), PDB code: 6vfb 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) 34.99 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.198, 62.334, 118.756, 90, 90, 90
R / Rfree (%) 16.7 / 18.2

Other elements in 6vfb:

The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) 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-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) (pdb code 6vfb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min), PDB code: 6vfb:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 6vfb

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Manganese binding site 1 out of 7 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)


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-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:19.3
occ:1.00
 O2G A:8GT510 1.9 18.9 0.5
OD1 A:ASP330 2.1 19.6 1.0
O21 A:PPV512 2.1 19.2 0.5
O2B A:8GT510 2.1 19.1 0.5
OD2 A:ASP332 2.2 18.4 1.0
O2A A:8GT510 2.2 32.7 0.5
O A:HOH692 2.3 20.8 1.0
O32 A:PPV512 2.4 29.7 0.5
OP1 P:8GM5 2.6 23.1 0.5
CG A:ASP332 3.1 18.2 1.0
CG A:ASP330 3.1 21.6 1.0
P1 A:PPV512 3.1 21.0 0.5
PG A:8GT510 3.2 20.8 0.5
O31 A:PPV512 3.2 21.2 0.5
PB A:8GT510 3.3 25.1 0.5
OD1 A:ASP332 3.5 19.0 1.0
PA A:8GT510 3.5 37.4 0.5
OD2 A:ASP330 3.5 24.1 1.0
MN P:MN101 3.5 22.9 1.0
O3B A:8GT510 3.6 24.6 0.5
P2 A:PPV512 3.7 25.6 0.5
O3A A:8GT510 3.7 28.3 0.5
P P:8GM5 3.8 24.5 0.5
OPP A:PPV512 3.8 23.6 0.5
O5' P:8GM5 3.9 32.8 0.5
O1G A:8GT510 4.0 25.7 0.5
O A:ASP330 4.0 19.8 1.0
ND1 A:HIS329 4.2 40.5 1.0
C5' P:8GM5 4.2 30.6 0.5
N A:GLY320 4.3 17.3 1.0
O A:HOH618 4.3 19.6 1.0
CE1 A:HIS329 4.3 43.1 1.0
C A:ASP330 4.3 17.9 1.0
O3G A:8GT510 4.3 21.0 0.5
O A:HOH612 4.4 29.8 1.0
O11 A:PPV512 4.5 23.0 0.5
CB A:ASP330 4.5 21.4 1.0
O1A A:8GT510 4.5 40.5 0.5
O12 A:PPV512 4.5 35.9 0.5
CB A:ASP332 4.5 16.6 1.0
CA A:GLY319 4.5 17.9 1.0
O5' A:8GT510 4.6 38.4 0.5
O1B A:8GT510 4.7 25.3 0.5
OP2 P:8GM5 4.7 28.8 0.5
N A:ASP330 4.7 21.0 1.0
O P:HOH201 4.7 29.0 1.0
O A:HOH775 4.7 20.9 0.5
CA A:ASP330 4.7 18.1 1.0
O22 A:PPV512 4.7 33.7 0.5
N A:ASP332 4.8 16.8 1.0
N A:VAL331 4.9 18.7 1.0
O3' P:DA4 4.9 27.7 0.5
C A:GLY319 5.0 19.6 1.0

Manganese binding site 2 out of 7 in 6vfb

Go back to Manganese Binding Sites List in 6vfb
Manganese binding site 2 out of 7 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)


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-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:84.7
occ:0.96
 NE2 A:HIS219 2.2 55.9 1.0
CD2 A:HIS219 3.2 52.6 1.0
CE1 A:HIS219 3.2 52.7 1.0
CD A:GLU218 3.7 50.7 1.0
ND1 A:HIS219 4.3 52.1 1.0
CG A:HIS219 4.3 51.2 1.0
CB A:GLU218 4.5 42.4 1.0
CG A:GLU218 4.7 50.3 1.0

Manganese binding site 3 out of 7 in 6vfb

Go back to Manganese Binding Sites List in 6vfb
Manganese binding site 3 out of 7 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)


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-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn507

b:58.5
occ:0.55
 O T:HOH201 2.1 47.4 0.6
OE2 A:GLU386 2.3 57.0 1.0
NE2 A:HIS459 2.6 34.5 0.6
O A:HOH771 2.7 33.7 0.6
CD A:GLU386 3.1 56.7 1.0
OE1 A:GLU386 3.1 57.7 1.0
CD2 A:HIS459 3.2 35.7 0.6
NE2 A:HIS459 3.5 35.9 0.5
CE1 A:HIS459 3.5 33.0 0.5
CE1 A:HIS459 3.7 36.2 0.6
OP1 T:DC8 3.8 42.6 1.0
CD2 A:HIS459 4.2 31.7 0.5
ND1 A:HIS459 4.2 31.1 0.5
C5' T:DC8 4.3 35.5 1.0
O A:HOH667 4.4 30.8 1.0
CG A:HIS459 4.5 27.8 0.6
CG A:GLU386 4.5 44.8 1.0
CG A:HIS459 4.7 28.7 0.5
ND1 A:HIS459 4.7 36.8 0.6
O A:HOH663 4.8 48.2 1.0
O5' T:DC8 4.9 42.0 1.0
P T:DC8 5.0 33.4 1.0

Manganese binding site 4 out of 7 in 6vfb

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Manganese binding site 4 out of 7 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)


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-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:56.3
occ:0.62
 N7 T:DG2 2.3 30.4 0.7
O T:HOH210 2.4 43.6 1.0
N7 T:DG2 2.5 29.5 0.3
O T:HOH204 2.6 47.6 1.0
C8 T:DG2 3.1 26.9 0.7
C5 T:DG2 3.4 25.2 0.7
C8 T:DG2 3.4 26.0 0.3
C5 T:DG2 3.5 25.2 0.3
O6 T:DG2 3.6 26.8 0.3
O6 T:DG2 3.8 26.5 0.7
C6 T:DG2 3.9 23.8 0.3
C6 T:DG2 3.9 22.9 0.7
O T:HOH211 4.0 39.2 1.0
N9 T:DG2 4.3 23.0 0.7
C4 T:DG2 4.4 24.1 0.7
O6 T:DG3 4.4 23.9 1.0
OP2 T:DG2 4.5 31.2 0.7
N9 T:DG2 4.6 25.9 0.3
C4 T:DG2 4.6 24.6 0.3
C6 T:DC1 4.9 25.6 0.5
C2' T:DC1 4.9 31.5 0.5
C5 T:DC1 5.0 25.4 0.5

Manganese binding site 5 out of 7 in 6vfb

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Manganese binding site 5 out of 7 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)


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-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:22.9
occ:1.00
 OP1 P:8GM5 1.6 23.1 0.5
OD2 A:ASP330 1.9 24.1 1.0
OD1 A:ASP332 2.2 19.0 1.0
OD2 A:ASP418 2.2 21.4 1.0
O P:HOH201 2.2 29.0 1.0
O A:HOH775 2.3 20.9 0.5
O2G A:8GT510 2.4 18.9 0.5
O3' P:DA4 2.4 27.7 0.5
P P:8GM5 2.5 24.5 0.5
CG A:ASP330 3.0 21.6 1.0
CG A:ASP332 3.2 18.2 1.0
CG A:ASP418 3.2 20.5 1.0
OD1 A:ASP330 3.3 19.6 1.0
PG A:8GT510 3.5 20.8 0.5
MN A:MN505 3.5 19.3 1.0
OD2 A:ASP332 3.6 18.4 1.0
OP2 P:8GM5 3.6 28.8 0.5
O5' P:8GM5 3.6 32.8 0.5
C3' P:DA4 3.6 25.2 0.5
O3G A:8GT510 3.8 21.0 0.5
C5' P:8GM5 3.9 30.6 0.5
C4' P:DA4 3.9 20.9 0.5
CB A:ASP418 3.9 18.1 1.0
C5' P:DA4 3.9 17.4 0.5
O1G A:8GT510 4.0 25.7 0.5
OD1 A:ASP418 4.2 21.7 1.0
CE1 A:HIS329 4.2 43.1 1.0
CB A:ASP330 4.4 21.4 1.0
CB A:ASP332 4.4 16.6 1.0
O5' P:DA4 4.5 19.1 0.5
NH2 A:ARG416 4.5 21.3 1.0
OP1 P:DA4 4.6 22.2 0.5
OP1 P:DA4 4.6 24.1 0.5
O2A A:8GT510 4.7 32.7 0.5
C2' P:DA4 4.8 21.5 0.5
O2B A:8GT510 4.8 19.1 0.5
CZ3 A:TRP434 4.9 36.0 1.0
O31 A:PPV512 4.9 21.2 0.5
O3B A:8GT510 4.9 24.6 0.5
NE2 A:HIS329 5.0 41.4 1.0

Manganese binding site 6 out of 7 in 6vfb

Go back to Manganese Binding Sites List in 6vfb
Manganese binding site 6 out of 7 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)


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-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn102

b:35.2
occ:0.26
 O3G A:8GT510 1.9 21.0 0.5
O3B A:8GT510 2.0 24.6 0.5
O31 A:PPV512 2.4 21.2 0.5
PG A:8GT510 2.5 20.8 0.5
OP2 P:8GM5 2.5 28.8 0.5
O8 P:8GM5 2.5 39.3 0.5
O1G A:8GT510 3.1 25.7 0.5
O5' P:8GM5 3.3 32.8 0.5
C4' A:8GT510 3.3 35.4 0.5
C5' A:8GT510 3.3 32.9 0.5
P P:8GM5 3.4 24.5 0.5
O A:HOH605 3.5 26.1 1.0
PB A:8GT510 3.5 25.1 0.5
C8 P:8GM5 3.6 36.3 0.5
O3' A:8GT510 3.7 43.6 0.5
P1 A:PPV512 3.7 21.0 0.5
O1B A:8GT510 3.9 25.3 0.5
O2G A:8GT510 3.9 18.9 0.5
O3A A:8GT510 3.9 28.3 0.5
C3' A:8GT510 3.9 38.8 0.5
O5' A:8GT510 4.1 38.4 0.5
N7 P:8GM5 4.1 36.5 0.5
O11 A:PPV512 4.1 23.0 0.5
OP1 P:8GM5 4.2 23.1 0.5
OPP A:PPV512 4.3 23.6 0.5
C3' P:8GM5 4.5 25.5 0.5
O2B A:8GT510 4.5 19.1 0.5
O4' A:8GT510 4.6 40.9 0.5
PA A:8GT510 4.6 37.4 0.5
O P:HOH201 4.6 29.0 1.0
C5' P:8GM5 4.6 30.6 0.5
O22 A:PPV512 4.6 33.7 0.5
CB A:LYS438 4.7 33.4 1.0
O2A A:8GT510 4.7 32.7 0.5
O3' P:DA4 4.8 27.7 0.5
N9 P:8GM5 4.8 32.2 0.5
O21 A:PPV512 4.9 19.2 0.5
P2 A:PPV512 4.9 25.6 0.5
CE1 A:HIS329 5.0 43.1 1.0
O4' P:DA4 5.0 23.7 0.5

Manganese binding site 7 out of 7 in 6vfb

Go back to Manganese Binding Sites List in 6vfb
Manganese binding site 7 out of 7 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)


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, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn101

b:80.9
occ:0.61
 N7 D:DG1 2.5 23.1 1.0
C8 D:DG1 3.5 24.0 1.0
C5 D:DG1 3.5 20.6 1.0
O6 D:DG1 3.5 24.1 1.0
C6 D:DG1 3.8 22.4 1.0
N4 D:DC2 4.1 26.6 1.0
O T:HOH210 4.1 43.6 1.0
NE A:ARG175 4.4 28.2 0.5
C4 D:DG1 4.6 20.4 1.0
N9 D:DG1 4.7 21.0 1.0
O A:HOH757 4.9 33.4 0.4
C4 D:DC2 4.9 23.5 1.0
O D:HOH211 4.9 43.1 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) To Be Published.
Page generated: Sun Oct 6 07:32:12 2024

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