Atomistry » Manganese » PDB 5svc-5uqn » 5tyy
Atomistry »
  Manganese »
    PDB 5svc-5uqn »
      5tyy »

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

Go back to Manganese Binding Sites List in 5tyy
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

Go back to Manganese Binding Sites List in 5tyy
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy