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Magnesium in PDB 6byr: Structures of the Pka Ri Alpha Holoenzyme with the Flhcc Driver J-Pkac Alpha or Native Pkac Alpha

Enzymatic activity of Structures of the Pka Ri Alpha Holoenzyme with the Flhcc Driver J-Pkac Alpha or Native Pkac Alpha

All present enzymatic activity of Structures of the Pka Ri Alpha Holoenzyme with the Flhcc Driver J-Pkac Alpha or Native Pkac Alpha:
2.7.11.11;

Protein crystallography data

The structure of Structures of the Pka Ri Alpha Holoenzyme with the Flhcc Driver J-Pkac Alpha or Native Pkac Alpha, PDB code: 6byr was solved by B.Cao, T.W.Lu, J.A.Martinez Fiesco, M.Tomasini, L.Fan, S.M.Simon, S.S.Taylor, P.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.91 / 3.66
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 166.504, 166.504, 332.701, 90.00, 90.00, 120.00
R / Rfree (%) 20 / 25

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structures of the Pka Ri Alpha Holoenzyme with the Flhcc Driver J-Pkac Alpha or Native Pkac Alpha (pdb code 6byr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structures of the Pka Ri Alpha Holoenzyme with the Flhcc Driver J-Pkac Alpha or Native Pkac Alpha, PDB code: 6byr:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6byr

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Magnesium binding site 1 out of 4 in the Structures of the Pka Ri Alpha Holoenzyme with the Flhcc Driver J-Pkac Alpha or Native Pkac Alpha


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structures of the Pka Ri Alpha Holoenzyme with the Flhcc Driver J-Pkac Alpha or Native Pkac Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:94.7
occ:0.95
 O1G A:ATP501 1.9 0.5 0.8
O1B A:ATP501 2.0 0.9 0.8
OD2 A:ASP239 2.3 99.0 1.0
OD1 A:ASP239 2.6 86.8 1.0
CG A:ASP239 2.8 90.6 1.0
PG A:ATP501 3.1 0.4 0.8
PB A:ATP501 3.1 0.6 0.8
O3B A:ATP501 3.3 0.0 0.8
OD2 A:ASP221 3.5 89.2 1.0
O2G A:ATP501 3.7 0.2 0.8
MG A:MG503 3.9 86.6 0.6
O2B A:ATP501 4.0 0.1 0.8
CD2 A:PHE109 4.2 0.0 1.0
CB A:ASP239 4.2 84.7 1.0
O1A A:ATP501 4.2 91.7 0.8
CE2 A:PHE109 4.3 0.9 1.0
O3G A:ATP501 4.3 0.0 0.8
O3A A:ATP501 4.3 0.1 0.8
NZ A:LYS127 4.6 83.2 1.0
CB B:ALA97 4.7 93.3 1.0
PA A:ATP501 4.7 95.5 0.8
CG A:ASP221 4.7 89.3 1.0
CA A:GLY241 4.8 81.6 1.0
O2A A:ATP501 4.9 87.9 0.8
N A:GLY241 4.9 76.0 1.0
CE2 A:PHE242 4.9 82.7 1.0

Magnesium binding site 2 out of 4 in 6byr

Go back to Magnesium Binding Sites List in 6byr
Magnesium binding site 2 out of 4 in the Structures of the Pka Ri Alpha Holoenzyme with the Flhcc Driver J-Pkac Alpha or Native Pkac Alpha


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structures of the Pka Ri Alpha Holoenzyme with the Flhcc Driver J-Pkac Alpha or Native Pkac Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:86.6
occ:0.63
 O1A A:ATP501 2.0 91.7 0.8
OD1 A:ASN226 2.1 84.7 1.0
O2G A:ATP501 2.1 0.2 0.8
O3B A:ATP501 2.4 0.0 0.8
OD2 A:ASP239 2.8 99.0 1.0
PG A:ATP501 2.8 0.4 0.8
CG A:ASN226 2.9 81.0 1.0
ND2 A:ASN226 3.0 85.3 1.0
PA A:ATP501 3.4 95.5 0.8
CG A:ASP239 3.6 90.6 1.0
PB A:ATP501 3.6 0.6 0.8
O1G A:ATP501 3.6 0.5 0.8
O3' A:ATP501 3.8 85.2 0.8
O1B A:ATP501 3.8 0.9 0.8
O3A A:ATP501 3.8 0.1 0.8
MG A:MG502 3.9 94.7 0.9
CB A:ASP239 3.9 84.7 1.0
CE A:LYS223 4.1 84.1 1.0
O3G A:ATP501 4.1 0.0 0.8
CB A:ASN226 4.3 70.8 1.0
O5' A:ATP501 4.3 81.0 0.8
NZ A:LYS223 4.4 89.8 1.0
O2A A:ATP501 4.5 87.9 0.8
OD2 A:ASP221 4.5 89.2 1.0
OD1 A:ASP239 4.6 86.8 1.0
C5' A:ATP501 4.7 79.7 0.8
O A:GLU225 4.7 84.4 1.0
C3' A:ATP501 4.7 77.9 0.8
O2B A:ATP501 4.9 0.1 0.8
CA A:ASN226 4.9 73.1 1.0

Magnesium binding site 3 out of 4 in 6byr

Go back to Magnesium Binding Sites List in 6byr
Magnesium binding site 3 out of 4 in the Structures of the Pka Ri Alpha Holoenzyme with the Flhcc Driver J-Pkac Alpha or Native Pkac Alpha


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structures of the Pka Ri Alpha Holoenzyme with the Flhcc Driver J-Pkac Alpha or Native Pkac Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:85.7
occ:1.00
 O3G C:ATP501 1.9 1.0 0.8
O2B C:ATP501 2.0 0.7 0.8
OD2 C:ASP239 2.6 98.0 1.0
OD1 C:ASP239 2.6 93.0 1.0
CG C:ASP239 2.9 92.9 1.0
PG C:ATP501 3.1 0.2 0.8
PB C:ATP501 3.1 0.3 0.8
O3B C:ATP501 3.3 0.4 0.8
OD2 C:ASP221 3.7 88.9 1.0
O2G C:ATP501 3.8 97.2 0.8
MG C:MG503 3.9 92.5 0.6
O1B C:ATP501 4.0 0.7 0.8
CD2 C:PHE109 4.1 0.5 1.0
CE2 C:PHE109 4.1 98.5 1.0
O2A C:ATP501 4.3 99.1 0.8
CB C:ASP239 4.3 87.4 1.0
O1G C:ATP501 4.3 0.4 0.8
O3A C:ATP501 4.4 0.4 0.8
CA C:GLY241 4.4 79.7 1.0
NZ C:LYS127 4.5 95.5 1.0
N C:GLY241 4.6 79.5 1.0
PA C:ATP501 4.7 97.7 0.8
O C:ASP239 4.8 87.1 1.0
CB D:ALA97 4.8 91.0 1.0
CG C:ASP221 4.9 81.8 1.0
O1A C:ATP501 4.9 85.8 0.8
CZ C:PHE242 5.0 77.7 1.0
CE2 C:PHE242 5.0 73.6 1.0

Magnesium binding site 4 out of 4 in 6byr

Go back to Magnesium Binding Sites List in 6byr
Magnesium binding site 4 out of 4 in the Structures of the Pka Ri Alpha Holoenzyme with the Flhcc Driver J-Pkac Alpha or Native Pkac Alpha


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structures of the Pka Ri Alpha Holoenzyme with the Flhcc Driver J-Pkac Alpha or Native Pkac Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:92.5
occ:0.57
 OD1 C:ASN226 2.0 94.8 1.0
O2A C:ATP501 2.0 99.1 0.8
O2G C:ATP501 2.1 97.2 0.8
O3B C:ATP501 2.5 0.4 0.8
PG C:ATP501 2.8 0.2 0.8
CG C:ASN226 2.9 85.5 1.0
OD2 C:ASP239 3.1 98.0 1.0
ND2 C:ASN226 3.1 80.8 1.0
PA C:ATP501 3.5 97.7 0.8
O3G C:ATP501 3.6 1.0 0.8
CG C:ASP239 3.6 92.9 1.0
PB C:ATP501 3.6 0.3 0.8
O2B C:ATP501 3.8 0.7 0.8
O3A C:ATP501 3.9 0.4 0.8
MG C:MG502 3.9 85.7 1.0
CB C:ASP239 3.9 87.4 1.0
O1G C:ATP501 4.1 0.4 0.8
CE C:LYS223 4.1 76.3 1.0
CB C:ASN226 4.3 80.0 1.0
O5' C:ATP501 4.4 97.2 0.8
OD2 C:ASP221 4.4 88.9 1.0
OD1 C:ASP239 4.5 93.0 1.0
O1A C:ATP501 4.5 85.8 0.8
C5' C:ATP501 4.6 94.7 0.8
NZ C:LYS223 4.6 79.0 1.0
O C:GLU225 4.7 82.6 1.0
O3' C:ATP501 4.7 94.3 0.8
C3' C:ATP501 4.8 87.9 0.8
CA C:ASN226 4.9 79.6 1.0
O1B C:ATP501 4.9 0.7 0.8

Reference:

B.Cao, T.W.Lu, J.A.Martinez Fiesco, M.Tomasini, L.Fan, S.M.Simon, S.S.Taylor, P.Zhang. Structures of the Pka Ri Alpha Holoenzyme with the Flhcc Driver J-Pkac Alpha or Wild-Type Pkac Alpha. Structure V. 27 816 2019.
ISSN: ISSN 0969-2126
PubMed: 30905674
DOI: 10.1016/J.STR.2019.03.001
Page generated: Mon Sep 30 20:03:05 2024

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