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Manganese in PDB 6vf4: Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 Min)

Enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 Min), PDB code: 6vf4 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) 32.48 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.085, 68.757, 110.531, 90, 90, 90
R / Rfree (%) 16.8 / 19.2

Other elements in 6vf4:

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 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 Reaction State Ternary Complex, 50 Mm MN2+ (30 Min) (pdb code 6vf4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 Min), PDB code: 6vf4:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 6vf4

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Manganese binding site 1 out of 5 in the Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 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 Reaction State Ternary Complex, 50 Mm MN2+ (30 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:22.6
occ:1.00
 OD2 A:ASP330 1.7 27.6 1.0
OP1 P:8GM5 1.7 19.7 0.4
OD2 A:ASP418 2.1 20.8 1.0
OD1 A:ASP332 2.2 21.7 1.0
O P:HOH202 2.3 28.8 1.0
O1A A:8GT511 2.7 18.4 0.6
P P:8GM5 2.7 22.6 0.4
O3' P:DA4 2.8 24.7 0.6
O3' P:DA4 2.8 24.5 0.4
CG A:ASP330 2.8 27.5 1.0
CG A:ASP332 3.1 20.6 1.0
CG A:ASP418 3.2 21.1 1.0
OD1 A:ASP330 3.2 26.2 1.0
OD2 A:ASP332 3.5 20.1 1.0
PA A:8GT511 3.5 23.3 0.6
MN A:MN502 3.5 20.7 1.0
OP2 P:8GM5 3.7 23.7 0.4
O2A A:8GT511 3.8 25.1 0.6
CB A:ASP418 3.8 18.9 1.0
C3' P:DA4 3.9 24.6 0.6
C3' P:DA4 3.9 24.9 0.4
O5' A:8GT511 3.9 25.1 0.6
O5' P:8GM5 4.0 24.6 0.4
C5' P:DA4 4.0 23.3 0.4
C4' P:DA4 4.1 24.3 0.4
C5' P:DA4 4.1 23.7 0.6
OD1 A:ASP418 4.1 21.9 1.0
CB A:ASP330 4.2 24.6 1.0
C4' P:DA4 4.2 24.6 0.6
C5' P:8GM5 4.4 24.1 0.4
CB A:ASP332 4.4 18.0 1.0
C5' A:8GT511 4.5 24.9 0.6
OP1 P:DA4 4.5 23.9 0.6
NH2 A:ARG416 4.6 20.1 1.0
OP1 P:DA4 4.7 24.0 0.4
O3G A:8GT511 4.7 30.1 0.6
CZ3 A:TRP434 4.7 24.4 1.0
O5' P:DA4 4.8 24.1 0.4
O5' P:DA4 4.8 24.1 0.6
O A:VAL331 4.8 18.6 1.0
O32 A:PPV506 4.9 30.5 0.1
O21 A:PPV506 4.9 25.7 0.4
O3A A:8GT511 5.0 29.2 0.6

Manganese binding site 2 out of 5 in 6vf4

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Manganese binding site 2 out of 5 in the Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 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 Reaction State Ternary Complex, 50 Mm MN2+ (30 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:20.7
occ:1.00
 O1A A:8GT511 1.6 18.4 0.6
O A:HOH632 2.0 23.8 1.0
OD2 A:ASP332 2.1 20.1 1.0
OD1 A:ASP330 2.1 26.2 1.0
O32 A:PPV506 2.1 30.5 0.1
O1B A:8GT511 2.2 27.9 0.6
O21 A:PPV506 2.2 25.7 0.4
O3G A:8GT511 2.2 30.1 0.6
OP1 P:8GM5 2.6 19.7 0.4
PA A:8GT511 3.0 23.3 0.6
CG A:ASP332 3.1 20.6 1.0
CG A:ASP330 3.1 27.5 1.0
P1 A:PPV506 3.2 28.8 0.4
PB A:8GT511 3.2 28.3 0.6
O3A A:8GT511 3.4 29.2 0.6
O31 A:PPV506 3.4 30.4 0.4
P2 A:PPV506 3.4 33.2 0.1
OD1 A:ASP332 3.5 21.7 1.0
PG A:8GT511 3.5 32.7 0.6
MN A:MN501 3.5 22.6 1.0
OD2 A:ASP330 3.5 27.6 1.0
OPP A:PPV506 3.5 30.6 0.1
O3B A:8GT511 3.8 33.5 0.6
P P:8GM5 3.8 22.6 0.4
O2G A:8GT511 4.0 35.3 0.6
O A:ASP330 4.0 20.3 1.0
O5' P:8GM5 4.1 24.6 0.4
O5' A:8GT511 4.1 25.1 0.6
O2A A:8GT511 4.1 25.1 0.6
O A:HOH621 4.2 18.8 1.0
O12 A:PPV506 4.3 36.0 0.1
N A:GLY320 4.3 17.2 1.0
C5' A:8GT511 4.3 24.9 0.6
C A:ASP330 4.3 20.7 1.0
CB A:ASP332 4.4 18.0 1.0
CB A:ASP330 4.4 24.6 1.0
O A:HOH601 4.4 32.8 1.0
O22 A:PPV506 4.5 35.8 0.1
CA A:GLY319 4.5 16.4 1.0
C5' P:8GM5 4.5 24.1 0.4
O11 A:PPV506 4.5 31.3 0.4
O2B A:8GT511 4.6 30.5 0.6
O P:HOH202 4.6 28.8 1.0
O1G A:8GT511 4.6 37.0 0.6
OP2 P:8GM5 4.7 23.7 0.4
CA A:ASP330 4.7 22.8 1.0
N A:ASP330 4.7 23.8 1.0
N A:ASP332 4.8 15.8 1.0
N A:VAL331 4.9 18.4 1.0
O3' P:DA4 5.0 24.5 0.4
C A:GLY319 5.0 16.8 1.0
C A:VAL331 5.0 17.7 1.0

Manganese binding site 3 out of 5 in 6vf4

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Manganese binding site 3 out of 5 in the Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 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 Reaction State Ternary Complex, 50 Mm MN2+ (30 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:55.1
occ:0.57
 OP3 D:DG1 2.2 37.9 1.0
O A:HOH695 2.4 60.0 1.0
ND1 A:HIS208 2.4 34.8 1.0
CE1 A:HIS208 3.2 34.8 1.0
CG A:HIS208 3.4 33.4 1.0
P D:DG1 3.4 33.6 1.0
OP1 D:DG1 3.7 33.7 1.0
CB A:HIS208 3.8 29.4 1.0
O D:HOH107 3.9 48.4 1.0
O D:HOH104 4.1 51.0 1.0
OP2 D:DG1 4.1 35.1 1.0
NE2 A:HIS208 4.3 34.0 1.0
CD2 A:HIS208 4.4 33.7 1.0
NH2 A:ARG211 4.4 87.3 1.0
NH1 A:ARG211 4.6 88.7 1.0
O5' D:DG1 4.6 30.4 1.0
CA A:HIS208 4.7 29.1 1.0
C5' D:DG1 5.0 28.4 1.0

Manganese binding site 4 out of 5 in 6vf4

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Manganese binding site 4 out of 5 in the Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 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 Reaction State Ternary Complex, 50 Mm MN2+ (30 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:29.1
occ:0.57
 O A:HOH786 2.1 37.9 0.9
OE2 A:GLU386 2.2 36.1 1.0
O A:HOH761 2.2 35.0 0.9
NE2 A:HIS459 2.3 40.0 1.0
O T:HOH202 2.4 39.5 1.0
OE1 A:GLU386 2.7 42.9 1.0
CD A:GLU386 2.8 39.0 1.0
CD2 A:HIS459 3.1 39.8 1.0
CE1 A:HIS459 3.4 41.1 1.0
O A:HOH651 4.1 36.6 1.0
O A:HOH612 4.3 29.5 1.0
O A:HOH785 4.3 49.4 1.0
CG A:GLU386 4.3 36.7 1.0
OP1 T:DC8 4.3 30.5 1.0
CG A:HIS459 4.4 36.0 1.0
ND1 A:HIS459 4.5 39.2 1.0
OE1 A:GLN426 4.6 27.6 1.0
C5' T:DC8 4.6 25.0 1.0

Manganese binding site 5 out of 5 in 6vf4

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Manganese binding site 5 out of 5 in the Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 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 Reaction State Ternary Complex, 50 Mm MN2+ (30 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:70.0
occ:0.90
 O T:HOH201 2.4 51.6 1.0
O T:HOH203 2.4 42.7 0.8
N7 T:DG2 2.8 34.9 1.0
C8 T:DG2 3.6 34.5 1.0
O T:HOH206 3.8 39.7 1.0
C5 T:DG2 3.8 33.3 1.0
O6 T:DG2 4.0 31.7 1.0
C6 T:DG2 4.3 31.0 1.0
OP2 T:DG2 4.4 49.6 1.0
O6 T:DG3 4.4 27.6 1.0
N9 T:DG2 4.8 34.1 1.0
C2' T:DC1 4.9 48.0 1.0
C6 T:DC1 4.9 40.6 1.0
C4 T:DG2 5.0 32.5 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 Min) To Be Published.
Page generated: Sun Oct 6 07:30:45 2024

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