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Manganese in PDB 7ksu: Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN)

Enzymatic activity of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN)

All present enzymatic activity of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN), PDB code: 7ksu 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) 41.82 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.985, 68.882, 109.747, 90, 90, 90
R / Rfree (%) 17.3 / 19.2

Other elements in 7ksu:

The structure of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN) 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:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN) (pdb code 7ksu). 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:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN), PDB code: 7ksu:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 7ksu

Go back to Manganese Binding Sites List in 7ksu
Manganese binding site 1 out of 7 in the Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN)


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:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:21.4
occ:1.00
 OD2 A:ASP330 2.0 27.4 1.0
OD2 A:ASP418 2.0 21.0 1.0
OD1 A:ASP332 2.1 21.3 1.0
OP1 P:DG5 2.2 23.6 1.0
O P:HOH201 2.3 24.0 1.0
O3' P:DA4 2.7 22.7 1.0
CG A:ASP330 2.9 25.0 1.0
P P:DG5 3.0 24.2 1.0
CG A:ASP332 3.1 20.9 1.0
CG A:ASP418 3.1 22.0 1.0
OD1 A:ASP330 3.2 22.8 1.0
OD2 A:ASP332 3.4 20.0 1.0
MN A:MN502 3.5 19.1 1.0
CB A:ASP418 3.8 19.9 1.0
C3' P:DA4 3.9 21.6 1.0
OP2 P:DG5 4.0 22.5 1.0
OD1 A:ASP418 4.0 21.7 1.0
C4' P:DA4 4.1 20.4 1.0
C5' P:DA4 4.1 19.5 1.0
O5' P:DG5 4.2 19.7 1.0
O A:HOH628 4.2 38.2 1.0
CB A:ASP330 4.3 22.8 1.0
C5' P:DG5 4.4 21.3 1.0
CB A:ASP332 4.4 17.7 1.0
NH2 A:ARG416 4.5 22.0 1.0
OP1 P:DA4 4.6 23.3 1.0
O32 A:PPV507 4.6 22.6 0.7
CZ3 A:TRP434 4.7 20.6 1.0
O12 A:PPV507 4.8 22.9 0.3
O5' P:DA4 4.8 21.6 1.0
O A:VAL331 4.9 20.0 1.0
N A:ASP418 4.9 19.3 1.0
CA A:ASP332 4.9 17.6 1.0

Manganese binding site 2 out of 7 in 7ksu

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Manganese binding site 2 out of 7 in the Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN)


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:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:19.1
occ:1.00
 O12 A:PPV507 2.1 22.9 0.3
O A:HOH699 2.1 20.3 1.0
O21 A:PPV507 2.1 18.6 0.7
O11 A:PPV507 2.1 19.7 0.3
OD2 A:ASP332 2.2 20.0 1.0
OD1 A:ASP330 2.2 22.8 1.0
OP1 P:DG5 2.3 23.6 1.0
O32 A:PPV507 2.3 22.6 0.7
P1 A:PPV507 3.1 19.7 0.3
CG A:ASP332 3.2 20.9 1.0
CG A:ASP330 3.3 25.0 1.0
O21 A:PPV507 3.4 21.8 0.3
P2 A:PPV507 3.4 23.8 0.3
P1 A:PPV507 3.4 21.2 0.7
OPP A:PPV507 3.5 21.4 0.3
MN A:MN501 3.5 21.4 1.0
OD1 A:ASP332 3.6 21.3 1.0
P2 A:PPV507 3.6 24.1 0.7
P P:DG5 3.6 24.2 1.0
OPP A:PPV507 3.7 20.2 0.7
OD2 A:ASP330 3.7 27.4 1.0
O A:HOH608 3.9 22.7 0.7
C5' P:DG5 4.0 21.3 1.0
O A:HOH628 4.0 38.2 1.0
O5' P:DG5 4.0 19.7 1.0
O22 A:PPV507 4.1 25.4 0.3
O11 A:PPV507 4.2 20.7 0.7
O A:HOH608 4.2 19.7 0.3
O A:ASP330 4.3 20.9 1.0
O A:HOH616 4.3 20.1 1.0
N A:GLY320 4.5 18.4 1.0
O31 A:PPV507 4.5 19.8 0.3
OP2 P:DG5 4.5 22.5 1.0
O P:HOH201 4.5 24.0 1.0
C A:ASP330 4.5 20.7 1.0
CB A:ASP332 4.5 17.7 1.0
O32 A:PPV507 4.5 24.9 0.3
O22 A:PPV507 4.5 25.9 0.7
O31 A:PPV507 4.6 19.6 0.7
CB A:ASP330 4.6 22.8 1.0
O12 A:PPV507 4.6 26.3 0.7
CA A:GLY319 4.6 18.2 1.0
O3' P:DA4 4.7 22.7 1.0
CA A:ASP330 4.9 21.3 1.0
N A:ASP330 4.9 18.8 1.0
N A:ASP332 4.9 17.3 1.0

Manganese binding site 3 out of 7 in 7ksu

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Manganese binding site 3 out of 7 in the Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN)


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:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:29.3
occ:0.52
 O A:HOH800 2.1 32.9 0.8
OE2 A:GLU386 2.2 44.3 1.0
O T:HOH203 2.3 41.4 1.0
O A:HOH774 2.3 45.1 0.9
NE2 A:HIS459 2.3 41.3 1.0
OE1 A:GLU386 2.6 46.0 1.0
CD A:GLU386 2.7 41.5 1.0
CD2 A:HIS459 3.1 40.8 1.0
CE1 A:HIS459 3.5 40.0 1.0
O A:HOH663 4.2 35.5 1.0
OP1 T:DC8 4.2 33.2 1.0
CG A:GLU386 4.3 39.2 1.0
CG A:HIS459 4.3 39.4 1.0
O A:HOH623 4.4 28.4 1.0
ND1 A:HIS459 4.5 41.9 1.0
C5' T:DC8 4.6 24.8 1.0
OE1 A:GLN426 4.7 29.2 1.0

Manganese binding site 4 out of 7 in 7ksu

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Manganese binding site 4 out of 7 in the Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN)


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:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:40.5
occ:0.39
 O A:HOH810 2.2 63.1 1.0
O D:HOH105 2.2 49.6 0.9
OP3 D:DG1 2.2 31.4 1.0
ND1 A:HIS208 2.4 38.2 1.0
CE1 A:HIS208 3.1 38.6 1.0
CG A:HIS208 3.4 35.2 1.0
P D:DG1 3.4 32.4 1.0
O D:HOH108 3.6 46.4 1.0
OP1 D:DG1 3.6 34.1 1.0
CB A:HIS208 3.8 30.4 1.0
O D:HOH102 4.0 52.5 1.0
OP2 D:DG1 4.0 34.4 1.0
NE2 A:HIS208 4.2 37.8 1.0
CD2 A:HIS208 4.3 36.6 1.0
O A:HOH705 4.5 51.9 1.0
O5' D:DG1 4.7 30.9 1.0
CA A:HIS208 4.7 30.2 1.0
C5' D:DG1 5.0 29.7 1.0

Manganese binding site 5 out of 7 in 7ksu

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Manganese binding site 5 out of 7 in the Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN)


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:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:53.9
occ:0.62
 O A:HOH735 1.9 59.8 1.0
O A:HOH602 2.0 57.1 1.0
NE2 A:HIS219 2.1 62.9 1.0
O A:HOH709 2.4 52.6 0.9
OE1 A:GLU218 2.6 68.4 1.0
CE1 A:HIS219 3.1 59.7 1.0
CD2 A:HIS219 3.1 57.9 1.0
CD A:GLU218 3.7 65.7 1.0
ND1 A:HIS219 4.2 59.0 1.0
CG A:HIS219 4.2 54.9 1.0
OE2 A:GLU218 4.3 67.6 1.0
CB A:GLU218 4.5 46.9 1.0
CG A:GLU218 4.8 57.6 1.0

Manganese binding site 6 out of 7 in 7ksu

Go back to Manganese Binding Sites List in 7ksu
Manganese binding site 6 out of 7 in the Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN)


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:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:41.2
occ:0.63
 O T:HOH224 2.2 45.2 0.8
O T:HOH205 2.3 44.5 0.9
O T:HOH201 2.5 51.1 1.0
N7 T:DG2 2.6 37.8 1.0
C8 T:DG2 3.5 36.6 1.0
O T:HOH204 3.7 43.4 1.0
C5 T:DG2 3.7 35.4 1.0
O6 T:DG2 4.0 31.4 1.0
OP2 T:DG2 4.2 60.1 1.0
C6 T:DG2 4.3 31.5 1.0
O6 T:DG3 4.4 27.2 1.0
O D:HOH106 4.5 49.3 1.0
N9 T:DG2 4.7 35.6 1.0
C3' T:DC1 4.7 53.1 1.0
C6 T:DC1 4.9 50.9 1.0
C4 T:DG2 4.9 34.4 1.0

Manganese binding site 7 out of 7 in 7ksu

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Manganese binding site 7 out of 7 in the Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN)


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:Ct Product State Ternary Complex, 10 Mm MN2+ (4MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:30.6
occ:0.65
 O P:HOH212 1.8 33.4 0.7
O22 A:PPV507 2.1 25.9 0.7
O A:HOH778 2.2 32.4 0.7
OP2 P:DG5 2.2 22.5 1.0
O P:HOH208 2.4 29.4 0.7
P2 A:PPV507 3.5 24.1 0.7
P P:DG5 3.6 24.2 1.0
O A:HOH628 3.7 38.2 1.0
O P:HOH211 3.8 32.2 1.0
O21 A:PPV507 3.9 21.8 0.3
O32 A:PPV507 4.0 22.6 0.7
O P:HOH201 4.2 24.0 1.0
OPP A:PPV507 4.2 20.2 0.7
OP1 P:DG5 4.3 23.6 1.0
O5' P:DG5 4.3 19.7 1.0
O A:HOH806 4.3 49.5 1.0
OP2 P:DA4 4.5 23.0 1.0
O32 A:PPV507 4.6 24.9 0.3
O12 A:PPV507 4.6 26.3 0.7
O3' P:DA4 4.7 22.7 1.0
O12 A:PPV507 4.8 22.9 0.3
C3' P:DA4 4.8 21.6 1.0
O5' P:DA4 4.9 21.6 1.0
O A:HOH739 4.9 50.5 1.0
OP1 P:DA4 4.9 23.3 1.0
P P:DA4 5.0 23.5 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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