Atomistry » Manganese » PDB 7ksu-7lrd » 7kt2
Atomistry »
  Manganese »
    PDB 7ksu-7lrd »
      7kt2 »

Manganese in PDB 7kt2: Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN)

Enzymatic activity of Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN)

All present enzymatic activity of Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN), PDB code: 7kt2 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) 34.96 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.893, 68.866, 110.319, 90, 90, 90
R / Rfree (%) 16.8 / 18.9

Other elements in 7kt2:

The structure of Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN) (pdb code 7kt2). 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, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN), PDB code: 7kt2:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 7kt2

Go back to Manganese Binding Sites List in 7kt2
Manganese binding site 1 out of 7 in the Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN)


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, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:12.7
occ:0.94
 O1G A:DGT511 2.1 14.9 1.0
OD1 A:ASP330 2.1 15.0 1.0
OD2 A:ASP332 2.1 14.4 1.0
O A:HOH735 2.2 16.1 1.0
O2B A:DGT511 2.2 17.1 0.9
OP1 P:DG5 2.3 23.2 1.0
CG A:ASP332 3.2 15.4 1.0
CG A:ASP330 3.2 16.2 1.0
PG A:DGT511 3.3 16.5 1.0
PB A:DGT511 3.5 14.9 0.6
MN A:MN503 3.5 15.7 1.0
O3B A:DGT511 3.5 19.0 1.0
OD1 A:ASP332 3.5 14.8 1.0
OD2 A:ASP330 3.6 21.6 1.0
P P:DG5 3.7 23.4 1.0
O A:HOH644 3.9 25.6 1.0
O5' P:DG5 4.0 23.7 1.0
C5' P:DG5 4.1 23.9 1.0
O A:HOH707 4.1 27.1 1.0
O3G A:DGT511 4.1 23.9 1.0
O A:ASP330 4.3 14.6 1.0
O A:HOH620 4.3 16.0 1.0
N A:GLY320 4.4 11.8 1.0
C A:ASP330 4.5 14.3 1.0
CB A:ASP332 4.5 12.1 1.0
OP2 P:DG5 4.5 23.2 1.0
O P:HOH202 4.5 20.9 1.0
O3A A:DGT511 4.5 23.8 1.0
O1B A:DGT511 4.5 18.2 0.7
CB A:ASP330 4.5 14.3 1.0
O2G A:DGT511 4.6 18.1 1.0
CA A:GLY319 4.7 11.7 1.0
O3' P:DA4 4.7 23.4 1.0
O1A A:DGT511 4.8 28.2 0.9
N A:ASP330 4.8 15.1 1.0
CA A:ASP330 4.9 16.7 1.0
N A:ASP332 4.9 13.4 1.0
N A:VAL331 5.0 14.4 1.0

Manganese binding site 2 out of 7 in 7kt2

Go back to Manganese Binding Sites List in 7kt2
Manganese binding site 2 out of 7 in the Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN)


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, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:15.7
occ:1.00
 OD2 A:ASP330 2.1 21.6 1.0
OD2 A:ASP418 2.1 16.7 1.0
OD1 A:ASP332 2.1 14.8 1.0
OP1 P:DG5 2.1 23.2 1.0
O P:HOH202 2.2 20.9 1.0
O3' P:DA4 2.6 23.4 1.0
P P:DG5 2.9 23.4 1.0
CG A:ASP330 3.0 16.2 1.0
CG A:ASP418 3.1 14.9 1.0
CG A:ASP332 3.1 15.4 1.0
OD1 A:ASP330 3.2 15.0 1.0
OD2 A:ASP332 3.5 14.4 1.0
MN A:MN502 3.5 12.7 0.9
CB A:ASP418 3.8 15.3 1.0
C3' P:DA4 3.8 23.4 1.0
OP2 P:DG5 3.9 23.2 1.0
C4' P:DA4 4.0 23.3 1.0
OD1 A:ASP418 4.0 17.3 1.0
C5' P:DA4 4.0 22.9 1.0
O5' P:DG5 4.1 23.7 1.0
O A:HOH707 4.2 27.1 1.0
C5' P:DG5 4.2 23.9 1.0
CB A:ASP330 4.3 14.3 1.0
CB A:ASP332 4.4 12.1 1.0
O2B A:DGT511 4.5 17.1 0.9
NH2 A:ARG416 4.6 20.6 1.0
OP1 P:DA4 4.7 25.7 1.0
CZ3 A:TRP434 4.8 19.9 1.0
O5' P:DA4 4.8 22.8 1.0
CA A:ASP332 5.0 12.8 1.0
C2' P:DA4 5.0 23.7 1.0
N A:ASP418 5.0 13.9 1.0

Manganese binding site 3 out of 7 in 7kt2

Go back to Manganese Binding Sites List in 7kt2
Manganese binding site 3 out of 7 in the Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN)


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, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:28.9
occ:0.32
 O D:HOH219 1.8 46.4 0.9
OP3 D:DG1 2.1 27.5 1.0
O D:HOH208 2.3 46.3 1.0
ND1 A:HIS208 2.4 30.9 1.0
CE1 A:HIS208 3.2 33.5 1.0
CG A:HIS208 3.3 29.0 1.0
P D:DG1 3.4 27.1 1.0
O D:HOH215 3.7 44.5 1.0
OP1 D:DG1 3.7 31.1 1.0
CB A:HIS208 3.7 26.2 1.0
O D:HOH202 4.1 50.0 1.0
OP2 D:DG1 4.1 31.3 1.0
NE2 A:HIS208 4.2 30.0 1.0
CD2 A:HIS208 4.3 36.0 1.0
O A:HOH617 4.5 47.1 1.0
O5' D:DG1 4.6 24.8 1.0
CA A:HIS208 4.6 25.3 1.0
C5' D:DG1 4.8 26.5 1.0

Manganese binding site 4 out of 7 in 7kt2

Go back to Manganese Binding Sites List in 7kt2
Manganese binding site 4 out of 7 in the Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN)


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, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:55.1
occ:0.74
 NE2 A:HIS219 2.1 54.6 1.0
CE1 A:HIS219 3.1 54.5 1.0
CD2 A:HIS219 3.2 42.2 1.0
CD A:GLU218 4.0 46.3 1.0
ND1 A:HIS219 4.2 44.3 1.0
CG A:HIS219 4.3 43.9 1.0
CB A:GLU218 4.8 31.3 1.0
CG A:GLU218 5.0 45.6 1.0

Manganese binding site 5 out of 7 in 7kt2

Go back to Manganese Binding Sites List in 7kt2
Manganese binding site 5 out of 7 in the Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN)


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, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:30.8
occ:0.40
 OE2 A:GLU386 2.2 38.8 1.0
O A:HOH817 2.2 40.9 1.0
O A:HOH841 2.2 32.1 0.5
OE1 A:GLU386 2.3 50.1 1.0
O T:HOH103 2.4 39.7 1.0
CD A:GLU386 2.6 34.5 1.0
CE1 A:HIS459 2.7 45.0 1.0
ND1 A:HIS459 3.5 47.8 1.0
NE2 A:HIS459 3.5 39.9 1.0
O A:HOH841 3.6 37.2 0.5
O A:HOH662 4.1 34.4 1.0
CG A:GLU386 4.2 37.5 1.0
OP1 T:DC8 4.3 32.6 1.0
O A:HOH604 4.4 27.3 1.0
CG A:HIS459 4.6 29.9 1.0
CD2 A:HIS459 4.6 43.5 1.0
C5' T:DC8 4.6 23.9 1.0
OE1 A:GLN426 4.8 25.2 1.0

Manganese binding site 6 out of 7 in 7kt2

Go back to Manganese Binding Sites List in 7kt2
Manganese binding site 6 out of 7 in the Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN)


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, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:16.6
occ:0.49
 O P:HOH212 1.7 30.9 0.8
O1B A:DGT511 2.1 18.2 0.7
OP2 P:DG5 2.1 23.2 1.0
O A:HOH717 2.1 29.4 0.8
O P:HOH210 2.2 29.0 1.0
PB A:DGT511 3.5 14.9 0.6
P P:DG5 3.5 23.4 1.0
O A:HOH707 3.8 27.1 1.0
O P:HOH214 4.0 34.3 1.0
O3B A:DGT511 4.0 19.0 1.0
O3' A:DGT511 4.1 35.6 0.6
O2B A:DGT511 4.2 17.1 0.9
OP1 P:DG5 4.3 23.2 1.0
O P:HOH202 4.3 20.9 1.0
O5' P:DG5 4.3 23.7 1.0
OP2 P:DA4 4.5 22.4 1.0
O3A A:DGT511 4.6 23.8 1.0
C5' A:DGT511 4.6 35.4 0.8
O3' P:DA4 4.6 23.4 1.0
C4' A:DGT511 4.6 29.3 0.8
C3' A:DGT511 4.7 33.5 0.6
C3' P:DA4 4.7 23.4 1.0
O5' P:DA4 4.8 22.8 1.0
OP1 P:DA4 4.8 25.7 1.0
P P:DA4 5.0 22.4 1.0

Manganese binding site 7 out of 7 in 7kt2

Go back to Manganese Binding Sites List in 7kt2
Manganese binding site 7 out of 7 in the Dna Polymerase Mu, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN)


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, Dgtp:at Product State Ternary Complex, 50 Mm MN2+ (225MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn101

b:64.8
occ:0.50
 N7 D:DG1 2.4 23.2 1.0
O D:HOH211 2.5 45.8 1.0
O D:HOH214 2.5 46.8 1.0
C8 D:DG1 3.3 23.4 1.0
C5 D:DG1 3.6 20.9 1.0
O6 D:DG1 3.8 26.0 1.0
C6 D:DG1 4.1 23.3 1.0
O D:HOH209 4.5 43.4 1.0
N9 D:DG1 4.6 22.9 1.0
CG A:ARG175 4.6 24.6 1.0
OP2 D:DG1 4.6 31.3 1.0
C4 D:DG1 4.7 19.5 1.0
O A:HOH822 4.7 35.4 1.0
CD A:ARG175 4.8 29.4 1.0
N4 D:DC2 4.9 25.9 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Watching A Double Strand Break Repair Polymerase Insert A Pro-Mutagenic Oxidized Nucleotide. Nat Commun V. 12 2059 2021.
ISSN: ESSN 2041-1723
PubMed: 33824325
DOI: 10.1038/S41467-021-21354-6
Page generated: Sun Oct 6 09:28:26 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy