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Manganese in PDB 7kt1: Dna Polymerase Mu, Dgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (180MIN)

Enzymatic activity of Dna Polymerase Mu, Dgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (180MIN)

All present enzymatic activity of Dna Polymerase Mu, Dgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (180MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, Dgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (180MIN), PDB code: 7kt1 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) 43.01 / 1.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.754, 68.793, 110.223, 90, 90, 90
R / Rfree (%) 16.5 / 18.9

Other elements in 7kt1:

The structure of Dna Polymerase Mu, Dgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (180MIN) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Mu, Dgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (180MIN) (pdb code 7kt1). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Dna Polymerase Mu, Dgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (180MIN), PDB code: 7kt1:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 7kt1

Go back to Manganese Binding Sites List in 7kt1
Manganese binding site 1 out of 6 in the Dna Polymerase Mu, Dgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (180MIN)


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 Reaction State Ternary Complex, 50 Mm MN2+ (180MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:20.1
occ:1.00
 OD2 A:ASP330 2.0 23.4 1.0
OP1 P:DG5 2.0 17.7 0.6
OD2 A:ASP418 2.1 20.1 1.0
OD1 A:ASP332 2.1 18.2 1.0
O A:HOH617 2.2 28.1 1.0
O3' P:DA4 2.6 24.4 0.4
O3' P:DA4 2.6 24.6 0.6
O1A A:DGT501 2.8 17.7 0.4
P P:DG5 2.9 19.9 0.6
CG A:ASP330 3.0 23.3 1.0
CG A:ASP418 3.1 19.7 1.0
CG A:ASP332 3.1 18.3 1.0
OD1 A:ASP330 3.3 20.1 1.0
OD2 A:ASP332 3.5 17.9 1.0
MN A:MN503 3.5 18.7 1.0
PA A:DGT501 3.7 20.8 0.4
C3' P:DA4 3.7 25.4 0.4
C3' P:DA4 3.8 25.4 0.6
CB A:ASP418 3.8 18.6 1.0
OP2 P:DG5 3.9 21.9 0.6
O2A A:DGT501 3.9 21.4 0.4
C4' P:DA4 3.9 25.7 0.4
C4' P:DA4 3.9 25.7 0.6
C5' P:DA4 4.0 26.0 0.4
C5' P:DA4 4.0 26.0 0.6
O5' P:DG5 4.0 23.5 0.6
OD1 A:ASP418 4.1 21.8 1.0
O A:HOH699 4.1 24.3 0.6
C5' A:DGT501 4.1 25.4 0.4
C5' P:DG5 4.2 25.4 0.6
CB A:ASP330 4.3 21.4 1.0
O5' A:DGT501 4.3 23.7 0.4
CB A:ASP332 4.4 16.3 1.0
CE1 A:HIS329 4.5 24.1 0.4
NH2 A:ARG416 4.5 24.2 1.0
O2B A:DGT501 4.5 24.9 0.6
OP1 P:DA4 4.7 28.7 0.4
O5' P:DA4 4.7 26.8 0.4
CZ3 A:TRP434 4.7 25.3 1.0
O5' P:DA4 4.8 26.8 0.6
OP1 P:DA4 4.9 28.6 0.6
C2' P:DA4 5.0 25.9 0.6
C2' P:DA4 5.0 26.0 0.4
CA A:ASP332 5.0 16.6 1.0
O A:VAL331 5.0 18.7 1.0

Manganese binding site 2 out of 6 in 7kt1

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Manganese binding site 2 out of 6 in the Dna Polymerase Mu, Dgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (180MIN)


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 Reaction State Ternary Complex, 50 Mm MN2+ (180MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:18.7
occ:1.00
 O1A A:DGT501 1.5 17.7 0.4
OD2 A:ASP332 2.1 17.9 1.0
O2B A:DGT501 2.1 18.5 0.4
OD1 A:ASP330 2.2 20.1 1.0
O A:HOH647 2.2 20.6 1.0
O1G A:DGT501 2.2 16.5 0.6
O2B A:DGT501 2.2 24.9 0.6
OP1 P:DG5 2.4 17.7 0.6
PA A:DGT501 2.9 20.8 0.4
O3G A:DGT501 3.0 29.3 0.4
PB A:DGT501 3.1 19.4 0.4
CG A:ASP332 3.1 18.3 1.0
CG A:ASP330 3.2 23.3 1.0
O3A A:DGT501 3.3 20.5 0.4
PG A:DGT501 3.4 19.4 0.6
OD1 A:ASP332 3.5 18.2 1.0
PB A:DGT501 3.5 23.3 0.6
MN A:MN502 3.5 20.1 1.0
OD2 A:ASP330 3.6 23.4 1.0
O3B A:DGT501 3.6 20.0 0.6
P P:DG5 3.7 19.9 0.6
O5' A:DGT501 3.8 23.7 0.4
PG A:DGT501 3.8 26.6 0.4
O3B A:DGT501 3.9 22.2 0.4
O A:HOH645 4.0 24.5 0.6
O1G A:DGT501 4.0 25.5 0.4
O2A A:DGT501 4.1 21.4 0.4
O A:HOH699 4.1 24.3 0.6
O5' P:DG5 4.1 23.5 0.6
O3G A:DGT501 4.1 19.5 0.6
C5' A:DGT501 4.1 25.4 0.4
C5' P:DG5 4.2 25.4 0.6
O A:ASP330 4.2 18.5 1.0
O A:HOH608 4.3 19.1 1.0
ND1 A:HIS329 4.3 23.7 0.4
N A:GLY320 4.4 16.3 1.0
C A:ASP330 4.4 19.6 1.0
O1B A:DGT501 4.4 19.8 0.4
CE1 A:HIS329 4.5 24.1 0.4
O A:HOH617 4.5 28.1 1.0
CB A:ASP330 4.5 21.4 1.0
CB A:ASP332 4.5 16.3 1.0
OP2 P:DG5 4.6 21.9 0.6
O1B A:DGT501 4.6 22.4 0.6
O3A A:DGT501 4.6 27.6 0.6
O2G A:DGT501 4.7 20.4 0.6
CA A:GLY319 4.7 16.9 1.0
O1A A:DGT501 4.7 27.2 0.6
O3' P:DA4 4.8 24.6 0.6
O3' P:DA4 4.8 24.4 0.4
CA A:ASP330 4.8 20.4 1.0
N A:ASP330 4.8 19.6 1.0
N A:ASP332 4.9 16.9 1.0
N A:VAL331 5.0 18.6 1.0

Manganese binding site 3 out of 6 in 7kt1

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Manganese binding site 3 out of 6 in the Dna Polymerase Mu, Dgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (180MIN)


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 Reaction State Ternary Complex, 50 Mm MN2+ (180MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:43.4
occ:0.50
 O D:HOH118 1.8 51.1 1.0
OP3 D:DG1 2.1 36.6 1.0
ND1 A:HIS208 2.4 36.5 1.0
O D:HOH103 2.5 45.0 1.0
CE1 A:HIS208 3.2 37.1 1.0
P D:DG1 3.3 35.3 1.0
CG A:HIS208 3.3 34.6 1.0
O D:HOH113 3.6 51.0 1.0
OP1 D:DG1 3.6 37.8 1.0
CB A:HIS208 3.7 31.1 1.0
OP2 D:DG1 4.0 38.8 1.0
O D:HOH105 4.1 50.7 1.0
NE2 A:HIS208 4.3 35.8 1.0
CD2 A:HIS208 4.4 35.5 1.0
O5' D:DG1 4.5 31.4 1.0
CA A:HIS208 4.6 30.9 1.0
C5' D:DG1 4.9 28.9 1.0

Manganese binding site 4 out of 6 in 7kt1

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Manganese binding site 4 out of 6 in the Dna Polymerase Mu, Dgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (180MIN)


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 Reaction State Ternary Complex, 50 Mm MN2+ (180MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:32.3
occ:0.33
 OE2 A:GLU386 2.3 41.7 1.0
O T:HOH201 2.3 50.8 1.0
O A:HOH789 2.4 47.2 1.0
NE2 A:HIS459 2.4 32.6 0.5
OE1 A:GLU386 2.9 47.0 1.0
CD A:GLU386 3.0 40.7 1.0
CE1 A:HIS459 3.0 32.3 0.5
CD2 A:HIS459 3.1 32.6 0.5
NE2 A:HIS459 3.5 32.4 0.5
CE1 A:HIS459 3.6 32.5 0.5
O A:HOH798 3.6 60.5 1.0
ND1 A:HIS459 3.7 31.7 0.5
O A:HOH670 4.1 39.9 1.0
OP1 T:DC8 4.1 39.9 1.0
CG A:HIS459 4.4 31.1 0.5
O A:HOH632 4.4 33.5 1.0
CD2 A:HIS459 4.4 32.4 0.5
CG A:GLU386 4.5 36.0 1.0
CG A:HIS459 4.6 30.8 0.5
ND1 A:HIS459 4.6 31.6 0.5
C5' T:DC8 4.6 32.1 1.0
OE1 A:GLN426 4.7 32.0 1.0

Manganese binding site 5 out of 6 in 7kt1

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Manganese binding site 5 out of 6 in the Dna Polymerase Mu, Dgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (180MIN)


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 Reaction State Ternary Complex, 50 Mm MN2+ (180MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:68.3
occ:0.89
 NE2 A:HIS219 2.2 54.7 1.0
OE1 A:GLU218 2.9 64.5 1.0
CE1 A:HIS219 3.1 53.2 1.0
CD2 A:HIS219 3.2 50.9 1.0
CD A:GLU218 4.2 61.8 1.0
ND1 A:HIS219 4.2 51.9 1.0
CG A:HIS219 4.3 49.2 1.0
CB A:GLU218 4.7 45.0 1.0
OE2 A:GLU218 4.9 64.6 1.0

Manganese binding site 6 out of 6 in 7kt1

Go back to Manganese Binding Sites List in 7kt1
Manganese binding site 6 out of 6 in the Dna Polymerase Mu, Dgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (180MIN)


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 Reaction State Ternary Complex, 50 Mm MN2+ (180MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:25.4
occ:0.64
 O P:HOH212 2.0 28.5 0.6
OP2 P:DG5 2.1 21.9 0.6
O1B A:DGT501 2.1 22.4 0.6
O A:HOH742 2.2 27.5 0.6
O2A A:DGT501 2.2 21.4 0.4
O P:HOH213 2.3 27.0 0.6
PB A:DGT501 3.4 23.3 0.6
P P:DG5 3.5 19.9 0.6
PA A:DGT501 3.6 20.8 0.4
O3A A:DGT501 3.7 20.5 0.4
O A:HOH699 3.8 24.3 0.6
O P:HOH213 3.9 27.8 0.4
O P:HOH211 4.0 39.5 1.0
O3B A:DGT501 4.1 20.0 0.6
O3' A:DGT501 4.2 38.1 0.6
CE1 A:HIS329 4.2 24.1 0.4
O A:HOH617 4.2 28.1 1.0
OP1 P:DG5 4.2 17.7 0.6
O2B A:DGT501 4.3 24.9 0.6
O5' P:DG5 4.3 23.5 0.6
O A:HOH813 4.4 46.5 1.0
O3G A:DGT501 4.4 29.3 0.4
OP2 P:DA4 4.4 26.8 0.4
O3A A:DGT501 4.4 27.6 0.6
OP2 P:DA4 4.5 26.7 0.6
O1A A:DGT501 4.6 17.7 0.4
O5' A:DGT501 4.6 23.7 0.4
O3' P:DA4 4.6 24.6 0.6
C4' A:DGT501 4.6 33.5 0.6
C3' P:DA4 4.7 25.4 0.6
C3' A:DGT501 4.7 34.9 0.6
C5' A:DGT501 4.7 31.5 0.6
OP1 P:DA4 4.7 28.6 0.6
O5' P:DA4 4.7 26.8 0.4
O5' P:DA4 4.7 26.8 0.6
ND1 A:HIS329 4.8 23.7 0.4
C3' P:DA4 4.8 25.4 0.4
O3' P:DA4 4.8 24.4 0.4
OP1 P:DA4 4.8 28.7 0.4
NE2 A:HIS329 4.9 24.6 0.4
P P:DA4 4.9 27.9 0.4
P P:DA4 4.9 28.1 0.6

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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