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Manganese in PDB 6vf7: Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min)

Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min), PDB code: 6vf7 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) 35.04 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.159, 68.927, 110.446, 90, 90, 90
R / Rfree (%) 16.6 / 19.7

Other elements in 6vf7:

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 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-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) (pdb code 6vf7). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min), PDB code: 6vf7:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 6vf7

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Manganese binding site 1 out of 8 in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 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-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:29.9
occ:0.52
O2G A:8DG508 2.2 27.1 1.0
O A:HOH674 2.2 25.1 0.7
O A:HOH820 2.3 44.0 0.8
ND1 A:HIS329 2.5 43.4 1.0
O A:HOH646 2.8 25.9 0.7
CG A:HIS329 3.5 36.1 1.0
CE1 A:HIS329 3.5 45.3 1.0
PG A:8DG508 3.5 25.5 1.0
CB A:HIS329 3.7 26.6 1.0
O1G A:8DG508 3.8 27.0 1.0
O1A A:8DG508 4.2 25.4 1.0
O3B A:8DG508 4.4 22.5 1.0
O3G A:8DG508 4.5 26.4 1.0
NE2 A:HIS329 4.6 39.7 1.0
CD2 A:HIS329 4.6 37.7 1.0
O3A A:8DG508 4.7 23.5 1.0
PA A:8DG508 4.9 23.2 1.0
O A:HOH826 5.0 41.3 1.0

Manganese binding site 2 out of 8 in 6vf7

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Manganese binding site 2 out of 8 in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 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-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:26.9
occ:1.00
OD2 A:ASP330 2.1 26.0 1.0
OD2 A:ASP418 2.3 17.4 1.0
OD1 A:ASP332 2.3 17.4 1.0
O P:HOH101 2.5 21.4 1.0
O2A A:8DG508 2.6 17.8 1.0
O3' P:DA4 2.7 17.6 1.0
CG A:ASP330 3.1 22.0 1.0
CG A:ASP332 3.3 18.6 1.0
CG A:ASP418 3.3 19.2 1.0
OD1 A:ASP330 3.4 21.1 1.0
PA A:8DG508 3.5 23.2 1.0
OD2 A:ASP332 3.7 17.4 1.0
MN A:MN503 3.7 18.7 1.0
C3' P:DA4 3.8 17.1 1.0
O5' A:8DG508 3.8 18.9 1.0
O1A A:8DG508 3.9 25.4 1.0
CB A:ASP418 4.0 20.6 1.0
C5' P:DA4 4.0 23.4 1.0
C4' P:DA4 4.0 17.4 1.0
OD1 A:ASP418 4.3 18.7 1.0
O A:HOH646 4.4 25.9 0.7
C5' A:8DG508 4.4 16.8 1.0
CB A:ASP330 4.5 17.0 1.0
CZ3 A:TRP434 4.5 19.4 1.0
OP1 P:DA4 4.5 19.5 1.0
NH2 A:ARG416 4.5 18.6 1.0
CB A:ASP332 4.6 15.7 1.0
O5' P:DA4 4.7 21.6 1.0
O1G A:8DG508 4.8 27.0 1.0
O3A A:8DG508 5.0 23.5 1.0

Manganese binding site 3 out of 8 in 6vf7

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Manganese binding site 3 out of 8 in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 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-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:18.7
occ:1.00
O2A A:8DG508 2.0 17.8 1.0
OD1 A:ASP330 2.1 21.1 1.0
O2B A:8DG508 2.1 18.2 1.0
OD2 A:ASP332 2.1 17.4 1.0
O A:HOH635 2.2 21.7 1.0
O1G A:8DG508 2.2 27.0 1.0
CG A:ASP332 3.2 18.6 1.0
CG A:ASP330 3.2 22.0 1.0
PB A:8DG508 3.2 22.0 1.0
PA A:8DG508 3.3 23.2 1.0
PG A:8DG508 3.5 25.5 1.0
OD1 A:ASP332 3.5 17.4 1.0
O3A A:8DG508 3.6 23.5 1.0
OD2 A:ASP330 3.6 26.0 1.0
O3B A:8DG508 3.7 22.5 1.0
MN A:MN502 3.7 26.9 1.0
O A:ASP330 3.9 20.7 1.0
O3G A:8DG508 4.1 26.4 1.0
O A:HOH646 4.1 25.9 0.7
O A:HOH689 4.2 19.6 1.0
C A:ASP330 4.2 22.6 1.0
O A:HOH686 4.3 24.6 1.0
N A:GLY320 4.3 18.4 1.0
O5' A:8DG508 4.3 18.9 1.0
C5' A:8DG508 4.4 16.8 1.0
O1A A:8DG508 4.4 25.4 1.0
CB A:ASP330 4.5 17.0 1.0
CB A:ASP332 4.5 15.7 1.0
CA A:GLY319 4.5 21.4 1.0
O1B A:8DG508 4.6 21.8 1.0
N A:ASP330 4.6 19.5 1.0
O2G A:8DG508 4.7 27.1 1.0
CA A:ASP330 4.7 18.1 1.0
N A:ASP332 4.8 18.9 1.0
N A:VAL331 4.8 17.8 1.0
O P:HOH101 4.9 21.4 1.0
C A:VAL331 5.0 19.6 1.0

Manganese binding site 4 out of 8 in 6vf7

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Manganese binding site 4 out of 8 in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 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-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:16.6
occ:0.57
OE2 A:GLU386 2.1 31.5 1.0
O A:HOH734 2.1 23.2 0.9
O A:HOH810 2.2 24.9 0.9
O T:HOH202 2.2 23.7 1.0
OE1 A:GLU386 2.3 27.5 1.0
NE2 A:HIS459 2.4 30.4 1.0
CD A:GLU386 2.5 29.4 1.0
CD2 A:HIS459 3.1 35.2 1.0
CE1 A:HIS459 3.5 28.9 1.0
CG A:GLU386 4.0 36.9 1.0
O A:HOH655 4.1 29.2 1.0
OP1 T:DC8 4.2 29.6 1.0
O A:HOH812 4.2 41.9 1.0
CG A:HIS459 4.4 30.5 1.0
O A:HOH712 4.4 22.2 1.0
OE1 A:GLN426 4.5 23.9 1.0
ND1 A:HIS459 4.5 29.8 1.0
C5' T:DC8 4.5 19.3 1.0
CB A:GLU386 4.9 25.9 1.0

Manganese binding site 5 out of 8 in 6vf7

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Manganese binding site 5 out of 8 in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 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-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:33.4
occ:0.60
O A:HOH790 1.9 43.9 1.0
O D:HOH208 2.0 39.2 1.0
O A:HOH805 2.1 46.1 0.7
OP3 D:DG1 2.2 35.1 1.0
ND1 A:HIS208 2.2 35.1 1.0
O D:HOH202 2.4 31.6 0.4
CE1 A:HIS208 3.0 30.3 1.0
CG A:HIS208 3.3 30.8 1.0
P D:DG1 3.4 34.1 1.0
OP1 D:DG1 3.5 28.2 1.0
CB A:HIS208 3.7 28.0 1.0
O D:HOH209 4.0 42.5 1.0
OP2 D:DG1 4.1 31.4 1.0
NE2 A:HIS208 4.2 31.6 1.0
O D:HOH202 4.2 35.4 0.6
CD2 A:HIS208 4.3 33.6 1.0
O A:HOH837 4.4 48.1 1.0
O5' D:DG1 4.6 30.4 1.0
CA A:HIS208 4.6 26.2 1.0
C5' D:DG1 4.8 27.6 1.0

Manganese binding site 6 out of 8 in 6vf7

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Manganese binding site 6 out of 8 in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 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-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:47.6
occ:0.69
O A:HOH641 2.1 54.4 1.0
NE2 A:HIS219 2.3 58.6 1.0
CE1 A:HIS219 3.2 55.6 1.0
CD2 A:HIS219 3.3 43.1 1.0
ND1 A:HIS219 4.3 48.1 1.0
CG A:HIS219 4.4 45.9 1.0
CB A:GLU218 4.7 46.1 1.0

Manganese binding site 7 out of 8 in 6vf7

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Manganese binding site 7 out of 8 in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 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-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:54.3
occ:0.71
O T:HOH212 2.3 48.9 1.0
O T:HOH203 2.4 59.0 1.0
N7 T:DG2 2.6 38.8 1.0
C8 T:DG2 3.5 36.6 1.0
C5 T:DG2 3.7 32.5 1.0
O6 T:DG2 3.9 31.8 1.0
O T:HOH201 3.9 43.5 1.0
C6 T:DG2 4.2 31.2 1.0
OP2 T:DG2 4.2 55.5 1.0
O6 T:DG3 4.3 29.5 1.0
N9 T:DG2 4.8 35.2 1.0
O5' T:DC1 4.8 52.3 1.0
C4 T:DG2 4.9 30.7 1.0
C3' T:DC1 4.9 57.2 1.0
C6 T:DC1 5.0 56.5 1.0

Manganese binding site 8 out of 8 in 6vf7

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Manganese binding site 8 out of 8 in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min)


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, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn101

b:89.8
occ:0.94
O D:HOH212 2.4 55.7 1.0
N7 D:DG1 2.5 30.3 1.0
O D:HOH211 2.5 51.3 1.0
C8 D:DG1 3.3 28.9 1.0
C5 D:DG1 3.6 26.0 1.0
O6 D:DG1 3.9 28.2 1.0
C6 D:DG1 4.2 27.2 1.0
OP2 D:DG1 4.5 31.4 1.0
CG A:ARG175 4.5 30.2 1.0
N9 D:DG1 4.6 31.1 1.0
CD A:ARG175 4.7 43.4 1.0
C4 D:DG1 4.7 27.4 1.0
O A:HOH809 4.8 29.1 1.0
N4 D:DC2 4.9 29.5 1.0

Reference:

J.A.Jamsen, A.Sassa, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) To Be Published.
Page generated: Sun Oct 6 07:32:12 2024

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