Atomistry » Manganese » PDB 6vf5-6wij » 6vfa
Atomistry »
  Manganese »
    PDB 6vf5-6wij »
      6vfa »

Manganese in PDB 6vfa: Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min)

Enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min), PDB code: 6vfa 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 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.079, 62.215, 118.925, 90, 90, 90
R / Rfree (%) 17.5 / 20.3

Other elements in 6vfa:

The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 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, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min) (pdb code 6vfa). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min), PDB code: 6vfa:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 6vfa

Go back to Manganese Binding Sites List in 6vfa
Manganese binding site 1 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 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, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:19.4
occ:1.00
 OD2 A:ASP330 2.1 21.4 1.0
OD1 A:ASP332 2.1 17.9 1.0
OD2 A:ASP418 2.2 19.5 1.0
O P:HOH106 2.3 19.9 1.0
O A:HOH785 2.3 21.5 1.0
O1G A:8GT508 2.3 17.8 1.0
CG A:ASP330 3.1 18.4 1.0
CG A:ASP332 3.2 20.5 1.0
CG A:ASP418 3.3 20.6 1.0
PG A:8GT508 3.4 21.6 1.0
OD1 A:ASP330 3.4 19.0 1.0
MN A:MN502 3.6 18.4 1.0
OD2 A:ASP332 3.6 18.8 1.0
O2G A:8GT508 3.7 24.1 1.0
CB A:ASP418 3.9 16.6 1.0
O3G A:8GT508 4.0 23.6 1.0
OD1 A:ASP418 4.2 18.6 1.0
CE1 A:HIS329 4.2 25.4 1.0
CB A:ASP332 4.4 15.6 1.0
CB A:ASP330 4.4 15.8 1.0
OP1 P:DA4 4.5 21.4 1.0
NH2 A:ARG416 4.6 18.1 1.0
O3B A:8GT508 4.8 21.5 1.0
NE2 A:HIS329 4.8 27.3 1.0
CZ3 A:TRP434 4.9 30.7 1.0

Manganese binding site 2 out of 8 in 6vfa

Go back to Manganese Binding Sites List in 6vfa
Manganese binding site 2 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 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, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:18.4
occ:1.00
 O1G A:8GT508 2.1 17.8 1.0
O2B A:8GT508 2.1 17.4 1.0
OD1 A:ASP330 2.1 19.0 1.0
OD2 A:ASP332 2.1 18.8 1.0
O A:HOH669 2.3 17.7 1.0
O2A A:8GT508 2.4 28.2 1.0
CG A:ASP332 3.1 20.5 1.0
CG A:ASP330 3.1 18.4 1.0
PB A:8GT508 3.2 20.7 1.0
PG A:8GT508 3.2 21.6 1.0
O3B A:8GT508 3.4 21.5 1.0
OD1 A:ASP332 3.4 17.9 1.0
OD2 A:ASP330 3.5 21.4 1.0
MN A:MN501 3.6 19.4 1.0
PA A:8GT508 3.7 31.9 1.0
O3A A:8GT508 3.8 25.2 1.0
O3G A:8GT508 3.9 23.6 1.0
O A:ASP330 4.1 19.2 1.0
ND1 A:HIS329 4.2 25.6 1.0
CE1 A:HIS329 4.2 25.4 1.0
O A:HOH645 4.3 18.8 1.0
N A:GLY320 4.3 19.7 1.0
C A:ASP330 4.3 18.7 1.0
O A:HOH777 4.3 23.6 1.0
CB A:ASP332 4.5 15.6 1.0
O2G A:8GT508 4.5 24.1 1.0
CB A:ASP330 4.5 15.8 1.0
CA A:GLY319 4.5 20.3 1.0
O1B A:8GT508 4.5 21.8 1.0
O1A A:8GT508 4.6 40.2 1.0
N A:ASP330 4.6 18.7 1.0
CA A:ASP330 4.7 17.4 1.0
O5' A:8GT508 4.8 44.6 1.0
N A:ASP332 4.8 15.7 1.0
N A:VAL331 4.9 18.3 1.0
O A:HOH785 4.9 21.5 1.0
O P:HOH106 4.9 19.9 1.0
C A:GLY319 5.0 17.9 1.0

Manganese binding site 3 out of 8 in 6vfa

Go back to Manganese Binding Sites List in 6vfa
Manganese binding site 3 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 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, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:37.4
occ:0.62
 O A:HOH816 1.9 37.3 0.8
O A:HOH742 2.0 38.9 0.8
NE2 A:HIS152 2.1 54.5 1.0
CE1 A:HIS152 2.9 54.4 1.0
O A:HOH616 3.2 51.3 1.0
CD2 A:HIS152 3.2 52.2 1.0
ND1 A:HIS152 4.1 54.0 1.0
CG A:HIS152 4.3 50.5 1.0
O A:PRO190 4.4 34.3 1.0
O A:HOH630 4.4 29.6 1.0
O A:THR150 4.5 27.3 1.0

Manganese binding site 4 out of 8 in 6vfa

Go back to Manganese Binding Sites List in 6vfa
Manganese binding site 4 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 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, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:31.2
occ:0.50
 O D:HOH212 2.0 38.3 1.0
OP3 D:DG1 2.1 35.9 1.0
O D:HOH215 2.2 44.4 1.0
O A:HOH795 2.3 45.6 1.0
ND1 A:HIS208 2.3 32.6 1.0
CE1 A:HIS208 3.2 33.9 1.0
CG A:HIS208 3.3 31.5 1.0
P D:DG1 3.4 30.4 1.0
OP1 D:DG1 3.7 28.2 1.0
CB A:HIS208 3.7 27.9 1.0
O D:HOH210 4.0 40.1 1.0
OP2 D:DG1 4.1 28.4 1.0
O D:HOH205 4.1 43.6 1.0
NE2 A:HIS208 4.3 32.8 1.0
CD2 A:HIS208 4.4 32.9 1.0
O5' D:DG1 4.5 25.8 1.0
CA A:HIS208 4.7 28.4 1.0
C5' D:DG1 4.8 25.8 1.0

Manganese binding site 5 out of 8 in 6vfa

Go back to Manganese Binding Sites List in 6vfa
Manganese binding site 5 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 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, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:83.1
occ:1.00
 NE2 A:HIS219 2.3 52.7 1.0
O A:HOH787 2.4 50.2 1.0
OE1 A:GLU218 3.0 62.2 1.0
CE1 A:HIS219 3.1 53.5 1.0
CD2 A:HIS219 3.4 52.1 1.0
CD A:GLU218 4.1 59.8 1.0
ND1 A:HIS219 4.3 53.8 1.0
CG A:HIS219 4.4 52.7 1.0
CB A:GLU218 4.7 47.3 1.0
OE2 A:GLU218 4.7 60.6 1.0
CG A:GLU218 5.0 54.0 1.0

Manganese binding site 6 out of 8 in 6vfa

Go back to Manganese Binding Sites List in 6vfa
Manganese binding site 6 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 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, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:36.9
occ:0.55
 O A:HOH809 2.0 42.3 0.8
O T:HOH201 2.2 42.2 1.0
OE2 A:GLU386 2.3 42.3 1.0
O A:HOH783 2.3 39.6 0.9
NE2 A:HIS459 2.5 43.9 1.0
CD A:GLU386 3.0 42.6 1.0
OE1 A:GLU386 3.0 45.3 1.0
CD2 A:HIS459 3.1 50.2 1.0
CE1 A:HIS459 3.7 44.0 1.0
OP1 T:DC8 4.1 37.9 1.0
O A:HOH684 4.3 31.2 1.0
CG A:HIS459 4.4 39.6 1.0
C5' T:DC8 4.4 32.6 1.0
CG A:GLU386 4.5 38.5 1.0
O A:HOH723 4.5 41.2 1.0
OE1 A:GLN426 4.6 30.4 1.0
ND1 A:HIS459 4.6 43.1 1.0
O A:HOH789 4.9 45.1 1.0
O5' T:DC8 5.0 33.9 1.0

Manganese binding site 7 out of 8 in 6vfa

Go back to Manganese Binding Sites List in 6vfa
Manganese binding site 7 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 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, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:55.5
occ:0.79
 O T:HOH226 2.1 55.0 1.0
N7 T:DG2 2.3 30.0 1.0
O T:HOH203 2.3 36.8 0.9
O T:HOH210 2.6 49.5 1.0
C8 T:DG2 3.2 26.9 1.0
C5 T:DG2 3.4 25.4 1.0
O6 T:DG2 3.7 26.1 1.0
C6 T:DG2 3.9 24.4 1.0
O T:HOH215 4.0 48.4 1.0
O6 T:DG3 4.3 27.6 1.0
N9 T:DG2 4.4 25.6 1.0
C4 T:DG2 4.5 23.2 1.0
OP2 T:DG2 4.8 45.1 1.0

Manganese binding site 8 out of 8 in 6vfa

Go back to Manganese Binding Sites List in 6vfa
Manganese binding site 8 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn101

b:84.6
occ:0.98
 N7 D:DG1 2.2 22.2 1.0
O D:HOH217 2.5 40.7 1.0
O D:HOH201 3.0 44.7 1.0
C8 D:DG1 3.1 22.4 1.0
C5 D:DG1 3.2 22.6 1.0
O6 D:DG1 3.5 22.5 1.0
C6 D:DG1 3.8 22.8 1.0
N4 D:DC2 4.2 23.7 1.0
N9 D:DG1 4.3 22.5 1.0
C4 D:DG1 4.4 20.3 1.0
O D:HOH208 4.4 42.8 1.0
O T:HOH203 4.6 36.8 0.9
OP2 D:DG1 4.8 28.4 1.0
CG A:ARG175 4.8 24.8 1.0
O A:HOH804 4.8 32.5 1.0
C4 D:DC2 4.9 24.8 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min) To Be Published.
Page generated: Sun Oct 6 07:32:12 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