Manganese in PDB 6vf5: Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MN2+ (120 Min)

Enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MN2+ (120 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MN2+ (120 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MN2+ (120 Min), PDB code: 6vf5 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) 40.62 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.982, 68.718, 110.413, 90, 90, 90
R / Rfree (%) 16.5 / 19.1

Other elements in 6vf5:

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MN2+ (120 Min) 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-Oxorgtp:at Product State Ternary Complex, 50 Mm MN2+ (120 Min) (pdb code 6vf5). 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-Oxorgtp:at Product State Ternary Complex, 50 Mm MN2+ (120 Min), PDB code: 6vf5:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 6vf5

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Manganese binding site 1 out of 7 in the Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MN2+ (120 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 Product State Ternary Complex, 50 Mm MN2+ (120 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:14.4
occ:1.00
 OD2 A:ASP330 2.1 13.7 0.7
OD2 A:ASP332 2.1 14.2 1.0
O3 A:OXL513 2.2 13.0 1.0
O A:HOH633 2.2 16.1 1.0
O4 A:OXL513 2.2 18.2 1.0
OP1 P:8GM5 2.3 16.7 1.0
OD1 A:ASP330 2.4 12.5 0.3
CG A:ASP330 2.9 15.4 0.7
C1 A:OXL513 3.0 17.8 1.0
C2 A:OXL513 3.0 25.9 1.0
CG A:ASP332 3.1 14.9 1.0
OD1 A:ASP330 3.2 17.7 0.7
CG A:ASP330 3.3 19.1 0.3
MN A:MN502 3.3 15.8 1.0
OD1 A:ASP332 3.4 14.5 1.0
P P:8GM5 3.5 15.9 1.0
OD2 A:ASP330 3.6 15.3 0.3
O5' P:8GM5 3.7 14.1 1.0
O A:ASP330 4.1 13.2 0.7
C5' P:8GM5 4.1 17.8 1.0
O P:HOH101 4.1 24.7 1.0
O A:HOH828 4.1 18.7 1.0
OP2 P:8GM5 4.2 16.7 0.9
O2 A:OXL513 4.2 40.9 1.0
O1 A:OXL513 4.2 18.4 1.0
O A:HOH601 4.3 16.2 1.0
O A:HOH613 4.3 14.8 1.0
CB A:ASP330 4.3 15.9 0.7
N A:GLY320 4.4 11.9 1.0
CA A:GLY319 4.4 13.5 1.0
CB A:ASP332 4.4 12.0 1.0
C A:ASP330 4.5 13.2 0.7
O A:HOH729 4.5 24.1 1.0
O A:ASP330 4.6 13.1 0.3
CB A:ASP330 4.7 13.9 0.3
O3' P:DA4 4.7 15.3 1.0
C A:ASP330 4.7 13.3 0.3
O A:HOH758 4.9 13.9 0.7
N A:ASP332 5.0 12.6 1.0
CA A:ASP330 5.0 13.6 0.7
C A:GLY319 5.0 13.0 1.0

Manganese binding site 2 out of 7 in 6vf5

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Manganese binding site 2 out of 7 in the Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MN2+ (120 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 Product State Ternary Complex, 50 Mm MN2+ (120 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:15.8
occ:1.00
 OD2 A:ASP330 1.5 15.3 0.3
OD1 A:ASP332 2.1 14.5 1.0
OD2 A:ASP418 2.1 14.9 1.0
OP1 P:8GM5 2.1 16.7 1.0
O A:HOH601 2.2 16.2 1.0
OD2 A:ASP330 2.2 13.7 0.7
O A:HOH758 2.4 13.9 0.7
CG A:ASP330 2.6 19.1 0.3
OD1 A:ASP330 3.0 12.5 0.3
CG A:ASP418 3.0 16.2 1.0
CG A:ASP332 3.1 14.9 1.0
CG A:ASP330 3.2 15.4 0.7
P P:8GM5 3.2 15.9 1.0
MN A:MN501 3.3 14.4 1.0
O3' P:DA4 3.5 15.3 1.0
OD2 A:ASP332 3.5 14.2 1.0
CB A:ASP330 3.8 15.9 0.7
OD1 A:ASP418 3.8 16.0 1.0
CB A:ASP418 3.8 14.2 1.0
CB A:ASP330 3.9 13.9 0.3
OP2 P:8GM5 4.0 16.7 0.9
OD1 A:ASP330 4.2 17.7 0.7
O P:HOH101 4.2 24.7 1.0
C5' P:DA4 4.3 16.5 1.0
O A:VAL331 4.4 14.0 1.0
CB A:ASP332 4.4 12.0 1.0
NH2 A:ARG416 4.4 17.1 1.0
O4 A:OXL513 4.5 18.2 1.0
C3' P:DA4 4.5 15.9 1.0
O5' P:8GM5 4.5 14.1 1.0
OP1 P:DA4 4.6 17.0 1.0
C4' P:DA4 4.6 14.4 1.0
C A:VAL331 4.7 14.0 1.0
N A:ASP418 4.7 13.9 1.0
N A:VAL331 4.8 14.4 1.0
CA A:ASP332 4.9 12.4 1.0
CA A:ASP418 4.9 14.1 1.0
C A:ASP330 4.9 13.2 0.7
O A:HOH633 4.9 16.1 1.0
N A:ASP332 4.9 12.6 1.0
CA A:ASP330 5.0 13.6 0.7

Manganese binding site 3 out of 7 in 6vf5

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Manganese binding site 3 out of 7 in the Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MN2+ (120 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 Product State Ternary Complex, 50 Mm MN2+ (120 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:30.0
occ:0.62
 O D:HOH201 1.4 30.4 0.8
O D:HOH213 1.8 35.5 1.0
OP3 D:DG1 2.1 33.2 1.0
ND1 A:HIS208 2.2 34.9 1.0
O A:HOH809 2.3 35.9 0.7
CE1 A:HIS208 3.0 33.7 1.0
CG A:HIS208 3.3 28.7 1.0
P D:DG1 3.3 28.8 1.0
OP1 D:DG1 3.5 29.2 1.0
CB A:HIS208 3.7 24.8 1.0
O D:HOH217 3.8 41.2 1.0
OP2 D:DG1 4.1 30.6 1.0
NE2 A:HIS208 4.2 33.3 1.0
CD2 A:HIS208 4.3 33.7 1.0
O D:HOH205 4.4 49.9 1.0
O5' D:DG1 4.5 25.9 1.0
CA A:HIS208 4.6 23.9 1.0
C5' D:DG1 4.8 24.8 1.0

Manganese binding site 4 out of 7 in 6vf5

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Manganese binding site 4 out of 7 in the Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MN2+ (120 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 Product State Ternary Complex, 50 Mm MN2+ (120 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:55.9
occ:0.91
 NE2 A:HIS219 2.2 43.0 1.0
O A:HOH786 2.3 54.0 0.8
O A:HOH793 2.3 44.9 0.8
O A:HOH823 2.4 43.7 0.8
CE1 A:HIS219 3.2 44.9 1.0
CD2 A:HIS219 3.2 39.9 1.0
ND1 A:HIS219 4.3 39.1 1.0
CG A:HIS219 4.3 40.3 1.0
CB A:GLU218 4.8 37.2 1.0

Manganese binding site 5 out of 7 in 6vf5

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Manganese binding site 5 out of 7 in the Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MN2+ (120 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 Product State Ternary Complex, 50 Mm MN2+ (120 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:19.5
occ:0.74
 O A:HOH743 2.2 22.2 0.8
O A:HOH819 2.2 24.3 0.8
OE2 A:GLU386 2.2 27.5 1.0
NE2 A:HIS459 2.2 23.7 1.0
O T:HOH205 2.3 25.1 0.9
OE1 A:GLU386 2.6 38.9 1.0
CD A:GLU386 2.8 28.1 1.0
CD2 A:HIS459 3.1 24.0 1.0
CE1 A:HIS459 3.3 26.2 1.0
O A:HOH661 4.3 28.5 1.0
OP1 T:DC8 4.3 25.4 1.0
CG A:GLU386 4.3 29.1 1.0
CG A:HIS459 4.3 21.3 1.0
ND1 A:HIS459 4.4 25.9 1.0
O A:HOH617 4.4 20.8 1.0
O A:HOH831 4.4 38.1 1.0
OE1 A:GLN426 4.5 23.5 1.0
C5' T:DC8 4.5 20.7 1.0

Manganese binding site 6 out of 7 in 6vf5

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Manganese binding site 6 out of 7 in the Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MN2+ (120 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 Product State Ternary Complex, 50 Mm MN2+ (120 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:48.0
occ:0.72
 O T:HOH201 2.3 35.7 0.9
O T:HOH203 2.5 37.9 0.9
N7 T:DG2 2.7 28.9 1.0
C8 T:DG2 3.5 31.5 1.0
O T:HOH204 3.6 36.0 1.0
C5 T:DG2 3.8 27.0 1.0
O6 T:DG2 4.1 26.8 1.0
OP2 T:DG2 4.2 42.1 1.0
C6 T:DG2 4.3 24.3 1.0
O6 T:DG3 4.4 25.0 1.0
O D:HOH211 4.6 46.7 1.0
N9 T:DG2 4.8 30.2 1.0
O5' T:DC1 4.8 47.8 1.0
C6 T:DC1 4.9 38.8 1.0
C3' T:DC1 4.9 40.6 1.0
C4 T:DG2 4.9 24.9 1.0

Manganese binding site 7 out of 7 in 6vf5

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Manganese binding site 7 out of 7 in the Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MN2+ (120 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 Product State Ternary Complex, 50 Mm MN2+ (120 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn101

b:62.0
occ:0.61
 N7 D:DG1 2.4 24.3 1.0
O D:HOH216 2.7 43.4 1.0
O D:HOH211 2.7 46.7 1.0
C8 D:DG1 3.2 25.6 1.0
C5 D:DG1 3.5 21.9 1.0
O6 D:DG1 3.9 24.6 1.0
C6 D:DG1 4.1 23.4 1.0
O D:HOH208 4.3 46.8 1.0
OP2 D:DG1 4.4 30.6 1.0
N9 D:DG1 4.5 24.8 1.0
N4 D:DC2 4.6 26.2 1.0
C4 D:DG1 4.6 21.2 1.0
CG A:ARG175 4.7 23.7 1.0
CD A:ARG175 4.8 36.6 1.0
CL A:CL507 4.9 46.8 0.9

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MN2+ (120 Min) To Be Published.
Page generated: Fri Sep 24 16:03:06 2021

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