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Manganese in PDB 7kt5: Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)

Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN), PDB code: 7kt5 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) 34.93 / 1.46
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.996, 68.701, 110.125, 90, 90, 90
R / Rfree (%) 16.2 / 18.3

Other elements in 7kt5:

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN) also contains other interesting chemical elements:

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

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN) (pdb code 7kt5). 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-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN), PDB code: 7kt5:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 7kt5

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Manganese binding site 1 out of 7 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)


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 Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:13.8
occ:1.00
 O A:HOH621 2.0 15.4 1.0
OD2 A:ASP330 2.1 13.7 0.5
OD2 A:ASP332 2.1 13.5 1.0
O12 A:GOA514 2.1 14.0 1.0
O2 A:GOA514 2.2 15.3 0.9
OP1 P:8OG5 2.3 16.6 1.0
OD1 A:ASP330 2.3 14.7 0.5
CG A:ASP330 3.0 15.3 0.5
C1 A:GOA514 3.0 12.1 1.0
CG A:ASP332 3.1 13.3 1.0
C2 A:GOA514 3.1 15.4 0.9
OD1 A:ASP330 3.3 13.8 0.5
MN A:MN502 3.3 14.9 0.9
CG A:ASP330 3.4 17.6 0.5
OD1 A:ASP332 3.4 15.0 1.0
P P:8OG5 3.5 16.0 1.0
O5' P:8OG5 3.8 12.1 1.0
OD2 A:ASP330 3.9 22.0 0.5
O A:ASP330 3.9 14.4 0.5
C5' P:8OG5 4.1 14.2 1.0
O A:HOH851 4.1 19.2 1.0
O P:HOH101 4.2 25.0 1.0
OP2 P:8OG5 4.2 16.6 1.0
O A:HOH669 4.3 17.6 1.0
O11 A:GOA514 4.3 15.1 1.0
CB A:ASP330 4.3 16.2 0.5
O A:HOH632 4.4 15.1 1.0
N A:GLY320 4.4 11.8 1.0
C A:ASP330 4.4 14.3 0.5
O A:ASP330 4.5 13.7 0.5
CB A:ASP332 4.5 12.5 1.0
CA A:GLY319 4.5 12.0 1.0
O A:HOH660 4.5 26.2 1.0
CB A:ASP330 4.6 16.6 0.5
C A:ASP330 4.6 14.4 0.5
O3' P:DA4 4.7 13.5 1.0
N A:ASP332 5.0 13.2 1.0
O A:HOH773 5.0 12.1 0.5
CA A:ASP330 5.0 15.7 0.5

Manganese binding site 2 out of 7 in 7kt5

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Manganese binding site 2 out of 7 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)


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 Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:14.9
occ:0.92
 OD2 A:ASP330 1.8 22.0 0.5
OP1 P:8OG5 2.1 16.6 1.0
OD2 A:ASP418 2.1 13.9 1.0
OD1 A:ASP332 2.1 15.0 1.0
O A:HOH669 2.2 17.6 1.0
OD2 A:ASP330 2.3 13.7 0.5
O A:HOH773 2.5 12.1 0.5
CG A:ASP330 2.5 17.6 0.5
OD1 A:ASP330 2.7 14.7 0.5
CG A:ASP418 3.1 14.7 1.0
CG A:ASP332 3.1 13.3 1.0
P P:8OG5 3.2 16.0 1.0
O3' P:DA4 3.3 13.5 1.0
CG A:ASP330 3.3 15.3 0.5
MN A:MN501 3.3 13.8 1.0
OD2 A:ASP332 3.5 13.5 1.0
CB A:ASP418 3.9 13.8 1.0
CB A:ASP330 3.9 16.2 0.5
OD1 A:ASP418 3.9 15.8 1.0
CB A:ASP330 3.9 16.6 0.5
OP2 P:8OG5 3.9 16.6 1.0
O P:HOH101 4.2 25.0 1.0
OD1 A:ASP330 4.3 13.8 0.5
C5' P:DA4 4.3 14.9 1.0
C3' P:DA4 4.4 14.2 1.0
O A:VAL331 4.4 14.3 1.0
NH2 A:ARG416 4.4 16.9 1.0
CB A:ASP332 4.5 12.5 1.0
O5' P:8OG5 4.5 12.1 1.0
C4' P:DA4 4.5 13.0 1.0
O2 A:GOA514 4.5 15.3 0.9
OP1 P:DA4 4.6 16.7 1.0
C A:VAL331 4.8 14.0 1.0
N A:ASP418 4.8 13.4 1.0
O A:HOH621 4.9 15.4 1.0
C5' P:8OG5 4.9 14.2 1.0
CA A:ASP418 4.9 14.1 1.0
CA A:ASP332 4.9 11.9 1.0
N A:VAL331 5.0 14.6 1.0
C A:ASP330 5.0 14.3 0.5
CZ3 A:TRP434 5.0 14.5 1.0

Manganese binding site 3 out of 7 in 7kt5

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Manganese binding site 3 out of 7 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)


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 Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:19.9
occ:0.81
 OE2 A:GLU386 2.1 26.2 1.0
O T:HOH205 2.2 24.0 1.0
O A:HOH734 2.2 24.5 1.0
O A:HOH841 2.2 26.7 1.0
NE2 A:HIS459 2.3 21.9 1.0
OE1 A:GLU386 2.3 23.3 1.0
CD A:GLU386 2.5 26.5 1.0
CD2 A:HIS459 3.2 20.7 1.0
CE1 A:HIS459 3.3 20.4 1.0
CG A:GLU386 4.0 32.1 1.0
O A:HOH706 4.2 26.5 1.0
O A:HOH830 4.2 42.2 1.0
OP1 T:DC8 4.3 23.4 1.0
CG A:HIS459 4.3 19.6 1.0
O A:HOH848 4.4 39.8 1.0
ND1 A:HIS459 4.4 20.7 1.0
O A:HOH646 4.4 21.1 1.0
OE1 A:GLN426 4.5 23.2 1.0
C5' T:DC8 4.6 20.4 1.0
CB A:GLU386 4.9 24.6 1.0

Manganese binding site 4 out of 7 in 7kt5

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Manganese binding site 4 out of 7 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)


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 Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:52.1
occ:0.81
 O A:HOH843 2.2 55.7 0.7
O A:HOH782 2.2 49.5 1.0
O A:HOH774 2.2 59.6 1.0
NE2 A:HIS219 2.2 45.9 1.0
CE1 A:HIS219 3.2 47.4 1.0
CD2 A:HIS219 3.2 43.1 1.0
ND1 A:HIS219 4.3 44.0 1.0
CG A:HIS219 4.4 40.6 1.0
CB A:GLU218 4.7 34.9 1.0

Manganese binding site 5 out of 7 in 7kt5

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Manganese binding site 5 out of 7 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)


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-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:30.1
occ:0.67
 O D:HOH216 1.9 36.1 0.8
O D:HOH217 2.1 35.0 0.8
OP3 D:DG1 2.2 29.5 1.0
O D:HOH207 2.2 32.1 0.8
O A:HOH832 2.2 42.8 0.8
ND1 A:HIS208 2.3 31.8 1.0
CE1 A:HIS208 3.1 30.7 1.0
CG A:HIS208 3.4 28.3 1.0
P D:DG1 3.4 28.5 1.0
OP1 D:DG1 3.6 30.2 1.0
O D:HOH213 3.7 44.4 1.0
CB A:HIS208 3.7 25.0 1.0
O A:HOH866 4.1 45.4 1.0
OP2 D:DG1 4.1 30.4 1.0
O D:HOH206 4.2 46.2 1.0
NE2 A:HIS208 4.3 30.2 1.0
CD2 A:HIS208 4.4 30.4 1.0
O5' D:DG1 4.5 24.2 1.0
CA A:HIS208 4.6 24.8 1.0
C5' D:DG1 4.8 23.3 1.0

Manganese binding site 6 out of 7 in 7kt5

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Manganese binding site 6 out of 7 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)


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-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:38.7
occ:0.58
 O T:HOH201 2.2 40.4 1.0
O T:HOH204 2.3 49.7 0.8
O T:HOH202 2.4 44.5 0.9
N7 T:DG2 2.6 30.7 1.0
C8 T:DG2 3.4 29.1 1.0
O T:HOH203 3.6 37.6 1.0
C5 T:DG2 3.7 27.4 1.0
O6 T:DG2 4.1 27.9 1.0
OP2 T:DG2 4.1 44.8 1.0
C6 T:DG2 4.3 26.3 1.0
O6 T:DG3 4.4 23.7 1.0
O D:HOH208 4.5 52.2 1.0
N9 T:DG2 4.7 28.8 1.0
C4 T:DG2 4.8 26.6 1.0
O5' T:DC1 4.9 42.4 1.0
C6 T:DC1 4.9 35.5 1.0
C2' T:DC1 4.9 42.4 1.0
C3' T:DC1 5.0 43.1 1.0

Manganese binding site 7 out of 7 in 7kt5

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Manganese binding site 7 out of 7 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)


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-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn101

b:53.1
occ:0.53
 N7 D:DG1 2.3 23.2 1.0
O D:HOH208 2.8 52.2 1.0
C8 D:DG1 3.1 23.2 1.0
C5 D:DG1 3.5 21.5 1.0
O6 D:DG1 3.8 23.8 1.0
C6 D:DG1 4.0 21.4 1.0
N9 D:DG1 4.4 22.2 1.0
OP2 D:DG1 4.5 30.4 1.0
N4 D:DC2 4.5 25.4 1.0
C4 D:DG1 4.6 20.6 1.0
CG A:ARG175 4.8 24.7 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN) To Be Published.
Page generated: Sun Oct 6 09:28:26 2024

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