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Manganese in PDB 5tyw: Dna Polymerase Mu Reactant Complex, MN2+ (10 Min)

Enzymatic activity of Dna Polymerase Mu Reactant Complex, MN2+ (10 Min)

All present enzymatic activity of Dna Polymerase Mu Reactant Complex, MN2+ (10 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu Reactant Complex, MN2+ (10 Min), PDB code: 5tyw 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) 25.06 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.983, 68.718, 109.871, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.8

Other elements in 5tyw:

The structure of Dna Polymerase Mu Reactant Complex, MN2+ (10 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 Reactant Complex, MN2+ (10 Min) (pdb code 5tyw). 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 Reactant Complex, MN2+ (10 Min), PDB code: 5tyw:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 5tyw

Go back to Manganese Binding Sites List in 5tyw
Manganese binding site 1 out of 6 in the Dna Polymerase Mu Reactant Complex, MN2+ (10 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 Reactant Complex, MN2+ (10 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:23.0
occ:1.00
 OD2 A:ASP330 1.9 31.1 1.0
OD2 A:ASP418 2.0 19.2 1.0
OP1 P:DT5 2.1 23.5 0.7
OD1 A:ASP332 2.1 19.6 1.0
O P:HOH203 2.3 26.7 1.0
O1A A:TTP501 2.5 24.4 0.3
O3' P:DA4 2.7 26.4 0.3
O3' P:DA4 2.7 26.6 0.7
CG A:ASP330 2.8 29.4 1.0
P P:DT5 2.9 26.3 0.7
CG A:ASP418 3.1 21.7 1.0
CG A:ASP332 3.1 22.6 1.0
OD1 A:ASP330 3.1 24.4 1.0
OD2 A:ASP332 3.4 20.1 1.0
MN A:MN504 3.5 24.3 1.0
PA A:TTP501 3.5 28.3 0.3
O2A A:TTP501 3.7 29.8 0.3
C3' P:DA4 3.8 24.3 0.3
CB A:ASP418 3.8 19.6 1.0
C3' P:DA4 3.8 24.2 0.7
OP2 P:DT5 3.9 28.6 0.7
C5' P:DA4 3.9 23.4 0.3
C4' P:DA4 4.0 23.0 0.7
C5' P:DA4 4.0 23.4 0.7
O5' A:TTP501 4.0 25.2 0.3
C4' P:DA4 4.0 23.0 0.3
OD1 A:ASP418 4.0 21.7 1.0
O5' P:DT5 4.1 25.2 0.7
CB A:ASP330 4.2 20.2 1.0
C5' A:TTP501 4.3 23.7 0.3
C5' P:DT5 4.4 23.6 0.7
CB A:ASP332 4.5 15.8 1.0
NH2 A:ARG416 4.5 19.2 1.0
CE1 A:HIS329 4.6 27.7 0.3
OP1 P:DA4 4.6 21.7 0.3
OP1 P:DA4 4.6 21.7 0.7
O5' P:DA4 4.7 23.6 0.3
CZ3 A:TRP434 4.7 20.4 1.0
O5' P:DA4 4.7 23.7 0.7
O1G A:TTP501 4.7 31.1 0.3
O A:VAL331 4.9 16.4 1.0
O1B A:TTP501 4.9 24.9 0.3
O3A A:TTP501 5.0 30.8 0.3
O31 A:PPV502 5.0 31.4 0.6
N A:ASP418 5.0 16.9 1.0

Manganese binding site 2 out of 6 in 5tyw

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Manganese binding site 2 out of 6 in the Dna Polymerase Mu Reactant Complex, MN2+ (10 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 Reactant Complex, MN2+ (10 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:24.3
occ:1.00
 O1A A:TTP501 1.8 24.4 0.3
OD1 A:ASP330 2.1 24.4 1.0
O A:HOH683 2.2 21.7 1.0
O1B A:TTP501 2.2 24.9 0.3
O1G A:TTP501 2.2 31.1 0.3
OD2 A:ASP332 2.2 20.1 1.0
O12 A:PPV502 2.2 21.9 0.7
O31 A:PPV502 2.3 31.4 0.6
OP1 P:DT5 2.4 23.5 0.7
PA A:TTP501 3.1 28.3 0.3
PB A:TTP501 3.1 26.2 0.3
CG A:ASP330 3.2 29.4 1.0
CG A:ASP332 3.2 22.6 1.0
P2 A:PPV502 3.3 26.3 0.7
PG A:TTP501 3.3 42.3 0.3
O3A A:TTP501 3.3 30.8 0.3
O32 A:PPV502 3.4 32.8 0.7
O3B A:TTP501 3.5 32.6 0.3
MN A:MN503 3.5 23.0 1.0
P1 A:PPV502 3.5 44.4 0.6
OD1 A:ASP332 3.6 19.6 1.0
OD2 A:ASP330 3.7 31.1 1.0
P P:DT5 3.7 26.3 0.7
OPP A:PPV502 3.9 34.2 0.6
O2G A:TTP501 4.0 33.7 0.3
O A:ASP330 4.0 19.6 1.0
O5' P:DT5 4.1 25.2 0.7
O5' A:TTP501 4.1 25.2 0.3
C5' A:TTP501 4.1 23.7 0.3
O2A A:TTP501 4.1 29.8 0.3
O11 A:PPV502 4.1 33.8 0.6
C5' P:DT5 4.2 23.6 0.7
CE1 A:HIS329 4.3 27.7 0.3
N A:GLY320 4.3 16.1 1.0
ND1 A:HIS329 4.3 32.4 0.3
C A:ASP330 4.4 20.1 1.0
O A:HOH606 4.4 24.5 0.7
O A:HOH616 4.4 18.3 1.0
O2B A:TTP501 4.4 25.6 0.3
MN P:MN101 4.5 44.3 0.6
O P:HOH203 4.5 26.7 1.0
CB A:ASP330 4.5 20.2 1.0
O3G A:TTP501 4.5 38.1 0.3
CB A:ASP332 4.5 15.8 1.0
CA A:GLY319 4.6 16.7 1.0
O22 A:PPV502 4.6 25.8 0.7
OP2 P:DT5 4.6 28.6 0.7
O21 A:PPV502 4.7 38.5 0.6
N A:ASP330 4.8 18.9 1.0
CA A:ASP330 4.8 21.1 1.0
O3' P:DA4 4.8 26.6 0.7
O3' P:DA4 4.8 26.4 0.3
N A:ASP332 4.9 15.8 1.0
N A:VAL331 4.9 17.0 1.0

Manganese binding site 3 out of 6 in 5tyw

Go back to Manganese Binding Sites List in 5tyw
Manganese binding site 3 out of 6 in the Dna Polymerase Mu Reactant Complex, MN2+ (10 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 Reactant Complex, MN2+ (10 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:76.6
occ:1.00
 OE2 A:GLU386 2.3 36.2 1.0
OE1 A:GLU386 2.6 48.1 1.0
O T:HOH201 2.7 38.7 1.0
CD A:GLU386 2.8 37.4 1.0
O A:HOH856 2.8 44.0 1.0
O A:HOH819 2.8 41.7 1.0
CE1 A:HIS459 3.1 35.8 1.0
NE2 A:HIS459 3.6 37.0 1.0
ND1 A:HIS459 3.8 39.2 1.0
OP1 T:DC8 4.1 34.8 1.0
CG A:GLU386 4.3 33.3 1.0
O A:HOH713 4.3 38.4 1.0
O T:HOH228 4.4 42.5 1.0
O A:HOH626 4.4 27.9 1.0
C5' T:DC8 4.5 27.3 1.0
CD2 A:HIS459 4.6 37.5 1.0
CG A:HIS459 4.7 28.6 1.0
OE1 A:GLN426 5.0 29.2 1.0

Manganese binding site 4 out of 6 in 5tyw

Go back to Manganese Binding Sites List in 5tyw
Manganese binding site 4 out of 6 in the Dna Polymerase Mu Reactant Complex, MN2+ (10 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 Reactant Complex, MN2+ (10 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:81.1
occ:1.00
 NE2 A:HIS219 2.4 57.7 1.0
OE1 A:GLU218 2.8 68.3 1.0
CE1 A:HIS219 3.2 53.5 1.0
CD2 A:HIS219 3.4 49.7 1.0
CD A:GLU218 4.1 72.7 1.0
ND1 A:HIS219 4.4 50.5 1.0
CG A:HIS219 4.5 44.8 1.0
CB A:GLU218 4.7 45.0 1.0
OE2 A:GLU218 4.9 68.8 1.0

Manganese binding site 5 out of 6 in 5tyw

Go back to Manganese Binding Sites List in 5tyw
Manganese binding site 5 out of 6 in the Dna Polymerase Mu Reactant Complex, MN2+ (10 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 Reactant Complex, MN2+ (10 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:75.4
occ:1.00
 O T:HOH203 2.4 48.0 1.0
N7 T:DG2 2.8 30.9 1.0
C8 T:DG2 3.6 31.5 1.0
O T:HOH202 3.7 37.9 1.0
C5 T:DG2 3.9 30.1 1.0
O6 T:DG2 4.1 32.6 1.0
OP2 T:DG2 4.3 44.8 1.0
C6 T:DG2 4.4 28.2 1.0
O6 T:DG3 4.4 26.6 1.0
O D:HOH113 4.6 45.4 1.0
C2' T:DC1 4.6 48.6 1.0
C6 T:DC1 4.9 42.7 1.0
C3' T:DC1 4.9 53.7 1.0
N9 T:DG2 4.9 31.1 1.0

Manganese binding site 6 out of 6 in 5tyw

Go back to Manganese Binding Sites List in 5tyw
Manganese binding site 6 out of 6 in the Dna Polymerase Mu Reactant Complex, MN2+ (10 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 Reactant Complex, MN2+ (10 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:44.3
occ:0.55
 O2A A:TTP501 1.8 29.8 0.3
O3A A:TTP501 1.9 30.8 0.3
O A:HOH603 2.0 29.4 0.6
OP2 P:DT5 2.2 28.6 0.7
O32 A:PPV502 2.3 32.8 0.7
PA A:TTP501 2.3 28.3 0.3
O A:HOH818 2.3 28.4 0.6
O P:HOH212 2.5 29.9 0.6
P P:DT5 3.1 26.3 0.7
O3G A:TTP501 3.4 38.1 0.3
O1A A:TTP501 3.4 24.4 0.3
PB A:TTP501 3.4 26.2 0.3
O31 A:PPV502 3.5 31.4 0.6
O5' A:TTP501 3.5 25.2 0.3
O1G A:TTP501 3.5 31.1 0.3
O5' P:DT5 3.5 25.2 0.7
OP1 P:DT5 3.5 23.5 0.7
CE1 A:HIS329 3.6 27.7 0.3
PG A:TTP501 3.7 42.3 0.3
P2 A:PPV502 3.7 26.3 0.7
O21 A:PPV502 3.8 38.5 0.6
O3B A:TTP501 3.8 32.6 0.3
P1 A:PPV502 4.0 44.4 0.6
ND1 A:HIS329 4.1 32.4 0.3
C5M A:TTP501 4.2 28.1 0.3
O2B A:TTP501 4.2 25.6 0.3
C7 P:DT5 4.2 28.2 0.7
O P:HOH203 4.3 26.7 1.0
OPP A:PPV502 4.3 34.2 0.6
O1B A:TTP501 4.3 24.9 0.3
O12 A:PPV502 4.5 21.9 0.7
MN A:MN504 4.5 24.3 1.0
NE2 A:HIS329 4.5 28.6 0.3
O22 A:PPV502 4.5 25.8 0.7
O3' P:DA4 4.6 26.6 0.7
C5' A:TTP501 4.7 23.7 0.3
O A:HOH702 4.8 19.9 1.0
C5' P:DT5 4.8 23.6 0.7
O3' P:DA4 4.9 26.4 0.3

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 02:58:30 2024

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