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Manganese in PDB 5tyz: Dna Polymerase Mu Product Complex, MN2+ (960 Min)

Enzymatic activity of Dna Polymerase Mu Product Complex, MN2+ (960 Min)

All present enzymatic activity of Dna Polymerase Mu Product Complex, MN2+ (960 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu Product Complex, MN2+ (960 Min), PDB code: 5tyz 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) 21.98 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.934, 68.653, 109.999, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.5

Other elements in 5tyz:

The structure of Dna Polymerase Mu Product Complex, MN2+ (960 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+ (960 Min) (pdb code 5tyz). 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 Product Complex, MN2+ (960 Min), PDB code: 5tyz:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 5tyz

Go back to Manganese Binding Sites List in 5tyz
Manganese binding site 1 out of 6 in the Dna Polymerase Mu Product Complex, MN2+ (960 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+ (960 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:23.3
occ:1.00
 O A:HOH628 2.0 23.8 1.0
OD2 A:ASP332 2.1 22.2 1.0
OD1 A:ASP330 2.1 27.1 1.0
OP1 P:DT5 2.2 20.6 1.0
O11 A:GOA513 2.2 25.9 1.0
O2 A:GOA513 2.2 40.6 1.0
C1 A:GOA513 3.0 24.5 1.0
CG A:ASP332 3.1 21.6 1.0
C2 A:GOA513 3.1 35.3 1.0
CG A:ASP330 3.2 32.5 1.0
MN A:MN502 3.3 28.8 1.0
OD1 A:ASP332 3.4 23.1 1.0
P P:DT5 3.5 30.3 1.0
OD2 A:ASP330 3.6 35.9 1.0
O5' P:DT5 3.9 28.0 1.0
C5' P:DT5 4.0 29.9 1.0
O A:HOH819 4.1 19.0 0.6
O12 A:GOA513 4.2 26.5 1.0
O A:ASP330 4.3 22.9 1.0
O A:HOH608 4.3 24.0 1.0
N A:GLY320 4.3 21.5 1.0
OP2 P:DT5 4.4 30.5 1.0
O P:HOH105 4.4 29.7 1.0
O A:HOH819 4.4 21.3 0.5
CB A:ASP332 4.4 18.9 1.0
CA A:GLY319 4.5 21.4 1.0
C A:ASP330 4.5 25.8 1.0
CB A:ASP330 4.5 30.0 1.0
O3' P:DA4 4.6 26.3 1.0
CA A:ASP330 4.9 28.9 1.0
N A:ASP332 5.0 19.6 1.0

Manganese binding site 2 out of 6 in 5tyz

Go back to Manganese Binding Sites List in 5tyz
Manganese binding site 2 out of 6 in the Dna Polymerase Mu Product Complex, MN2+ (960 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+ (960 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:28.8
occ:1.00
 OD2 A:ASP330 1.8 35.9 1.0
OD2 A:ASP418 2.1 23.4 1.0
OD1 A:ASP332 2.1 23.1 1.0
OP1 P:DT5 2.1 20.6 1.0
O P:HOH105 2.3 29.7 1.0
CG A:ASP330 2.7 32.5 1.0
O3' P:DA4 2.8 26.3 1.0
P P:DT5 3.0 30.3 1.0
OD1 A:ASP330 3.0 27.1 1.0
CG A:ASP418 3.1 25.3 1.0
CG A:ASP332 3.1 21.6 1.0
MN A:MN501 3.3 23.3 1.0
OD2 A:ASP332 3.4 22.2 1.0
CB A:ASP418 3.8 25.0 1.0
OP2 P:DT5 4.0 30.5 1.0
C3' P:DA4 4.0 23.9 1.0
OD1 A:ASP418 4.0 25.8 1.0
CB A:ASP330 4.1 30.0 1.0
C5' P:DA4 4.1 28.9 1.0
C4' P:DA4 4.1 25.4 1.0
O5' P:DT5 4.3 28.0 1.0
CB A:ASP332 4.5 18.9 1.0
C5' P:DT5 4.5 29.9 1.0
NH2 A:ARG416 4.5 24.7 1.0
O2 A:GOA513 4.6 40.6 1.0
O A:VAL331 4.6 21.5 1.0
OP1 P:DA4 4.7 24.2 1.0
CZ3 A:TRP434 4.8 23.3 1.0
O A:HOH628 4.9 23.8 1.0
N A:ASP418 4.9 22.1 1.0
O5' P:DA4 4.9 23.9 1.0
C A:VAL331 4.9 20.0 1.0
CA A:ASP332 5.0 19.4 1.0
CA A:ASP418 5.0 24.0 1.0

Manganese binding site 3 out of 6 in 5tyz

Go back to Manganese Binding Sites List in 5tyz
Manganese binding site 3 out of 6 in the Dna Polymerase Mu Product Complex, MN2+ (960 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+ (960 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:51.3
occ:0.44
 OP3 D:DG1 2.3 37.8 1.0
O A:HOH820 2.5 40.2 0.5
ND1 A:HIS208 2.5 38.6 1.0
O D:HOH111 2.7 67.0 1.0
CE1 A:HIS208 3.3 36.5 1.0
CG A:HIS208 3.3 37.5 1.0
P D:DG1 3.6 37.7 1.0
CB A:HIS208 3.6 37.7 1.0
O D:HOH104 3.6 50.8 1.0
OP1 D:DG1 4.0 40.9 1.0
OP2 D:DG1 4.1 35.6 1.0
O D:HOH103 4.3 47.8 1.0
NE2 A:HIS208 4.3 36.1 1.0
CD2 A:HIS208 4.3 35.2 1.0
O A:HOH820 4.4 38.0 0.5
CA A:HIS208 4.5 39.8 1.0
O5' D:DG1 4.7 33.3 1.0

Manganese binding site 4 out of 6 in 5tyz

Go back to Manganese Binding Sites List in 5tyz
Manganese binding site 4 out of 6 in the Dna Polymerase Mu Product Complex, MN2+ (960 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+ (960 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:88.8
occ:1.00
 O A:HOH634 1.8 52.2 1.0
NE2 A:HIS219 2.3 55.7 1.0
OE1 A:GLU218 2.7 86.1 1.0
CE1 A:HIS219 3.1 56.3 1.0
O A:HOH857 3.3 65.6 1.0
CD2 A:HIS219 3.5 52.3 1.0
CD A:GLU218 4.0 84.1 1.0
ND1 A:HIS219 4.3 55.5 1.0
CG A:HIS219 4.5 52.6 1.0
OE2 A:GLU218 4.7 86.8 1.0
CB A:GLU218 4.7 65.4 1.0
CG A:GLU218 5.0 77.1 1.0

Manganese binding site 5 out of 6 in 5tyz

Go back to Manganese Binding Sites List in 5tyz
Manganese binding site 5 out of 6 in the Dna Polymerase Mu Product Complex, MN2+ (960 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+ (960 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:40.3
occ:0.48
 OE2 A:GLU386 2.3 44.3 1.0
O A:HOH791 2.3 49.8 1.0
NE2 A:HIS459 2.4 42.5 1.0
O T:HOH201 2.5 43.5 1.0
O A:HOH821 2.5 40.6 1.0
OE1 A:GLU386 2.6 46.5 1.0
CD A:GLU386 2.8 44.1 1.0
CD2 A:HIS459 3.1 43.9 1.0
CE1 A:HIS459 3.5 43.4 1.0
O A:HOH720 4.1 44.2 1.0
OP1 T:DC8 4.2 34.5 1.0
CG A:GLU386 4.3 42.8 1.0
CG A:HIS459 4.4 38.8 1.0
O A:HOH630 4.4 33.1 1.0
ND1 A:HIS459 4.5 44.6 1.0
OE1 A:GLN426 4.7 35.1 1.0
C5' T:DC8 4.7 30.0 1.0

Manganese binding site 6 out of 6 in 5tyz

Go back to Manganese Binding Sites List in 5tyz
Manganese binding site 6 out of 6 in the Dna Polymerase Mu Product Complex, MN2+ (960 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+ (960 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:86.6
occ:1.00
 O T:HOH210 2.4 50.6 1.0
O T:HOH203 2.5 58.9 1.0
N7 T:DG2 2.7 37.1 1.0
C8 T:DG2 3.5 39.4 1.0
O T:HOH202 3.6 41.6 1.0
C5 T:DG2 3.8 36.2 1.0
O6 T:DG2 4.0 35.7 1.0
OP2 T:DG2 4.1 68.9 1.0
C6 T:DG2 4.3 35.5 1.0
O6 T:DG3 4.4 32.7 1.0
C2' T:DC1 4.6 64.6 1.0
N9 T:DG2 4.8 38.2 1.0
C3' T:DC1 4.9 67.1 1.0
C4 T:DG2 4.9 36.3 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 02:59:48 2024

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