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Magnesium in PDB 6p7e: Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase

Enzymatic activity of Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase

All present enzymatic activity of Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase:
2.7.7.7;

Protein crystallography data

The structure of Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase, PDB code: 6p7e was solved by B.M.Foster, D.Rosenberg, H.Salvo, K.L.Stephens, B.J.Bintz, M.Hammel, T.Ellenberger, M.D.Gainey, J.R.Wallen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.13 / 3.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 100.724, 102.698, 148.885, 91.36, 96.83, 113.11
R / Rfree (%) 21.4 / 24.8

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase (pdb code 6p7e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase, PDB code: 6p7e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 6p7e

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Magnesium binding site 1 out of 12 in the Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:38.9
occ:1.00
 O2B A:TTP805 2.1 34.1 1.0
OD1 A:ASP475 2.1 47.0 1.0
O A:ALA476 2.1 44.8 1.0
OD2 A:ASP654 2.1 40.3 1.0
O2A A:TTP805 2.1 35.9 1.0
O1G A:TTP805 2.3 43.0 1.0
CG A:ASP654 3.2 40.7 1.0
CG A:ASP475 3.2 47.9 1.0
PB A:TTP805 3.2 39.0 1.0
C A:ALA476 3.3 42.8 1.0
PA A:TTP805 3.4 46.0 1.0
PG A:TTP805 3.6 42.0 1.0
O3A A:TTP805 3.7 54.9 1.0
OD1 A:ASP654 3.7 42.8 1.0
OD2 A:ASP475 3.8 58.5 1.0
O3B A:TTP805 3.9 41.9 1.0
N A:ALA476 3.9 35.5 1.0
C5' A:TTP805 3.9 33.8 1.0
CA A:ALA476 4.0 30.9 1.0
O5' A:TTP805 4.2 32.4 1.0
N A:SER477 4.3 44.0 1.0
CB A:ALA476 4.4 31.9 1.0
N A:GLY478 4.4 36.6 1.0
CB A:ASP654 4.4 36.0 1.0
MG A:MG803 4.5 56.4 1.0
C A:ASP475 4.5 42.4 1.0
CB A:ASP475 4.5 49.5 1.0
O3G A:TTP805 4.5 29.6 1.0
O1B A:TTP805 4.5 38.5 1.0
O1A A:TTP805 4.5 49.7 1.0
O2G A:TTP805 4.5 36.3 1.0
CA A:SER477 4.6 45.2 1.0
O A:ASP654 4.7 38.3 1.0
C A:SER477 4.8 42.2 1.0
N A:LEU479 4.8 37.2 1.0
CA A:ASP475 5.0 36.6 1.0
CB A:LEU479 5.0 35.4 1.0

Magnesium binding site 2 out of 12 in 6p7e

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Magnesium binding site 2 out of 12 in the Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:56.4
occ:1.00
 OD1 A:ASP654 2.2 42.8 1.0
OD2 A:ASP475 2.6 58.5 1.0
CB A:GLU655 3.3 30.3 1.0
CG A:ASP654 3.3 40.7 1.0
CG A:GLU655 3.5 38.8 1.0
O A:VAL652 3.5 39.5 1.0
O2A A:TTP805 3.5 35.9 1.0
CG A:ASP475 3.6 47.9 1.0
C3' I:DA822 3.6 33.6 1.0
C4' I:DA822 3.7 32.8 1.0
C5' I:DA822 3.7 35.5 1.0
CD A:GLU655 3.9 50.5 1.0
OD2 A:ASP654 3.9 40.3 1.0
N A:GLU655 3.9 36.1 1.0
C A:ASP654 4.0 33.9 1.0
OD1 A:ASP475 4.0 47.0 1.0
OE2 A:GLU655 4.0 48.9 1.0
N A:ASP654 4.2 33.1 1.0
CA A:GLU655 4.2 32.5 1.0
O A:ASP654 4.2 38.3 1.0
CA A:ASP654 4.4 33.0 1.0
MG A:MG802 4.5 38.9 1.0
CB A:ASP654 4.5 36.0 1.0
PA A:TTP805 4.5 46.0 1.0
OE1 A:GLU655 4.6 62.2 1.0
O1A A:TTP805 4.6 49.7 1.0
C A:VAL652 4.7 36.7 1.0
C2' I:DA822 4.8 32.3 1.0
CB A:ASP475 4.9 49.5 1.0
CG1 A:VAL652 4.9 27.7 1.0
C5' A:TTP805 4.9 33.8 1.0
O5' A:TTP805 5.0 32.4 1.0

Magnesium binding site 3 out of 12 in 6p7e

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Magnesium binding site 3 out of 12 in the Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:33.5
occ:1.00
 O A:HOH909 2.0 35.2 1.0
O A:HOH915 2.3 21.2 1.0
O A:HOH914 3.0 28.0 1.0
O A:HIS59 3.4 30.6 1.0
O A:HOH907 3.6 28.8 1.0
OD1 A:ASP65 3.7 32.5 1.0
OD2 A:ASP65 3.8 49.6 1.0
CB A:ALA5 4.1 39.4 1.0
CG A:ASP65 4.2 44.6 1.0
CD1 A:LEU125 4.2 40.2 1.0
C A:HIS59 4.5 30.8 1.0
CA A:ALA5 4.7 29.1 1.0
O A:ILE6 4.7 35.7 1.0
O3' A:TTP801 4.8 67.1 1.0
CB A:HIS59 4.8 31.2 1.0
N A:ILE6 4.8 35.3 1.0
N A:HIS59 4.8 29.6 1.0

Magnesium binding site 4 out of 12 in 6p7e

Go back to Magnesium Binding Sites List in 6p7e
Magnesium binding site 4 out of 12 in the Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:36.1
occ:1.00
 O2B B:TTP805 2.0 37.2 1.0
O2A B:TTP805 2.1 37.4 1.0
OD2 B:ASP475 2.1 42.5 1.0
OD1 B:ASP654 2.1 35.0 1.0
O1G B:TTP805 2.1 39.6 1.0
O B:ALA476 2.3 40.8 1.0
PB B:TTP805 3.1 36.6 1.0
CG B:ASP654 3.2 37.1 1.0
CG B:ASP475 3.2 41.2 1.0
PA B:TTP805 3.3 39.0 1.0
C B:ALA476 3.4 38.5 1.0
PG B:TTP805 3.4 43.0 1.0
O3A B:TTP805 3.5 45.5 1.0
MG B:MG803 3.6 64.6 1.0
OD2 B:ASP654 3.7 41.3 1.0
OD1 B:ASP475 3.7 49.5 1.0
O3B B:TTP805 3.7 35.6 1.0
C5' B:TTP805 4.0 28.4 1.0
N B:ALA476 4.0 37.0 1.0
CA B:ALA476 4.2 37.2 1.0
O5' B:TTP805 4.2 23.8 1.0
O2G B:TTP805 4.4 34.5 1.0
O1A B:TTP805 4.4 38.5 1.0
O1B B:TTP805 4.4 35.6 1.0
CB B:ASP654 4.4 33.1 1.0
O3G B:TTP805 4.4 35.9 1.0
CB B:ALA476 4.5 40.8 1.0
CB B:ASP475 4.5 38.2 1.0
N B:SER477 4.5 35.6 1.0
N B:GLY478 4.5 30.6 1.0
C B:ASP475 4.5 39.8 1.0
CA B:SER477 4.7 30.1 1.0
O B:ASP654 4.9 35.7 1.0
N B:LEU479 4.9 31.6 1.0
C B:SER477 4.9 32.2 1.0
CA B:ASP475 5.0 34.7 1.0

Magnesium binding site 5 out of 12 in 6p7e

Go back to Magnesium Binding Sites List in 6p7e
Magnesium binding site 5 out of 12 in the Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:64.6
occ:1.00
 OD1 B:ASP475 1.9 49.5 1.0
O B:HOH904 2.1 38.5 1.0
OD2 B:ASP654 2.5 41.3 1.0
O2A B:TTP805 2.7 37.4 1.0
CG B:ASP475 2.9 41.2 1.0
OD2 B:ASP475 3.2 42.5 1.0
CG B:ASP654 3.3 37.1 1.0
OD1 B:ASP654 3.5 35.0 1.0
MG B:MG802 3.6 36.1 1.0
CB B:GLU655 3.7 31.2 1.0
PA B:TTP805 3.9 39.0 1.0
C3' K:DA822 3.9 30.1 1.0
O1A B:TTP805 4.0 38.5 1.0
CG B:GLU655 4.0 30.4 1.0
C B:ASP654 4.2 30.8 1.0
CB B:ASP475 4.2 38.2 1.0
C4' K:DA822 4.3 24.0 1.0
C5' K:DA822 4.3 32.9 1.0
CD B:GLU655 4.3 44.5 1.0
O B:ASP654 4.3 35.7 1.0
N B:GLU655 4.4 30.6 1.0
O B:VAL652 4.4 42.6 1.0
OE2 B:GLU655 4.5 55.3 1.0
CB B:ASP654 4.6 33.1 1.0
CA B:GLU655 4.6 27.7 1.0
O5' B:TTP805 4.6 23.8 1.0
N B:ASP654 4.7 28.5 1.0
CA B:ASP654 4.7 30.9 1.0
O1G B:TTP805 4.7 39.6 1.0
C5' B:TTP805 4.7 28.4 1.0
OE1 B:GLU655 4.8 54.4 1.0
CA B:ASP475 5.0 34.7 1.0

Magnesium binding site 6 out of 12 in 6p7e

Go back to Magnesium Binding Sites List in 6p7e
Magnesium binding site 6 out of 12 in the Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg804

b:38.6
occ:1.00
 O B:HOH907 2.2 38.1 1.0
O B:HIS59 3.1 35.2 1.0
OD1 B:ASP65 3.2 38.7 1.0
OD2 B:ASP65 3.6 45.8 1.0
CG B:ASP65 3.8 37.8 1.0
C B:HIS59 4.3 29.3 1.0
O4' B:TTP801 4.5 74.1 1.0
C4' B:TTP801 4.7 69.8 1.0
CD2 B:TYR64 4.7 37.7 1.0
O B:ILE6 4.9 42.2 1.0
C1' B:TTP801 4.9 49.7 1.0
CB B:HIS59 5.0 29.8 1.0
CB B:ALA5 5.0 40.2 1.0
N B:HIS59 5.0 28.5 1.0

Magnesium binding site 7 out of 12 in 6p7e

Go back to Magnesium Binding Sites List in 6p7e
Magnesium binding site 7 out of 12 in the Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:43.5
occ:1.00
 O C:ALA476 1.9 60.3 1.0
OD1 C:ASP475 1.9 64.7 1.0
OD1 C:ASP654 1.9 54.9 1.0
O2B C:TTP805 2.3 56.2 1.0
O2A C:TTP805 2.5 54.1 1.0
O1G C:TTP805 2.6 56.4 1.0
C C:ALA476 3.0 62.5 1.0
CG C:ASP475 3.0 68.9 1.0
CG C:ASP654 3.1 55.5 1.0
N C:ALA476 3.5 50.5 1.0
PB C:TTP805 3.6 59.6 1.0
OD2 C:ASP475 3.6 77.3 1.0
CA C:ALA476 3.7 49.2 1.0
OD2 C:ASP654 3.7 55.5 1.0
PA C:TTP805 3.8 50.7 1.0
PG C:TTP805 3.9 58.8 1.0
CB C:ALA476 4.0 43.6 1.0
MG C:MG803 4.0 79.6 1.0
C C:ASP475 4.1 59.2 1.0
O3A C:TTP805 4.1 62.2 1.0
N C:SER477 4.1 61.3 1.0
CB C:ASP654 4.1 45.0 1.0
O3B C:TTP805 4.1 57.8 1.0
CB C:ASP475 4.2 62.4 1.0
O C:ASP654 4.3 56.1 1.0
C5' C:TTP805 4.3 40.6 1.0
N C:GLY478 4.5 62.7 1.0
CA C:SER477 4.5 57.1 1.0
O5' C:TTP805 4.6 42.5 1.0
CA C:ASP475 4.6 57.0 1.0
O C:ASP475 4.6 66.4 1.0
O1B C:TTP805 4.7 51.6 1.0
O2G C:TTP805 4.8 59.9 1.0
C C:SER477 4.8 59.4 1.0
N C:LEU479 4.8 55.0 1.0
O3G C:TTP805 4.9 49.2 1.0
O1A C:TTP805 4.9 56.0 1.0
CB C:LEU479 4.9 44.8 1.0
C C:ASP654 5.0 47.7 1.0

Magnesium binding site 8 out of 12 in 6p7e

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Magnesium binding site 8 out of 12 in the Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg803

b:79.6
occ:1.00
 OD2 C:ASP475 2.1 77.3 1.0
OD2 C:ASP654 2.8 55.5 1.0
O2A C:TTP805 3.0 54.1 1.0
CG C:ASP475 3.1 68.9 1.0
OD1 C:ASP475 3.5 64.7 1.0
CG C:ASP654 3.6 55.5 1.0
CB C:GLU655 3.7 44.3 1.0
C5' M:DA822 3.7 45.8 1.0
C3' M:DA822 3.7 47.9 1.0
OD1 C:ASP654 3.8 54.9 1.0
C4' M:DA822 3.9 44.2 1.0
CG C:GLU655 4.0 50.8 1.0
O1A C:TTP805 4.0 56.0 1.0
PA C:TTP805 4.0 50.7 1.0
MG C:MG802 4.0 43.5 1.0
CD C:GLU655 4.1 64.3 1.0
OE2 C:GLU655 4.3 75.0 1.0
O C:VAL652 4.5 50.2 1.0
CB C:ASP475 4.5 62.4 1.0
C C:ASP654 4.5 47.7 1.0
N C:GLU655 4.6 51.3 1.0
O C:ASP654 4.6 56.1 1.0
OE1 C:GLU655 4.6 63.8 1.0
CE1 C:HIS704 4.6 0.8 1.0
O5' C:TTP805 4.7 42.5 1.0
CA C:GLU655 4.7 47.2 1.0
CB C:ASP654 4.9 45.0 1.0
O5' M:DA822 4.9 37.7 1.0
OP1 M:DA822 4.9 69.8 1.0
C5' C:TTP805 5.0 40.6 1.0
N C:ASP654 5.0 47.0 1.0

Magnesium binding site 9 out of 12 in 6p7e

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Magnesium binding site 9 out of 12 in the Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg804

b:61.2
occ:1.00
 O C:HIS59 3.4 54.4 1.0
OD1 C:ASP65 3.5 61.0 1.0
O4' C:TTP801 3.9 93.0 1.0
C4' C:TTP801 4.0 92.0 1.0
O3' C:TTP801 4.0 94.0 1.0
C1' C:TTP801 4.1 74.1 1.0
OD2 C:ASP65 4.2 74.7 1.0
CG C:ASP65 4.3 69.8 1.0
C2' C:TTP801 4.4 79.0 1.0
C3' C:TTP801 4.4 90.0 1.0
CD2 C:TYR64 4.5 53.4 1.0
C C:HIS59 4.6 55.5 1.0
O C:ILE6 5.0 55.0 1.0

Magnesium binding site 10 out of 12 in 6p7e

Go back to Magnesium Binding Sites List in 6p7e
Magnesium binding site 10 out of 12 in the Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of T7 Dna Polymerase Bound to A Primer/Template Dna and A Peptide That Mimics the C-Terminal Tail of the Primase-Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:86.0
occ:1.00
 O D:ALA476 1.9 84.5 1.0
OD2 D:ASP654 2.0 81.4 1.0
O2B D:TTP805 2.0 87.1 1.0
OD1 D:ASP475 2.3 85.9 1.0
MG D:MG803 2.6 90.5 1.0
O2A D:TTP805 2.8 72.5 1.0
O1G D:TTP805 2.8 90.2 1.0
C D:ALA476 3.0 85.9 1.0
CG D:ASP654 3.1 83.3 1.0
CG D:ASP475 3.4 83.2 1.0
N D:ALA476 3.5 72.9 1.0
PB D:TTP805 3.5 92.9 1.0
CA D:ALA476 3.6 71.2 1.0
OD1 D:ASP654 3.7 89.5 1.0
CB D:ALA476 3.7 59.1 1.0
OD2 D:ASP475 3.9 85.2 1.0
PA D:TTP805 4.0 73.6 1.0
C5' D:TTP805 4.0 66.1 1.0
PG D:TTP805 4.1 96.0 1.0
CB D:ASP654 4.1 74.9 1.0
O3A D:TTP805 4.1 92.1 1.0
N D:SER477 4.1 84.5 1.0
C D:ASP475 4.2 77.4 1.0
O3B D:TTP805 4.2 85.8 1.0
O D:ASP654 4.3 69.2 1.0
N D:GLY478 4.4 85.0 1.0
CB D:ASP475 4.5 79.1 1.0
O1B D:TTP805 4.5 75.4 1.0
O5' D:TTP805 4.5 65.9 1.0
N D:LEU479 4.5 78.7 1.0
CA D:SER477 4.6 74.0 1.0
CB D:LEU479 4.6 80.3 1.0
C D:SER477 4.7 80.7 1.0
CA D:ASP475 4.7 76.2 1.0
O D:ASP475 4.8 79.1 1.0
O2G D:TTP805 4.9 95.2 1.0
C D:ASP654 5.0 70.5 1.0

Reference:

B.M.Foster, D.Rosenberg, H.Salvo, K.L.Stephens, B.J.Bintz, M.Hammel, T.Ellenberger, M.D.Gainey, J.R.Wallen. Combined Solution and Crystal Methods Reveal the Electrostatic Tethers That Provide A Flexible Platform For Replication Activities in the Bacteriophage T7 Replisome. Biochemistry V. 58 4466 2019.
ISSN: ISSN 0006-2960
PubMed: 31659895
DOI: 10.1021/ACS.BIOCHEM.9B00525
Page generated: Tue Oct 1 13:54:26 2024

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