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Manganese in PDB 7kt2: Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN)

Enzymatic activity of Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN)

All present enzymatic activity of Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN), PDB code: 7kt2 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 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.893, 68.866, 110.319, 90, 90, 90
R / Rfree (%) 16.8 / 18.9

Other elements in 7kt2:

The structure of Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN) (pdb code 7kt2). 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, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN), PDB code: 7kt2:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 7kt2

Go back to Manganese Binding Sites List in 7kt2
Manganese binding site 1 out of 7 in the Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN)


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, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:12.7
occ:0.94
 O1G A:DGT511 2.1 14.9 1.0
OD1 A:ASP330 2.1 15.0 1.0
OD2 A:ASP332 2.1 14.4 1.0
O A:HOH735 2.2 16.1 1.0
O2B A:DGT511 2.2 17.1 0.9
OP1 P:DG5 2.3 23.2 1.0
CG A:ASP332 3.2 15.4 1.0
CG A:ASP330 3.2 16.2 1.0
PG A:DGT511 3.3 16.5 1.0
PB A:DGT511 3.5 14.9 0.6
MN A:MN503 3.5 15.7 1.0
O3B A:DGT511 3.5 19.0 1.0
OD1 A:ASP332 3.5 14.8 1.0
OD2 A:ASP330 3.6 21.6 1.0
P P:DG5 3.7 23.4 1.0
O A:HOH644 3.9 25.6 1.0
O5' P:DG5 4.0 23.7 1.0
C5' P:DG5 4.1 23.9 1.0
O A:HOH707 4.1 27.1 1.0
O3G A:DGT511 4.1 23.9 1.0
O A:ASP330 4.3 14.6 1.0
O A:HOH620 4.3 16.0 1.0
N A:GLY320 4.4 11.8 1.0
C A:ASP330 4.5 14.3 1.0
CB A:ASP332 4.5 12.1 1.0
OP2 P:DG5 4.5 23.2 1.0
O P:HOH202 4.5 20.9 1.0
O3A A:DGT511 4.5 23.8 1.0
O1B A:DGT511 4.5 18.2 0.7
CB A:ASP330 4.5 14.3 1.0
O2G A:DGT511 4.6 18.1 1.0
CA A:GLY319 4.7 11.7 1.0
O3' P:DA4 4.7 23.4 1.0
O1A A:DGT511 4.8 28.2 0.9
N A:ASP330 4.8 15.1 1.0
CA A:ASP330 4.9 16.7 1.0
N A:ASP332 4.9 13.4 1.0
N A:VAL331 5.0 14.4 1.0

Manganese binding site 2 out of 7 in 7kt2

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Manganese binding site 2 out of 7 in the Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN)


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, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:15.7
occ:1.00
 OD2 A:ASP330 2.1 21.6 1.0
OD2 A:ASP418 2.1 16.7 1.0
OD1 A:ASP332 2.1 14.8 1.0
OP1 P:DG5 2.1 23.2 1.0
O P:HOH202 2.2 20.9 1.0
O3' P:DA4 2.6 23.4 1.0
P P:DG5 2.9 23.4 1.0
CG A:ASP330 3.0 16.2 1.0
CG A:ASP418 3.1 14.9 1.0
CG A:ASP332 3.1 15.4 1.0
OD1 A:ASP330 3.2 15.0 1.0
OD2 A:ASP332 3.5 14.4 1.0
MN A:MN502 3.5 12.7 0.9
CB A:ASP418 3.8 15.3 1.0
C3' P:DA4 3.8 23.4 1.0
OP2 P:DG5 3.9 23.2 1.0
C4' P:DA4 4.0 23.3 1.0
OD1 A:ASP418 4.0 17.3 1.0
C5' P:DA4 4.0 22.9 1.0
O5' P:DG5 4.1 23.7 1.0
O A:HOH707 4.2 27.1 1.0
C5' P:DG5 4.2 23.9 1.0
CB A:ASP330 4.3 14.3 1.0
CB A:ASP332 4.4 12.1 1.0
O2B A:DGT511 4.5 17.1 0.9
NH2 A:ARG416 4.6 20.6 1.0
OP1 P:DA4 4.7 25.7 1.0
CZ3 A:TRP434 4.8 19.9 1.0
O5' P:DA4 4.8 22.8 1.0
CA A:ASP332 5.0 12.8 1.0
C2' P:DA4 5.0 23.7 1.0
N A:ASP418 5.0 13.9 1.0

Manganese binding site 3 out of 7 in 7kt2

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Manganese binding site 3 out of 7 in the Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN)


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, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:28.9
occ:0.32
 O D:HOH219 1.8 46.4 0.9
OP3 D:DG1 2.1 27.5 1.0
O D:HOH208 2.3 46.3 1.0
ND1 A:HIS208 2.4 30.9 1.0
CE1 A:HIS208 3.2 33.5 1.0
CG A:HIS208 3.3 29.0 1.0
P D:DG1 3.4 27.1 1.0
O D:HOH215 3.7 44.5 1.0
OP1 D:DG1 3.7 31.1 1.0
CB A:HIS208 3.7 26.2 1.0
O D:HOH202 4.1 50.0 1.0
OP2 D:DG1 4.1 31.3 1.0
NE2 A:HIS208 4.2 30.0 1.0
CD2 A:HIS208 4.3 36.0 1.0
O A:HOH617 4.5 47.1 1.0
O5' D:DG1 4.6 24.8 1.0
CA A:HIS208 4.6 25.3 1.0
C5' D:DG1 4.8 26.5 1.0

Manganese binding site 4 out of 7 in 7kt2

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Manganese binding site 4 out of 7 in the Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN)


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, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:55.1
occ:0.74
 NE2 A:HIS219 2.1 54.6 1.0
CE1 A:HIS219 3.1 54.5 1.0
CD2 A:HIS219 3.2 42.2 1.0
CD A:GLU218 4.0 46.3 1.0
ND1 A:HIS219 4.2 44.3 1.0
CG A:HIS219 4.3 43.9 1.0
CB A:GLU218 4.8 31.3 1.0
CG A:GLU218 5.0 45.6 1.0

Manganese binding site 5 out of 7 in 7kt2

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Manganese binding site 5 out of 7 in the Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN)


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, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:30.8
occ:0.40
 OE2 A:GLU386 2.2 38.8 1.0
O A:HOH817 2.2 40.9 1.0
O A:HOH841 2.2 32.1 0.5
OE1 A:GLU386 2.3 50.1 1.0
O T:HOH103 2.4 39.7 1.0
CD A:GLU386 2.6 34.5 1.0
CE1 A:HIS459 2.7 45.0 1.0
ND1 A:HIS459 3.5 47.8 1.0
NE2 A:HIS459 3.5 39.9 1.0
O A:HOH841 3.6 37.2 0.5
O A:HOH662 4.1 34.4 1.0
CG A:GLU386 4.2 37.5 1.0
OP1 T:DC8 4.3 32.6 1.0
O A:HOH604 4.4 27.3 1.0
CG A:HIS459 4.6 29.9 1.0
CD2 A:HIS459 4.6 43.5 1.0
C5' T:DC8 4.6 23.9 1.0
OE1 A:GLN426 4.8 25.2 1.0

Manganese binding site 6 out of 7 in 7kt2

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Manganese binding site 6 out of 7 in the Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN)


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, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:16.6
occ:0.49
 O P:HOH212 1.7 30.9 0.8
O1B A:DGT511 2.1 18.2 0.7
OP2 P:DG5 2.1 23.2 1.0
O A:HOH717 2.1 29.4 0.8
O P:HOH210 2.2 29.0 1.0
PB A:DGT511 3.5 14.9 0.6
P P:DG5 3.5 23.4 1.0
O A:HOH707 3.8 27.1 1.0
O P:HOH214 4.0 34.3 1.0
O3B A:DGT511 4.0 19.0 1.0
O3' A:DGT511 4.1 35.6 0.6
O2B A:DGT511 4.2 17.1 0.9
OP1 P:DG5 4.3 23.2 1.0
O P:HOH202 4.3 20.9 1.0
O5' P:DG5 4.3 23.7 1.0
OP2 P:DA4 4.5 22.4 1.0
O3A A:DGT511 4.6 23.8 1.0
C5' A:DGT511 4.6 35.4 0.8
O3' P:DA4 4.6 23.4 1.0
C4' A:DGT511 4.6 29.3 0.8
C3' A:DGT511 4.7 33.5 0.6
C3' P:DA4 4.7 23.4 1.0
O5' P:DA4 4.8 22.8 1.0
OP1 P:DA4 4.8 25.7 1.0
P P:DA4 5.0 22.4 1.0

Manganese binding site 7 out of 7 in 7kt2

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Manganese binding site 7 out of 7 in the Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN)


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, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn101

b:64.8
occ:0.50
 N7 D:DG1 2.4 23.2 1.0
O D:HOH211 2.5 45.8 1.0
O D:HOH214 2.5 46.8 1.0
C8 D:DG1 3.3 23.4 1.0
C5 D:DG1 3.6 20.9 1.0
O6 D:DG1 3.8 26.0 1.0
C6 D:DG1 4.1 23.3 1.0
O D:HOH209 4.5 43.4 1.0
N9 D:DG1 4.6 22.9 1.0
CG A:ARG175 4.6 24.6 1.0
OP2 D:DG1 4.6 31.3 1.0
C4 D:DG1 4.7 19.5 1.0
O A:HOH822 4.7 35.4 1.0
CD A:ARG175 4.8 29.4 1.0
N4 D:DC2 4.9 25.9 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Watching A Double Strand Break Repair Polymerase Insert A Pro-Mutagenic Oxidized Nucleotide. Nat Commun V. 12 2059 2021.
ISSN: ESSN 2041-1723
PubMed: 33824325
DOI: 10.1038/S41467-021-21354-6
Page generated: Sun Oct 6 09:28:26 2024

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