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

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

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

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min), PDB code: 6vfa 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) 34.96 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.079, 62.215, 118.925, 90, 90, 90
R / Rfree (%) 17.5 / 20.3

Other elements in 6vfa:

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

Manganese binding site 1 out of 8 in 6vfa

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

b:19.4
occ:1.00
 OD2 A:ASP330 2.1 21.4 1.0
OD1 A:ASP332 2.1 17.9 1.0
OD2 A:ASP418 2.2 19.5 1.0
O P:HOH106 2.3 19.9 1.0
O A:HOH785 2.3 21.5 1.0
O1G A:8GT508 2.3 17.8 1.0
CG A:ASP330 3.1 18.4 1.0
CG A:ASP332 3.2 20.5 1.0
CG A:ASP418 3.3 20.6 1.0
PG A:8GT508 3.4 21.6 1.0
OD1 A:ASP330 3.4 19.0 1.0
MN A:MN502 3.6 18.4 1.0
OD2 A:ASP332 3.6 18.8 1.0
O2G A:8GT508 3.7 24.1 1.0
CB A:ASP418 3.9 16.6 1.0
O3G A:8GT508 4.0 23.6 1.0
OD1 A:ASP418 4.2 18.6 1.0
CE1 A:HIS329 4.2 25.4 1.0
CB A:ASP332 4.4 15.6 1.0
CB A:ASP330 4.4 15.8 1.0
OP1 P:DA4 4.5 21.4 1.0
NH2 A:ARG416 4.6 18.1 1.0
O3B A:8GT508 4.8 21.5 1.0
NE2 A:HIS329 4.8 27.3 1.0
CZ3 A:TRP434 4.9 30.7 1.0

Manganese binding site 2 out of 8 in 6vfa

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

b:18.4
occ:1.00
 O1G A:8GT508 2.1 17.8 1.0
O2B A:8GT508 2.1 17.4 1.0
OD1 A:ASP330 2.1 19.0 1.0
OD2 A:ASP332 2.1 18.8 1.0
O A:HOH669 2.3 17.7 1.0
O2A A:8GT508 2.4 28.2 1.0
CG A:ASP332 3.1 20.5 1.0
CG A:ASP330 3.1 18.4 1.0
PB A:8GT508 3.2 20.7 1.0
PG A:8GT508 3.2 21.6 1.0
O3B A:8GT508 3.4 21.5 1.0
OD1 A:ASP332 3.4 17.9 1.0
OD2 A:ASP330 3.5 21.4 1.0
MN A:MN501 3.6 19.4 1.0
PA A:8GT508 3.7 31.9 1.0
O3A A:8GT508 3.8 25.2 1.0
O3G A:8GT508 3.9 23.6 1.0
O A:ASP330 4.1 19.2 1.0
ND1 A:HIS329 4.2 25.6 1.0
CE1 A:HIS329 4.2 25.4 1.0
O A:HOH645 4.3 18.8 1.0
N A:GLY320 4.3 19.7 1.0
C A:ASP330 4.3 18.7 1.0
O A:HOH777 4.3 23.6 1.0
CB A:ASP332 4.5 15.6 1.0
O2G A:8GT508 4.5 24.1 1.0
CB A:ASP330 4.5 15.8 1.0
CA A:GLY319 4.5 20.3 1.0
O1B A:8GT508 4.5 21.8 1.0
O1A A:8GT508 4.6 40.2 1.0
N A:ASP330 4.6 18.7 1.0
CA A:ASP330 4.7 17.4 1.0
O5' A:8GT508 4.8 44.6 1.0
N A:ASP332 4.8 15.7 1.0
N A:VAL331 4.9 18.3 1.0
O A:HOH785 4.9 21.5 1.0
O P:HOH106 4.9 19.9 1.0
C A:GLY319 5.0 17.9 1.0

Manganese binding site 3 out of 8 in 6vfa

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

b:37.4
occ:0.62
 O A:HOH816 1.9 37.3 0.8
O A:HOH742 2.0 38.9 0.8
NE2 A:HIS152 2.1 54.5 1.0
CE1 A:HIS152 2.9 54.4 1.0
O A:HOH616 3.2 51.3 1.0
CD2 A:HIS152 3.2 52.2 1.0
ND1 A:HIS152 4.1 54.0 1.0
CG A:HIS152 4.3 50.5 1.0
O A:PRO190 4.4 34.3 1.0
O A:HOH630 4.4 29.6 1.0
O A:THR150 4.5 27.3 1.0

Manganese binding site 4 out of 8 in 6vfa

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

b:31.2
occ:0.50
 O D:HOH212 2.0 38.3 1.0
OP3 D:DG1 2.1 35.9 1.0
O D:HOH215 2.2 44.4 1.0
O A:HOH795 2.3 45.6 1.0
ND1 A:HIS208 2.3 32.6 1.0
CE1 A:HIS208 3.2 33.9 1.0
CG A:HIS208 3.3 31.5 1.0
P D:DG1 3.4 30.4 1.0
OP1 D:DG1 3.7 28.2 1.0
CB A:HIS208 3.7 27.9 1.0
O D:HOH210 4.0 40.1 1.0
OP2 D:DG1 4.1 28.4 1.0
O D:HOH205 4.1 43.6 1.0
NE2 A:HIS208 4.3 32.8 1.0
CD2 A:HIS208 4.4 32.9 1.0
O5' D:DG1 4.5 25.8 1.0
CA A:HIS208 4.7 28.4 1.0
C5' D:DG1 4.8 25.8 1.0

Manganese binding site 5 out of 8 in 6vfa

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

b:83.1
occ:1.00
 NE2 A:HIS219 2.3 52.7 1.0
O A:HOH787 2.4 50.2 1.0
OE1 A:GLU218 3.0 62.2 1.0
CE1 A:HIS219 3.1 53.5 1.0
CD2 A:HIS219 3.4 52.1 1.0
CD A:GLU218 4.1 59.8 1.0
ND1 A:HIS219 4.3 53.8 1.0
CG A:HIS219 4.4 52.7 1.0
CB A:GLU218 4.7 47.3 1.0
OE2 A:GLU218 4.7 60.6 1.0
CG A:GLU218 5.0 54.0 1.0

Manganese binding site 6 out of 8 in 6vfa

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

b:36.9
occ:0.55
 O A:HOH809 2.0 42.3 0.8
O T:HOH201 2.2 42.2 1.0
OE2 A:GLU386 2.3 42.3 1.0
O A:HOH783 2.3 39.6 0.9
NE2 A:HIS459 2.5 43.9 1.0
CD A:GLU386 3.0 42.6 1.0
OE1 A:GLU386 3.0 45.3 1.0
CD2 A:HIS459 3.1 50.2 1.0
CE1 A:HIS459 3.7 44.0 1.0
OP1 T:DC8 4.1 37.9 1.0
O A:HOH684 4.3 31.2 1.0
CG A:HIS459 4.4 39.6 1.0
C5' T:DC8 4.4 32.6 1.0
CG A:GLU386 4.5 38.5 1.0
O A:HOH723 4.5 41.2 1.0
OE1 A:GLN426 4.6 30.4 1.0
ND1 A:HIS459 4.6 43.1 1.0
O A:HOH789 4.9 45.1 1.0
O5' T:DC8 5.0 33.9 1.0

Manganese binding site 7 out of 8 in 6vfa

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

b:55.5
occ:0.79
 O T:HOH226 2.1 55.0 1.0
N7 T:DG2 2.3 30.0 1.0
O T:HOH203 2.3 36.8 0.9
O T:HOH210 2.6 49.5 1.0
C8 T:DG2 3.2 26.9 1.0
C5 T:DG2 3.4 25.4 1.0
O6 T:DG2 3.7 26.1 1.0
C6 T:DG2 3.9 24.4 1.0
O T:HOH215 4.0 48.4 1.0
O6 T:DG3 4.3 27.6 1.0
N9 T:DG2 4.4 25.6 1.0
C4 T:DG2 4.5 23.2 1.0
OP2 T:DG2 4.8 45.1 1.0

Manganese binding site 8 out of 8 in 6vfa

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

b:84.6
occ:0.98
 N7 D:DG1 2.2 22.2 1.0
O D:HOH217 2.5 40.7 1.0
O D:HOH201 3.0 44.7 1.0
C8 D:DG1 3.1 22.4 1.0
C5 D:DG1 3.2 22.6 1.0
O6 D:DG1 3.5 22.5 1.0
C6 D:DG1 3.8 22.8 1.0
N4 D:DC2 4.2 23.7 1.0
N9 D:DG1 4.3 22.5 1.0
C4 D:DG1 4.4 20.3 1.0
O D:HOH208 4.4 42.8 1.0
O T:HOH203 4.6 36.8 0.9
OP2 D:DG1 4.8 28.4 1.0
CG A:ARG175 4.8 24.8 1.0
O A:HOH804 4.8 32.5 1.0
C4 D:DC2 4.9 24.8 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:Ct 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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