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Manganese in PDB 5tyv: Dna Polymerase Mu Reactant Complex, MN2+ (7.5 Min)

Enzymatic activity of Dna Polymerase Mu Reactant Complex, MN2+ (7.5 Min)

All present enzymatic activity of Dna Polymerase Mu Reactant Complex, MN2+ (7.5 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu Reactant Complex, MN2+ (7.5 Min), PDB code: 5tyv 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) 23.21 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.947, 68.752, 109.994, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 21.8

Other elements in 5tyv:

The structure of Dna Polymerase Mu Reactant Complex, MN2+ (7.5 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+ (7.5 Min) (pdb code 5tyv). 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 Reactant Complex, MN2+ (7.5 Min), PDB code: 5tyv:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 5tyv

Go back to Manganese Binding Sites List in 5tyv
Manganese binding site 1 out of 7 in the Dna Polymerase Mu Reactant Complex, MN2+ (7.5 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+ (7.5 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:21.7
occ:1.00
 O1A A:TTP501 1.8 20.1 0.4
O A:HOH662 2.0 21.2 1.0
OD1 A:ASP330 2.1 22.3 1.0
OD2 A:ASP332 2.1 17.0 1.0
O21 A:PPV511 2.2 19.3 0.6
O1B A:TTP501 2.2 20.1 0.4
O1G A:TTP501 2.2 25.6 0.4
O32 A:PPV511 2.4 25.6 0.5
OP1 P:DT5 2.4 20.1 0.6
PA A:TTP501 3.1 23.7 0.4
P1 A:PPV511 3.2 22.3 0.6
CG A:ASP332 3.2 18.5 1.0
PB A:TTP501 3.2 21.5 0.4
O31 A:PPV511 3.2 25.2 0.6
CG A:ASP330 3.2 25.8 1.0
PG A:TTP501 3.4 31.3 0.4
O3A A:TTP501 3.5 25.4 0.4
MN A:MN503 3.5 23.3 1.0
P2 A:PPV511 3.6 31.4 0.5
OD1 A:ASP332 3.6 18.2 1.0
O3B A:TTP501 3.7 26.6 0.4
OD2 A:ASP330 3.7 32.4 1.0
P P:DT5 3.7 17.6 0.6
OPP A:PPV511 3.8 29.1 0.5
O2G A:TTP501 3.9 25.5 0.4
O A:ASP330 4.0 19.2 1.0
C5' A:TTP501 4.0 20.6 0.4
O5' A:TTP501 4.1 20.3 0.4
O5' P:DT5 4.1 20.2 0.6
O2A A:TTP501 4.2 25.1 0.4
O22 A:PPV511 4.2 27.4 0.5
O A:HOH785 4.2 27.3 0.5
C5' P:DT5 4.3 20.7 0.6
CE1 A:HIS329 4.3 25.1 0.4
N A:GLY320 4.3 18.9 1.0
C A:ASP330 4.3 20.8 1.0
ND1 A:HIS329 4.4 27.3 0.4
O A:HOH605 4.4 19.9 1.0
O11 A:PPV511 4.5 21.0 0.6
CB A:ASP332 4.5 17.0 1.0
CB A:ASP330 4.5 20.0 1.0
O2B A:TTP501 4.5 20.6 0.4
CA A:GLY319 4.5 16.0 1.0
O A:HOH619 4.6 28.7 1.0
O P:HOH204 4.6 26.5 1.0
MN P:MN101 4.6 35.2 0.5
O3G A:TTP501 4.6 29.1 0.4
OP2 P:DT5 4.6 22.9 0.6
N A:ASP330 4.7 19.6 1.0
O12 A:PPV511 4.7 29.2 0.5
CA A:ASP330 4.8 21.6 1.0
O3' P:DA4 4.8 24.9 0.6
N A:ASP332 4.9 17.3 1.0
N A:VAL331 4.9 19.0 1.0
O3' P:DA4 5.0 24.3 0.4

Manganese binding site 2 out of 7 in 5tyv

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Manganese binding site 2 out of 7 in the Dna Polymerase Mu Reactant Complex, MN2+ (7.5 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+ (7.5 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:23.3
occ:1.00
 OD2 A:ASP330 1.9 32.4 1.0
OP1 P:DT5 2.1 20.1 0.6
OD2 A:ASP418 2.1 20.4 1.0
OD1 A:ASP332 2.1 18.2 1.0
O P:HOH204 2.4 26.5 1.0
O1A A:TTP501 2.6 20.1 0.4
O3' P:DA4 2.7 24.9 0.6
O3' P:DA4 2.7 24.3 0.4
CG A:ASP330 2.8 25.8 1.0
P P:DT5 2.9 17.6 0.6
OD1 A:ASP330 3.1 22.3 1.0
CG A:ASP332 3.1 18.5 1.0
CG A:ASP418 3.2 20.4 1.0
OD2 A:ASP332 3.4 17.0 1.0
MN A:MN502 3.5 21.7 1.0
PA A:TTP501 3.6 23.7 0.4
C3' P:DA4 3.8 21.8 0.6
C3' P:DA4 3.8 22.1 0.4
O2A A:TTP501 3.8 25.1 0.4
OP2 P:DT5 3.8 22.9 0.6
CB A:ASP418 3.8 21.0 1.0
O5' A:TTP501 3.9 20.3 0.4
C5' P:DA4 4.0 23.2 0.4
C5' P:DA4 4.0 23.2 0.6
C4' P:DA4 4.0 23.7 0.6
C4' P:DA4 4.1 23.6 0.4
O5' P:DT5 4.1 20.2 0.6
OD1 A:ASP418 4.2 20.9 1.0
CB A:ASP330 4.2 20.0 1.0
C5' A:TTP501 4.3 20.6 0.4
C5' P:DT5 4.4 20.7 0.6
O A:HOH785 4.4 27.3 0.5
CB A:ASP332 4.5 17.0 1.0
CE1 A:HIS329 4.5 25.1 0.4
NH2 A:ARG416 4.6 19.5 1.0
OP1 P:DA4 4.6 23.3 0.4
OP1 P:DA4 4.7 23.3 0.6
O5' P:DA4 4.7 25.7 0.4
O5' P:DA4 4.7 25.8 0.6
CZ3 A:TRP434 4.7 22.3 1.0
O1G A:TTP501 4.8 25.6 0.4
O32 A:PPV511 4.9 25.6 0.5
O A:VAL331 4.9 17.4 1.0
O1B A:TTP501 5.0 20.1 0.4

Manganese binding site 3 out of 7 in 5tyv

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Manganese binding site 3 out of 7 in the Dna Polymerase Mu Reactant Complex, MN2+ (7.5 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+ (7.5 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:35.6
occ:0.51
 OE2 A:GLU386 2.3 32.4 1.0
O T:HOH202 2.4 37.6 1.0
O A:HOH791 2.5 39.9 1.0
OE1 A:GLU386 2.6 42.2 1.0
O A:HOH840 2.6 30.0 0.5
NE2 A:HIS459 2.8 34.4 1.0
CD A:GLU386 2.8 34.0 1.0
CD2 A:HIS459 3.4 35.8 1.0
CE1 A:HIS459 3.6 35.1 1.0
OP1 T:DC8 4.1 32.3 1.0
O A:HOH733 4.2 36.8 1.0
CG A:GLU386 4.3 30.6 1.0
O A:HOH624 4.4 26.9 1.0
CG A:HIS459 4.4 27.6 1.0
ND1 A:HIS459 4.4 38.0 1.0
C5' T:DC8 4.5 25.7 1.0
OE1 A:GLN426 4.7 29.4 1.0

Manganese binding site 4 out of 7 in 5tyv

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Manganese binding site 4 out of 7 in the Dna Polymerase Mu Reactant Complex, MN2+ (7.5 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+ (7.5 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:79.7
occ:1.00
 NE2 A:HIS219 2.4 57.4 1.0
OE1 A:GLU218 2.8 65.4 1.0
CE1 A:HIS219 3.2 56.4 1.0
CD2 A:HIS219 3.4 49.1 1.0
O A:HOH870 3.4 47.5 1.0
CD A:GLU218 4.0 68.3 1.0
ND1 A:HIS219 4.4 49.1 1.0
CG A:HIS219 4.5 45.5 1.0
CB A:GLU218 4.7 46.0 1.0
OE2 A:GLU218 4.8 70.6 1.0

Manganese binding site 5 out of 7 in 5tyv

Go back to Manganese Binding Sites List in 5tyv
Manganese binding site 5 out of 7 in the Dna Polymerase Mu Reactant Complex, MN2+ (7.5 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+ (7.5 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:55.4
occ:0.52
 O A:HOH833 2.2 38.4 0.5
OP3 D:DG1 2.3 32.8 1.0
ND1 A:HIS208 2.7 32.4 1.0
O D:HOH118 2.9 30.8 0.5
O D:HOH115 3.3 39.0 1.0
CG A:HIS208 3.4 31.6 1.0
CE1 A:HIS208 3.5 30.2 1.0
P D:DG1 3.6 31.9 1.0
CB A:HIS208 3.7 30.0 1.0
OP1 D:DG1 4.0 29.7 1.0
OP2 D:DG1 4.1 36.6 1.0
O D:HOH110 4.2 39.9 1.0
O A:HOH833 4.3 38.2 0.5
CD2 A:HIS208 4.4 34.2 1.0
NE2 A:HIS208 4.5 35.6 1.0
CA A:HIS208 4.5 29.9 1.0
O5' D:DG1 4.7 36.0 1.0
NH2 A:ARG211 4.8 54.1 1.0
N A:HIS208 5.0 30.9 1.0

Manganese binding site 6 out of 7 in 5tyv

Go back to Manganese Binding Sites List in 5tyv
Manganese binding site 6 out of 7 in the Dna Polymerase Mu Reactant Complex, MN2+ (7.5 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+ (7.5 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:65.6
occ:1.00
 O T:HOH203 2.4 38.2 1.0
O T:HOH201 2.6 40.9 1.0
N7 T:DG2 2.8 32.3 1.0
C8 T:DG2 3.7 34.8 1.0
C5 T:DG2 3.8 31.7 1.0
O T:HOH204 3.9 36.0 1.0
O6 T:DG2 3.9 31.2 1.0
C6 T:DG2 4.2 28.6 1.0
OP2 T:DG2 4.3 44.4 1.0
O6 T:DG3 4.4 28.1 1.0
C2' T:DC1 4.5 44.9 1.0
O D:HOH114 4.6 42.1 1.0
C6 T:DC1 4.7 38.0 1.0
C3' T:DC1 4.8 51.6 1.0
N9 T:DG2 4.9 34.0 1.0
C4 T:DG2 5.0 29.2 1.0
C5 T:DC1 5.0 31.6 1.0

Manganese binding site 7 out of 7 in 5tyv

Go back to Manganese Binding Sites List in 5tyv
Manganese binding site 7 out of 7 in the Dna Polymerase Mu Reactant Complex, MN2+ (7.5 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 Reactant Complex, MN2+ (7.5 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:35.2
occ:0.45
 O2A A:TTP501 1.8 25.1 0.4
O3A A:TTP501 1.9 25.4 0.4
O A:HOH609 2.1 23.7 0.5
O P:HOH216 2.2 21.9 0.5
PA A:TTP501 2.2 23.7 0.4
O A:HOH800 2.3 19.9 0.5
OP2 P:DT5 2.3 22.9 0.6
O31 A:PPV511 2.4 25.2 0.6
O A:HOH785 2.7 27.3 0.5
P P:DT5 3.2 17.6 0.6
O1A A:TTP501 3.3 20.1 0.4
PB A:TTP501 3.4 21.5 0.4
O5' A:TTP501 3.4 20.3 0.4
O5' P:DT5 3.5 20.2 0.6
O1G A:TTP501 3.6 25.6 0.4
OP1 P:DT5 3.6 20.1 0.6
O3G A:TTP501 3.6 29.1 0.4
O32 A:PPV511 3.6 25.6 0.5
CE1 A:HIS329 3.8 25.1 0.4
O12 A:PPV511 3.8 29.2 0.5
P1 A:PPV511 3.8 22.3 0.6
O3B A:TTP501 3.8 26.6 0.4
PG A:TTP501 3.9 31.3 0.4
P2 A:PPV511 4.1 31.4 0.5
C7 P:DT5 4.2 24.5 0.6
C5M A:TTP501 4.2 24.4 0.4
OPP A:PPV511 4.2 29.1 0.5
ND1 A:HIS329 4.2 27.3 0.4
O2B A:TTP501 4.3 20.6 0.4
O P:HOH204 4.3 26.5 1.0
O1B A:TTP501 4.3 20.1 0.4
MN A:MN502 4.6 21.7 1.0
C5' A:TTP501 4.6 20.6 0.4
O3' P:DA4 4.6 24.9 0.6
O11 A:PPV511 4.7 21.0 0.6
O21 A:PPV511 4.7 19.3 0.6
O A:HOH645 4.7 19.0 1.0
NE2 A:HIS329 4.8 26.6 0.4
C5' P:DT5 4.9 20.7 0.6
C6 A:TTP501 4.9 21.9 0.4

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 02:58:12 2024

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