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Magnesium in PDB 4elv: Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines

Enzymatic activity of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines

All present enzymatic activity of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines:
2.7.7.7;

Protein crystallography data

The structure of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines, PDB code: 4elv was solved by A.Marx, K.Diederichs, S.Obeid, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.29 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.213, 109.213, 91.047, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 21.6

Other elements in 4elv:

The structure of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines (pdb code 4elv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines, PDB code: 4elv:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4elv

Go back to Magnesium Binding Sites List in 4elv
Magnesium binding site 1 out of 3 in the Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:42.4
occ:1.00
O A:HOH1196 2.0 44.3 1.0
O A:HOH1048 2.1 31.0 1.0
O A:HOH1129 2.1 43.5 1.0
OE2 A:GLU786 2.1 30.3 0.5
O A:HOH1019 2.1 29.8 1.0
OD2 A:ASP610 2.2 31.6 1.0
CG A:ASP610 3.1 36.0 1.0
CD A:GLU786 3.1 34.6 0.5
OD1 A:ASP610 3.4 41.6 1.0
O11 A:0R7902 3.5 28.6 1.0
O A:HOH1199 3.6 88.9 1.0
CG A:GLU786 3.6 27.6 0.5
O A:HOH1200 4.0 44.8 1.0
CA A:CA908 4.1 26.9 1.0
OD1 A:ASP785 4.2 26.6 1.0
OE1 A:GLU786 4.3 36.3 0.5
O7 A:0R7902 4.4 32.7 1.0
O A:HOH1225 4.4 60.5 1.0
CB A:ASP610 4.5 24.8 1.0
O10 A:0R7902 4.6 39.2 1.0
P1 A:0R7902 4.6 29.9 1.0
OP1 B:0R8112 4.8 28.4 1.0
C5' B:0R8112 4.8 27.2 1.0
C3' B:0R8112 4.8 25.5 1.0
OD2 A:ASP785 4.9 36.0 1.0
O5' B:0R8112 4.9 25.4 1.0
OE1 A:GLU786 4.9 49.6 0.5
CG A:ASP785 5.0 30.0 1.0
NZ A:LYS663 5.0 35.8 1.0

Magnesium binding site 2 out of 3 in 4elv

Go back to Magnesium Binding Sites List in 4elv
Magnesium binding site 2 out of 3 in the Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:67.8
occ:1.00
O B:HOH337 2.2 34.6 1.0
O B:HOH338 2.2 69.9 1.0
O B:HOH335 2.2 20.2 1.0
O C:HOH444 2.2 82.0 1.0
O B:HOH336 2.2 39.7 1.0
O C:HOH437 2.9 67.6 1.0
O6 B:DG108 4.1 16.9 1.0
O B:HOH316 4.1 31.6 1.0
N7 B:DG107 4.3 16.0 1.0
O6 B:DG107 4.4 12.5 1.0
O C:HOH430 4.4 34.7 1.0
O C:HOH409 4.5 24.6 1.0
N4 C:DC209 4.6 14.9 1.0
O B:HOH315 4.8 33.4 1.0
C5 B:DC106 4.9 18.9 1.0

Magnesium binding site 3 out of 3 in 4elv

Go back to Magnesium Binding Sites List in 4elv
Magnesium binding site 3 out of 3 in the Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:75.7
occ:1.00
O C:HOH440 2.2 42.4 1.0
O C:HOH442 2.2 63.2 1.0
O C:HOH439 2.2 0.8 1.0
O C:HOH441 2.2 45.5 1.0
O C:HOH443 2.2 51.2 1.0
O6 C:DG214 3.5 29.7 1.0
O B:HOH330 3.5 49.1 1.0
N7 C:DG213 3.8 28.6 1.0
N7 C:DG214 4.1 27.7 1.0
O6 C:DG213 4.3 25.3 1.0
C6 C:DG214 4.4 23.4 1.0
C5 C:DG213 4.6 22.9 1.0
C5 C:DG214 4.6 24.8 1.0
C8 C:DG213 4.7 29.9 1.0
C6 C:DG213 4.8 19.0 1.0
O C:HOH427 4.9 37.4 1.0

Reference:

S.Obeid, H.Bu Kamp, W.Welte, K.Diederichs, A.Marx. Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines To Be Published.
Page generated: Fri Aug 16 14:31:18 2024

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