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Manganese in PDB 5tyx: Dna Polymerase Mu Product Complex, MN2+ (15 Min)

Enzymatic activity of Dna Polymerase Mu Product Complex, MN2+ (15 Min)

All present enzymatic activity of Dna Polymerase Mu Product Complex, MN2+ (15 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu Product Complex, MN2+ (15 Min), PDB code: 5tyx 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) 23.13 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.908, 68.736, 109.962, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 21.6

Other elements in 5tyx:

The structure of Dna Polymerase Mu Product Complex, 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 Product Complex, MN2+ (15 Min) (pdb code 5tyx). 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 Product Complex, MN2+ (15 Min), PDB code: 5tyx:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 5tyx

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Manganese binding site 1 out of 7 in the Dna Polymerase Mu Product Complex, 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 Product Complex, MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn702

b:24.0
occ:1.00
 OD2 A:ASP330 2.0 28.4 1.0
OD2 A:ASP418 2.1 19.6 1.0
OD1 A:ASP332 2.2 20.0 1.0
OP1 P:DT5 2.2 21.7 1.0
O P:HOH210 2.3 24.4 1.0
O3' P:DA4 2.6 24.4 1.0
CG A:ASP330 2.9 26.7 1.0
P P:DT5 2.9 25.6 1.0
CG A:ASP332 3.1 22.0 1.0
OD1 A:ASP330 3.1 22.1 1.0
CG A:ASP418 3.1 21.2 1.0
OD2 A:ASP332 3.4 18.5 1.0
MN A:MN703 3.4 19.9 1.0
C3' P:DA4 3.8 18.2 1.0
CB A:ASP418 3.8 21.5 1.0
OP2 P:DT5 3.9 23.8 1.0
C4' P:DA4 4.0 21.5 1.0
C5' P:DA4 4.0 21.3 1.0
OD1 A:ASP418 4.1 22.6 1.0
O5' P:DT5 4.2 21.9 1.0
CB A:ASP330 4.3 21.0 1.0
C5' P:DT5 4.4 20.1 1.0
CB A:ASP332 4.5 16.8 1.0
O A:HOH1019 4.5 32.6 0.6
NH2 A:ARG416 4.6 20.3 1.0
CZ3 A:TRP434 4.7 20.0 1.0
OP1 P:DA4 4.7 21.3 1.0
O5' P:DA4 4.8 22.3 1.0
O32 A:PPV701 4.9 22.8 0.7
O A:VAL331 4.9 17.0 1.0
C2' P:DA4 5.0 24.9 1.0

Manganese binding site 2 out of 7 in 5tyx

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Manganese binding site 2 out of 7 in the Dna Polymerase Mu Product Complex, 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 Product Complex, MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn703

b:19.9
occ:1.00
 OD2 A:ASP332 2.1 18.5 1.0
O A:HOH909 2.1 20.1 1.0
OP1 P:DT5 2.2 21.7 1.0
O21 A:PPV701 2.2 21.0 1.0
OD1 A:ASP330 2.2 22.1 1.0
O32 A:PPV701 2.3 22.8 0.7
P1 A:PPV701 3.2 26.3 1.0
CG A:ASP332 3.2 22.0 1.0
CG A:ASP330 3.3 26.7 1.0
O31 A:PPV701 3.3 32.7 1.0
MN A:MN702 3.4 24.0 1.0
P2 A:PPV701 3.4 34.4 0.7
P P:DT5 3.6 25.6 1.0
OD1 A:ASP332 3.6 20.0 1.0
OPP A:PPV701 3.7 29.6 0.7
OD2 A:ASP330 3.7 28.4 1.0
O5' P:DT5 4.0 21.9 1.0
O22 A:PPV701 4.0 31.6 0.7
C5' P:DT5 4.1 20.1 1.0
O A:ASP330 4.2 17.5 1.0
O A:HOH1019 4.3 32.6 0.6
N A:GLY320 4.3 19.4 1.0
O P:HOH210 4.3 24.4 1.0
O A:HOH835 4.4 20.2 1.0
OP2 P:DT5 4.5 23.8 1.0
O11 A:PPV701 4.5 22.2 1.0
CB A:ASP332 4.5 16.8 1.0
C A:ASP330 4.5 19.9 1.0
CA A:GLY319 4.6 18.0 1.0
CB A:ASP330 4.6 21.0 1.0
MN P:MN101 4.6 43.4 0.6
O3' P:DA4 4.6 24.4 1.0
O12 A:PPV701 4.7 36.1 0.7
O A:HOH810 4.8 29.9 1.0
N A:ASP330 4.9 21.0 1.0
CA A:ASP330 4.9 21.7 1.0
N A:ASP332 5.0 17.3 1.0

Manganese binding site 3 out of 7 in 5tyx

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Manganese binding site 3 out of 7 in the Dna Polymerase Mu Product Complex, 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 Product Complex, MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn704

b:82.2
occ:1.00
 NE2 A:HIS219 2.2 59.7 1.0
OE1 A:GLU218 3.0 69.0 1.0
CE1 A:HIS219 3.1 56.1 1.0
CD2 A:HIS219 3.4 50.9 1.0
CD A:GLU218 4.2 71.0 1.0
ND1 A:HIS219 4.3 50.9 1.0
CG A:HIS219 4.4 49.3 1.0
CB A:GLU218 4.7 46.6 1.0
OE2 A:GLU218 4.9 72.2 1.0

Manganese binding site 4 out of 7 in 5tyx

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Manganese binding site 4 out of 7 in the Dna Polymerase Mu Product Complex, 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 Product Complex, MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn705

b:53.3
occ:0.44
 OP3 D:DG1 2.2 34.7 1.0
ND1 A:HIS208 2.3 32.6 1.0
CE1 A:HIS208 3.1 28.6 1.0
CG A:HIS208 3.2 31.2 1.0
P D:DG1 3.4 35.2 1.0
O D:HOH107 3.6 39.2 1.0
CB A:HIS208 3.7 29.7 1.0
OP1 D:DG1 3.7 31.2 1.0
O D:HOH102 3.9 41.2 1.0
OP2 D:DG1 4.1 35.1 1.0
NE2 A:HIS208 4.1 32.3 1.0
CD2 A:HIS208 4.2 31.0 1.0
CA A:HIS208 4.6 28.4 1.0
O5' D:DG1 4.6 36.6 1.0
C5' D:DG1 4.9 29.9 1.0

Manganese binding site 5 out of 7 in 5tyx

Go back to Manganese Binding Sites List in 5tyx
Manganese binding site 5 out of 7 in the Dna Polymerase Mu Product Complex, 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 Product Complex, MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn706

b:28.9
occ:0.36
 OE2 A:GLU386 2.2 33.9 1.0
O A:HOH1005 2.2 40.6 1.0
O A:HOH1027 2.2 45.3 1.0
O T:HOH201 2.2 39.8 1.0
OE1 A:GLU386 2.2 41.0 1.0
NE2 A:HIS459 2.4 40.2 1.0
CD A:GLU386 2.5 34.1 1.0
CD2 A:HIS459 3.2 36.6 1.0
CE1 A:HIS459 3.5 35.1 1.0
CG A:GLU386 4.1 33.7 1.0
OP1 T:DC8 4.1 31.6 1.0
O A:HOH893 4.1 39.1 1.0
O A:HOH812 4.3 27.5 1.0
CG A:HIS459 4.4 31.6 1.0
C5' T:DC8 4.5 27.5 1.0
ND1 A:HIS459 4.5 39.9 1.0
OE1 A:GLN426 4.8 30.9 1.0
CB A:GLU386 4.9 35.3 1.0

Manganese binding site 6 out of 7 in 5tyx

Go back to Manganese Binding Sites List in 5tyx
Manganese binding site 6 out of 7 in the Dna Polymerase Mu Product Complex, 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 Product Complex, MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:51.5
occ:0.70
 O T:HOH222 2.2 39.2 0.7
O T:HOH235 2.2 42.3 0.7
O T:HOH227 2.2 39.1 0.7
N7 T:DG2 2.7 37.2 1.0
C8 T:DG2 3.5 37.2 1.0
C5 T:DG2 3.8 32.7 1.0
O T:HOH203 3.8 38.2 1.0
O6 T:DG2 4.0 32.2 1.0
OP2 T:DG2 4.2 49.1 1.0
O D:HOH112 4.3 46.2 1.0
C6 T:DG2 4.3 31.6 1.0
O6 T:DG3 4.4 28.6 1.0
C2' T:DC1 4.5 48.9 1.0
N9 T:DG2 4.8 35.3 1.0
C3' T:DC1 4.9 54.8 1.0
C4 T:DG2 4.9 32.7 1.0
C6 T:DC1 4.9 44.3 1.0

Manganese binding site 7 out of 7 in 5tyx

Go back to Manganese Binding Sites List in 5tyx
Manganese binding site 7 out of 7 in the Dna Polymerase Mu Product Complex, 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 Product Complex, MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:43.4
occ:0.60
 O A:HOH994 2.2 26.1 0.6
O P:HOH215 2.2 30.2 0.6
O A:HOH964 2.2 24.7 0.6
OP2 P:DT5 2.2 23.8 1.0
O31 A:PPV701 2.3 32.7 1.0
O A:HOH1019 3.1 32.6 0.6
P P:DT5 3.2 25.6 1.0
O5' P:DT5 3.6 21.9 1.0
OP1 P:DT5 3.6 21.7 1.0
P1 A:PPV701 3.7 26.3 1.0
O32 A:PPV701 3.9 22.8 0.7
OPP A:PPV701 4.1 29.6 0.7
C7 P:DT5 4.1 26.3 1.0
O A:HOH1052 4.2 44.7 1.0
O12 A:PPV701 4.3 36.1 0.7
P2 A:PPV701 4.4 34.4 0.7
O P:HOH210 4.5 24.4 1.0
O11 A:PPV701 4.5 22.2 1.0
O21 A:PPV701 4.5 21.0 1.0
MN A:MN703 4.6 19.9 1.0
O3' P:DA4 4.7 24.4 1.0
O A:HOH910 4.7 21.1 1.0
C5' P:DT5 4.9 20.1 1.0

Reference:

J.A.Jamsen, W.A.Beard, L.C.Pedersen, D.D.Shock, A.F.Moon, J.M.Krahn, K.Bebenek, T.A.Kunkel, S.H.Wilson. Time-Lapse Crystallography Snapshots of A Double-Strand Break Repair Polymerase in Action. Nat Commun V. 8 253 2017.
ISSN: ESSN 2041-1723
PubMed: 28811466
DOI: 10.1038/S41467-017-00271-7
Page generated: Sun Oct 6 02:59:07 2024

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