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Manganese in PDB 5tyy: Dna Polymerase Mu Product Complex, MN2+ (60 Min)

Enzymatic activity of Dna Polymerase Mu Product Complex, MN2+ (60 Min)

All present enzymatic activity of Dna Polymerase Mu Product Complex, MN2+ (60 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu Product Complex, MN2+ (60 Min), PDB code: 5tyy 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) 25.08 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.985, 68.670, 110.181, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 21.8

Other elements in 5tyy:

The structure of Dna Polymerase Mu Product Complex, MN2+ (60 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+ (60 Min) (pdb code 5tyy). 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+ (60 Min), PDB code: 5tyy:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 5tyy

Go back to Manganese Binding Sites List in 5tyy
Manganese binding site 1 out of 7 in the Dna Polymerase Mu Product Complex, MN2+ (60 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+ (60 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:17.4
occ:1.00
 O A:HOH722 2.1 18.4 1.0
OD2 A:ASP332 2.1 16.9 1.0
O12 A:PPV507 2.1 20.6 1.0
OP1 P:DT5 2.1 19.8 1.0
OD1 A:ASP330 2.2 20.2 1.0
O31 A:PPV507 2.3 24.8 0.7
CG A:ASP332 3.1 18.6 1.0
P2 A:PPV507 3.2 25.0 1.0
CG A:ASP330 3.3 23.5 1.0
O32 A:PPV507 3.4 29.6 1.0
MN A:MN502 3.4 21.6 1.0
P1 A:PPV507 3.4 43.6 0.7
OD1 A:ASP332 3.5 17.4 1.0
P P:DT5 3.5 21.7 1.0
OPP A:PPV507 3.7 30.1 0.7
OD2 A:ASP330 3.8 24.6 1.0
O5' P:DT5 4.1 18.0 1.0
C5' P:DT5 4.1 17.4 1.0
O11 A:PPV507 4.1 32.6 0.7
O A:HOH760 4.1 28.2 0.4
O A:ASP330 4.2 18.0 1.0
N A:GLY320 4.4 17.8 1.0
O A:HOH602 4.4 29.9 1.0
OP2 P:DT5 4.4 21.7 1.0
O A:HOH610 4.4 20.0 1.0
CB A:ASP332 4.4 14.5 1.0
O P:HOH204 4.5 19.6 1.0
C A:ASP330 4.5 19.2 1.0
O22 A:PPV507 4.5 21.2 1.0
MN P:MN101 4.5 33.3 0.4
O21 A:PPV507 4.5 37.3 0.7
CA A:GLY319 4.5 15.6 1.0
CB A:ASP330 4.6 18.6 1.0
O3' P:DA4 4.6 21.9 1.0
CA A:ASP330 4.9 20.7 1.0
N A:ASP330 4.9 19.9 1.0
N A:ASP332 4.9 15.4 1.0

Manganese binding site 2 out of 7 in 5tyy

Go back to Manganese Binding Sites List in 5tyy
Manganese binding site 2 out of 7 in the Dna Polymerase Mu Product Complex, MN2+ (60 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+ (60 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:21.6
occ:1.00
 OD2 A:ASP330 1.9 24.6 1.0
OD1 A:ASP332 2.1 17.4 1.0
OD2 A:ASP418 2.1 17.7 1.0
OP1 P:DT5 2.2 19.8 1.0
O P:HOH204 2.4 19.6 1.0
O3' P:DA4 2.7 21.9 1.0
CG A:ASP330 2.8 23.5 1.0
OD1 A:ASP330 2.9 20.2 1.0
P P:DT5 3.0 21.7 1.0
CG A:ASP332 3.1 18.6 1.0
CG A:ASP418 3.1 19.2 1.0
MN A:MN501 3.4 17.4 1.0
OD2 A:ASP332 3.4 16.9 1.0
CB A:ASP418 3.8 18.0 1.0
C3' P:DA4 3.9 17.7 1.0
OP2 P:DT5 4.0 21.7 1.0
OD1 A:ASP418 4.0 19.2 1.0
C5' P:DA4 4.1 19.7 1.0
C4' P:DA4 4.1 17.8 1.0
CB A:ASP330 4.2 18.6 1.0
O5' P:DT5 4.3 18.0 1.0
CB A:ASP332 4.4 14.5 1.0
O A:HOH760 4.4 28.2 0.4
C5' P:DT5 4.5 17.4 1.0
NH2 A:ARG416 4.5 19.0 1.0
OP1 P:DA4 4.7 17.9 1.0
CZ3 A:TRP434 4.7 17.6 1.0
O31 A:PPV507 4.8 24.8 0.7
O A:VAL331 4.8 18.1 1.0
O5' P:DA4 4.9 20.4 1.0
CA A:ASP332 4.9 15.7 1.0
N A:ASP418 4.9 16.9 1.0
CA A:ASP418 5.0 17.1 1.0
C A:VAL331 5.0 17.0 1.0

Manganese binding site 3 out of 7 in 5tyy

Go back to Manganese Binding Sites List in 5tyy
Manganese binding site 3 out of 7 in the Dna Polymerase Mu Product Complex, MN2+ (60 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+ (60 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:79.1
occ:1.00
 NE2 A:HIS219 2.3 57.0 1.0
OE1 A:GLU218 2.9 68.3 1.0
CE1 A:HIS219 3.1 54.5 1.0
CD2 A:HIS219 3.4 48.9 1.0
CD A:GLU218 4.1 68.2 1.0
ND1 A:HIS219 4.3 49.9 1.0
CG A:HIS219 4.4 46.4 1.0
CB A:GLU218 4.7 46.2 1.0
OE2 A:GLU218 4.9 73.0 1.0

Manganese binding site 4 out of 7 in 5tyy

Go back to Manganese Binding Sites List in 5tyy
Manganese binding site 4 out of 7 in the Dna Polymerase Mu Product Complex, MN2+ (60 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+ (60 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:52.7
occ:0.52
 OP3 D:DG1 2.2 33.4 1.0
O A:HOH839 2.4 44.2 1.0
ND1 A:HIS208 2.6 33.6 1.0
O D:HOH117 2.6 42.1 1.0
CE1 A:HIS208 3.3 31.9 1.0
CG A:HIS208 3.5 31.9 1.0
P D:DG1 3.5 32.8 1.0
O D:HOH114 3.5 39.1 1.0
CB A:HIS208 3.8 29.9 1.0
OP1 D:DG1 3.9 30.7 1.0
OP2 D:DG1 4.1 33.8 1.0
O D:HOH106 4.1 40.0 1.0
O A:HOH711 4.3 46.1 1.0
NE2 A:HIS208 4.3 33.6 1.0
CD2 A:HIS208 4.4 32.7 1.0
NH2 A:ARG211 4.6 55.5 1.0
O5' D:DG1 4.7 31.6 1.0
CA A:HIS208 4.8 29.2 1.0

Manganese binding site 5 out of 7 in 5tyy

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Manganese binding site 5 out of 7 in the Dna Polymerase Mu Product Complex, MN2+ (60 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+ (60 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:56.6
occ:1.00
 OE2 A:GLU386 2.3 32.6 1.0
O T:HOH201 2.5 36.8 1.0
O A:HOH799 2.5 37.9 1.0
O A:HOH848 2.6 39.2 1.0
OE1 A:GLU386 2.6 40.2 1.0
NE2 A:HIS459 2.7 33.5 1.0
CD A:GLU386 2.8 34.1 1.0
CD2 A:HIS459 3.3 32.9 1.0
CE1 A:HIS459 3.9 33.8 1.0
O A:HOH674 4.1 34.8 1.0
OP1 T:DC8 4.1 30.3 1.0
CG A:GLU386 4.3 30.8 1.0
O A:HOH617 4.4 26.3 1.0
O A:HOH847 4.6 41.3 1.0
CG A:HIS459 4.6 29.2 1.0
C5' T:DC8 4.6 26.6 1.0
ND1 A:HIS459 4.8 34.5 1.0
OE1 A:GLN426 4.8 28.3 1.0

Manganese binding site 6 out of 7 in 5tyy

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Manganese binding site 6 out of 7 in the Dna Polymerase Mu Product Complex, MN2+ (60 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+ (60 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:40.3
occ:0.56
 O T:HOH227 2.3 38.8 1.0
O T:HOH202 2.4 39.0 1.0
N7 T:DG2 2.7 34.5 1.0
C8 T:DG2 3.5 35.6 1.0
C5 T:DG2 3.8 30.9 1.0
O T:HOH203 3.8 35.1 1.0
O6 T:DG2 4.0 31.2 1.0
OP2 T:DG2 4.2 46.1 1.0
C6 T:DG2 4.3 30.4 1.0
O6 T:DG3 4.4 27.0 1.0
O D:HOH109 4.5 39.2 1.0
C2' T:DC1 4.6 45.0 1.0
N9 T:DG2 4.8 33.0 1.0
C4 T:DG2 4.9 31.6 1.0
C6 T:DC1 4.9 39.0 1.0
C3' T:DC1 4.9 50.1 1.0

Manganese binding site 7 out of 7 in 5tyy

Go back to Manganese Binding Sites List in 5tyy
Manganese binding site 7 out of 7 in the Dna Polymerase Mu Product Complex, MN2+ (60 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+ (60 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:33.3
occ:0.40
 O P:HOH214 2.1 23.2 0.4
OP2 P:DT5 2.2 21.7 1.0
O32 A:PPV507 2.2 29.6 1.0
O A:HOH797 2.3 20.5 0.4
O A:HOH601 2.3 28.0 0.4
O A:HOH760 2.7 28.2 0.4
P P:DT5 3.2 21.7 1.0
O21 A:PPV507 3.3 37.3 0.7
O31 A:PPV507 3.4 24.8 0.7
O P:HOH214 3.4 26.9 0.6
O5' P:DT5 3.6 18.0 1.0
OP1 P:DT5 3.6 19.8 1.0
P2 A:PPV507 3.7 25.0 1.0
P1 A:PPV507 3.9 43.6 0.7
O A:HOH862 4.1 41.9 1.0
C7 P:DT5 4.3 23.1 1.0
OPP A:PPV507 4.3 30.1 0.7
O12 A:PPV507 4.4 20.6 1.0
O22 A:PPV507 4.4 21.2 1.0
O P:HOH204 4.5 19.6 1.0
MN A:MN501 4.5 17.4 1.0
O A:HOH661 4.6 19.4 1.0
O3' P:DA4 4.7 21.9 1.0
C5' P:DT5 4.8 17.4 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 02:59:13 2024

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