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Manganese in PDB 6vf3: Dna Polymerase Mu, 8-Oxorgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min)

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

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

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min), PDB code: 6vf3 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) 33.39 / 1.52
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.198, 62.385, 118.58, 90, 90, 90
R / Rfree (%) 16.3 / 18

Other elements in 6vf3:

The structure of Dna Polymerase Mu, 8-Oxorgtp: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-Oxorgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) (pdb code 6vf3). 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-Oxorgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min), PDB code: 6vf3:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 6vf3

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Manganese binding site 1 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp: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-Oxorgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn507

b:18.3
occ:1.00
 OD1 A:ASP330 2.1 19.7 1.0
O1A A:8GT506 2.1 20.4 1.0
O2B A:8GT506 2.1 19.3 1.0
OD2 A:ASP332 2.2 18.3 1.0
O A:HOH692 2.2 18.6 1.0
O2G A:8GT506 2.3 28.5 1.0
CG A:ASP332 3.1 16.8 1.0
CG A:ASP330 3.1 20.0 1.0
PB A:8GT506 3.2 22.8 1.0
PA A:8GT506 3.3 23.8 1.0
OD1 A:ASP332 3.5 18.7 1.0
O3A A:8GT506 3.5 22.9 1.0
PG A:8GT506 3.5 28.1 1.0
OD2 A:ASP330 3.5 21.5 1.0
MN A:MN508 3.6 18.4 1.0
O3B A:8GT506 3.7 25.7 1.0
O A:ASP330 4.0 18.7 1.0
O3G A:8GT506 4.2 32.7 1.0
O A:HOH654 4.2 17.6 1.0
ND1 A:HIS329 4.3 32.2 1.0
C A:ASP330 4.3 18.9 1.0
O5' A:8GT506 4.3 31.2 1.0
N A:GLY320 4.3 16.5 1.0
O A:HOH646 4.3 24.1 1.0
CE1 A:HIS329 4.3 33.6 1.0
C5' A:8GT506 4.4 48.7 1.0
O2A A:8GT506 4.4 27.2 1.0
CB A:ASP330 4.5 18.6 1.0
CB A:ASP332 4.5 14.8 1.0
CA A:GLY319 4.5 15.6 1.0
O1B A:8GT506 4.6 26.7 1.0
N A:ASP330 4.6 18.2 1.0
CA A:ASP330 4.7 16.8 1.0
O1G A:8GT506 4.7 34.6 1.0
O P:HOH101 4.7 22.6 1.0
N A:ASP332 4.8 15.6 1.0
N A:VAL331 4.9 17.8 1.0

Manganese binding site 2 out of 8 in 6vf3

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Manganese binding site 2 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp: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-Oxorgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn508

b:18.4
occ:1.00
 OD2 A:ASP330 2.0 21.5 1.0
O P:HOH101 2.1 22.6 1.0
OD1 A:ASP332 2.1 18.7 1.0
OD2 A:ASP418 2.1 21.4 1.0
O A:HOH711 2.3 16.3 0.5
O1A A:8GT506 2.4 20.4 1.0
O3' P:DA4 2.6 30.9 0.5
CG A:ASP330 3.0 20.0 1.0
CG A:ASP332 3.2 16.8 1.0
CG A:ASP418 3.3 20.9 1.0
OD1 A:ASP330 3.4 19.7 1.0
PA A:8GT506 3.4 23.8 1.0
OD2 A:ASP332 3.6 18.3 1.0
MN A:MN507 3.6 18.3 1.0
O5' A:8GT506 3.7 31.2 1.0
C3' P:DA4 3.7 20.9 0.5
C5' P:DA4 3.9 14.6 0.5
CB A:ASP418 3.9 17.4 1.0
O2A A:8GT506 3.9 27.2 1.0
C4' P:DA4 4.0 15.6 0.5
C5' A:8GT506 4.0 48.7 1.0
OD1 A:ASP418 4.2 19.0 1.0
CE1 A:HIS329 4.2 33.6 1.0
OP1 P:DA4 4.3 16.3 0.5
CB A:ASP330 4.4 18.6 1.0
CB A:ASP332 4.4 14.8 1.0
OP1 P:DA4 4.5 31.3 0.5
O5' P:DA4 4.5 18.1 0.5
NH2 A:ARG416 4.5 19.9 1.0
CZ3 A:TRP434 4.8 27.7 1.0
O3A A:8GT506 4.9 22.9 1.0
NE2 A:HIS329 4.9 32.1 1.0
C2' P:DA4 5.0 19.3 0.5

Manganese binding site 3 out of 8 in 6vf3

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Manganese binding site 3 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp: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-Oxorgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn509

b:71.9
occ:0.82
 NE2 A:HIS219 2.2 63.7 1.0
CE1 A:HIS219 3.1 55.0 1.0
CD2 A:HIS219 3.2 58.1 1.0
CD A:GLU218 3.5 52.1 1.0
ND1 A:HIS219 4.2 58.9 1.0
CG A:HIS219 4.3 54.5 1.0
CB A:GLU218 4.4 35.1 1.0
CG A:GLU218 4.6 48.9 1.0

Manganese binding site 4 out of 8 in 6vf3

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Manganese binding site 4 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp: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-Oxorgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn510

b:25.8
occ:0.49
 O A:HOH819 2.0 38.1 0.7
O T:HOH205 2.0 36.0 0.7
OE2 A:GLU386 2.2 30.0 1.0
O A:HOH795 2.4 30.0 0.7
NE2 A:HIS459 2.4 46.5 1.0
CD A:GLU386 2.9 33.1 1.0
OE1 A:GLU386 3.0 47.3 1.0
CD2 A:HIS459 3.2 44.0 1.0
CE1 A:HIS459 3.5 45.9 1.0
OP1 T:DC8 4.1 31.9 1.0
O A:HOH677 4.3 35.1 1.0
O A:HOH695 4.3 25.8 1.0
CG A:GLU386 4.4 30.9 1.0
CG A:HIS459 4.4 27.7 1.0
C5' T:DC8 4.4 27.6 1.0
ND1 A:HIS459 4.5 44.7 1.0
OE1 A:GLN426 4.7 28.7 1.0

Manganese binding site 5 out of 8 in 6vf3

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Manganese binding site 5 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp: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-Oxorgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn511

b:32.9
occ:0.32
 OP3 D:DG1 2.1 29.8 1.0
ND1 A:HIS208 2.6 31.0 1.0
O D:HOH215 2.6 36.2 0.7
P D:DG1 3.4 26.6 1.0
CE1 A:HIS208 3.4 31.5 1.0
CG A:HIS208 3.4 28.6 1.0
O D:HOH211 3.7 41.8 1.0
CB A:HIS208 3.7 25.5 1.0
OP1 D:DG1 3.8 27.9 1.0
OP2 D:DG1 4.0 28.5 1.0
O A:HOH835 4.3 53.5 1.0
NE2 A:HIS208 4.4 29.4 1.0
CD2 A:HIS208 4.4 35.5 1.0
O5' D:DG1 4.6 23.9 1.0
CA A:HIS208 4.7 25.2 1.0
C5' D:DG1 5.0 24.1 1.0

Manganese binding site 6 out of 8 in 6vf3

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Manganese binding site 6 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp: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-Oxorgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn512

b:46.9
occ:0.50
 O A:HOH802 1.9 45.7 0.7
NE2 A:HIS152 2.3 49.8 1.0
O A:HOH607 2.7 37.3 0.6
CD2 A:HIS152 3.2 51.1 1.0
CE1 A:HIS152 3.4 53.0 1.0
O A:HOH651 4.4 32.8 1.0
CG A:HIS152 4.4 50.6 1.0
O A:HOH607 4.4 30.7 0.4
ND1 A:HIS152 4.4 50.9 1.0
O A:PRO190 4.5 37.2 1.0
O A:THR150 4.6 29.4 1.0

Manganese binding site 7 out of 8 in 6vf3

Go back to Manganese Binding Sites List in 6vf3
Manganese binding site 7 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp: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-Oxorgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:36.0
occ:0.38
 N7 T:DG2 2.2 27.6 0.4
N7 T:DG2 2.3 27.4 0.6
O T:HOH210 2.4 39.3 1.0
O T:HOH201 2.8 40.1 1.0
C8 T:DG2 3.1 28.4 0.6
C8 T:DG2 3.1 27.0 0.4
C5 T:DG2 3.2 23.0 0.4
C5 T:DG2 3.4 22.4 0.6
O6 T:DG2 3.6 24.5 0.4
C6 T:DG2 3.8 22.7 0.4
O6 T:DG2 3.9 21.0 0.6
C6 T:DG2 4.0 22.0 0.6
O T:HOH220 4.0 43.3 1.0
N9 T:DG2 4.3 23.6 0.4
N9 T:DG2 4.3 23.0 0.6
C4 T:DG2 4.3 20.6 0.4
O6 T:DG3 4.4 23.3 1.0
C4 T:DG2 4.4 23.0 0.6
OP2 T:DG2 4.5 27.2 0.6
C6 T:DC1 4.9 21.5 0.5
C5 T:DC1 4.9 18.8 0.5

Manganese binding site 8 out of 8 in 6vf3

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

b:73.0
occ:0.60
 N7 D:DG1 2.4 22.5 1.0
O D:HOH206 2.9 41.5 1.0
O D:HOH216 3.1 48.6 1.0
C8 D:DG1 3.3 22.6 1.0
C5 D:DG1 3.5 19.2 1.0
O6 D:DG1 3.8 24.0 1.0
C6 D:DG1 4.0 20.7 1.0
N4 D:DC2 4.1 24.4 1.0
O T:HOH210 4.4 39.3 1.0
N9 D:DG1 4.5 20.4 1.0
O D:HOH210 4.6 45.5 1.0
C4 D:DG1 4.6 20.0 1.0
OP2 D:DG1 4.8 28.5 1.0
C4 D:DC2 4.8 23.8 1.0
C5 D:DC2 5.0 23.0 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) To Be Published.
Page generated: Sun Oct 6 07:30:42 2024

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