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Magnesium in PDB 4x4q: Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccac and Ctp

Enzymatic activity of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccac and Ctp

All present enzymatic activity of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccac and Ctp:
2.7.7.72;

Protein crystallography data

The structure of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccac and Ctp, PDB code: 4x4q was solved by C.-D.Kuhn, L.Joshua-Tor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.51 / 3.15
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 111.484, 215.582, 58.469, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 28.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccac and Ctp (pdb code 4x4q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccac and Ctp, PDB code: 4x4q:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4x4q

Go back to Magnesium Binding Sites List in 4x4q
Magnesium binding site 1 out of 3 in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccac and Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccac and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:60.0
occ:1.00
 OD2 A:ASP61 2.2 79.8 1.0
O2B A:CTP503 2.4 60.3 1.0
O3G A:CTP503 2.5 72.2 1.0
O1A A:CTP503 2.6 65.6 1.0
CG A:ASP61 3.2 72.0 1.0
H A:SER47 3.5 84.7 1.0
OE1 A:GLU59 3.5 91.1 1.0
HB3 A:GLU59 3.6 96.3 1.0
OD1 A:ASP61 3.6 74.5 1.0
PB A:CTP503 3.7 56.4 1.0
OG A:SER47 3.7 75.4 1.0
O A:GLU59 3.7 66.9 1.0
HG A:SER47 3.8 90.5 1.0
PG A:CTP503 3.8 63.3 1.0
HG2 A:GLU59 3.9 99.2 1.0
PA A:CTP503 3.9 65.4 1.0
HA3 A:GLY46 4.1 82.2 1.0
H5'2 A:CTP503 4.1 70.2 1.0
O3B A:CTP503 4.1 64.5 1.0
O3A A:CTP503 4.3 75.8 1.0
CD A:GLU59 4.3 92.1 1.0
N A:SER47 4.3 70.6 1.0
CG A:GLU59 4.3 82.6 1.0
CB A:GLU59 4.3 80.3 1.0
CB A:ASP61 4.5 67.6 1.0
C A:GLU59 4.5 71.7 1.0
HB3 A:SER47 4.5 83.3 1.0
HB2 A:ASP61 4.6 81.1 1.0
H5'1 A:CTP503 4.6 70.2 1.0
O5' A:CTP503 4.6 57.1 1.0
CB A:SER47 4.6 69.4 1.0
H A:ASP61 4.7 87.4 1.0
C5' A:CTP503 4.7 58.5 1.0
O1G A:CTP503 4.7 62.3 1.0
H A:TYR48 4.8 79.5 1.0
O2G A:CTP503 4.8 70.5 1.0
O1B A:CTP503 4.8 58.6 1.0
CA A:GLY46 4.9 68.5 1.0
HA2 A:GLY46 4.9 82.2 1.0
N A:ASP61 5.0 72.8 1.0

Magnesium binding site 2 out of 3 in 4x4q

Go back to Magnesium Binding Sites List in 4x4q
Magnesium binding site 2 out of 3 in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccac and Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccac and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:72.5
occ:1.00
 OD1 A:ASP61 2.6 74.5 1.0
O2' B:C36 2.8 53.9 1.0
OD2 A:ASP110 2.9 81.9 1.0
O3' B:C36 2.9 67.2 1.0
HB3 A:ASP110 3.2 83.0 1.0
HO2' B:C36 3.3 64.6 1.0
HO3' B:C36 3.3 80.7 1.0
HB2 A:ASP110 3.5 83.0 1.0
HG21 A:VAL112 3.5 65.8 1.0
CG A:ASP110 3.6 79.8 1.0
CB A:ASP110 3.6 69.2 1.0
O A:HOH603 3.6 62.0 1.0
C2' B:C36 3.7 58.4 1.0
C3' B:C36 3.8 60.2 1.0
CG A:ASP61 3.8 72.0 1.0
H4' B:C36 4.0 68.9 1.0
O B:HOH201 4.0 60.7 1.0
HG23 A:VAL112 4.1 65.8 1.0
H2' B:C36 4.1 70.1 1.0
HE1 A:PHE63 4.1 71.1 1.0
O5' A:CTP503 4.1 57.1 1.0
CG2 A:VAL112 4.1 54.8 1.0
HB3 A:ASP61 4.2 81.1 1.0
O1A A:CTP503 4.2 65.6 1.0
H5'1 A:CTP503 4.3 70.2 1.0
HG22 A:VAL112 4.3 65.8 1.0
OE1 A:GLU59 4.4 91.1 1.0
C4' B:C36 4.5 57.4 1.0
CB A:ASP61 4.6 67.6 1.0
H3' B:C36 4.6 72.2 1.0
PA A:CTP503 4.7 65.4 1.0
OD2 A:ASP61 4.7 79.8 1.0
OD1 A:ASP110 4.7 81.9 1.0
C5' A:CTP503 4.8 58.5 1.0
HA A:ASP61 4.9 79.7 1.0
O2A A:CTP503 4.9 49.4 1.0
CE1 A:PHE63 4.9 59.3 1.0

Magnesium binding site 3 out of 3 in 4x4q

Go back to Magnesium Binding Sites List in 4x4q
Magnesium binding site 3 out of 3 in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccac and Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix Ending in Ccac and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:82.2
occ:1.00
 OE1 C:GLU59 2.1 94.2 1.0
O3G C:CTP501 2.6 97.0 1.0
O1G C:CTP501 2.8 0.7 1.0
O2A C:CTP501 2.8 94.6 1.0
HG C:SER47 2.9 94.0 1.0
OD1 C:ASP61 2.9 79.1 1.0
O2B C:CTP501 2.9 91.8 1.0
PG C:CTP501 3.2 0.9 1.0
CD C:GLU59 3.2 92.6 1.0
HB3 C:GLU59 3.4 0.8 1.0
H C:SER47 3.5 93.2 1.0
OG C:SER47 3.6 78.4 1.0
O3B C:CTP501 3.6 0.0 1.0
O C:GLU59 3.7 77.8 1.0
PB C:CTP501 3.8 0.1 1.0
CG C:ASP61 3.9 81.5 1.0
OE2 C:GLU59 3.9 91.4 1.0
OD2 C:ASP61 4.2 84.5 1.0
PA C:CTP501 4.2 0.7 1.0
CB C:GLU59 4.2 84.8 1.0
CG C:GLU59 4.3 85.6 1.0
N C:SER47 4.4 77.7 1.0
HB3 C:SER47 4.4 89.4 1.0
HA3 C:GLY46 4.4 91.0 1.0
O3A C:CTP501 4.5 0.1 1.0
CB C:SER47 4.5 74.5 1.0
O2G C:CTP501 4.6 90.2 1.0
C C:GLU59 4.6 77.5 1.0
HG3 C:GLU59 4.8 0.7 1.0
H C:TYR48 4.9 87.8 1.0
HB2 C:GLU59 4.9 0.8 1.0
O5' C:CTP501 4.9 93.4 1.0
CA C:GLU59 5.0 77.5 1.0
H5'1 C:CTP501 5.0 0.4 1.0
HG2 C:GLU59 5.0 0.7 1.0

Reference:

C.-D.Kuhn, J.E.Wilusz, Y.Zheng, P.A.Beal, L.Joshua-Tor. On-Enzyme Refolding Permits Small Rna and Trna Surveillance By the Cca-Adding Enzyme To Be Published.
Page generated: Tue Aug 20 14:03:34 2024

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