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Magnesium in PDB 3wfr: Trna Processing Enzyme Complex 2

Enzymatic activity of Trna Processing Enzyme Complex 2

All present enzymatic activity of Trna Processing Enzyme Complex 2:
2.7.7.72;

Protein crystallography data

The structure of Trna Processing Enzyme Complex 2, PDB code: 3wfr was solved by S.Yamashita, D.Takeshita, K.Tomita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 3.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 152.810, 154.590, 174.670, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 26.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Trna Processing Enzyme Complex 2 (pdb code 3wfr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Trna Processing Enzyme Complex 2, PDB code: 3wfr:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3wfr

Go back to Magnesium Binding Sites List in 3wfr
Magnesium binding site 1 out of 4 in the Trna Processing Enzyme Complex 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Trna Processing Enzyme Complex 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg603

b:45.8
occ:1.00
O1 E:POP602 2.1 74.2 0.5
O2B E:CTP601 2.1 74.5 0.5
OD2 E:ASP58 2.3 81.5 1.0
OD2 E:ASP60 2.3 97.5 1.0
OP1 A:C74 2.8 56.8 0.5
CG E:ASP58 3.0 76.8 1.0
CG E:ASP60 3.1 92.5 1.0
PB E:CTP601 3.2 73.8 0.5
OD1 E:ASP60 3.2 95.3 1.0
O E:ASP58 3.3 42.2 1.0
O4 E:POP602 3.4 0.1 0.5
O3A E:CTP601 3.4 69.3 0.5
O1A E:CTP601 3.5 43.3 0.5
P1 E:POP602 3.5 72.2 0.5
CB E:ASP58 3.6 65.2 1.0
O1G E:CTP601 3.7 0.8 0.5
OD1 E:ASP58 3.8 83.8 1.0
O3B E:CTP601 3.8 80.1 0.5
C E:ASP58 3.8 53.0 1.0
PA E:CTP601 4.0 44.9 0.5
O2 E:POP602 4.0 73.5 0.5
C5' E:CTP601 4.2 47.0 0.5
P A:C74 4.2 58.6 0.5
C5' A:C74 4.3 65.5 0.5
O5' E:CTP601 4.3 46.1 0.5
PG E:CTP601 4.3 0.8 0.5
CA E:ASP58 4.4 56.2 1.0
N E:GLY42 4.4 62.6 1.0
O E:POP602 4.4 82.7 0.5
O3 E:POP602 4.4 77.5 0.5
O1B E:CTP601 4.5 76.5 0.5
CA E:GLY42 4.5 62.9 1.0
P2 E:POP602 4.5 0.6 0.5
N E:TRP43 4.5 55.3 1.0
N E:VAL59 4.6 33.9 1.0
CB E:ASP60 4.6 79.8 1.0
O5' A:C74 4.6 66.8 0.5
N E:ASP60 4.7 62.5 1.0
O2G E:CTP601 4.7 0.0 0.5
C E:VAL59 4.8 55.5 1.0
CA E:VAL59 4.8 34.5 1.0
O3' A:A73 4.8 70.3 0.5
O3' A:A73 4.8 72.0 0.5
C E:GLY42 4.9 63.2 1.0

Magnesium binding site 2 out of 4 in 3wfr

Go back to Magnesium Binding Sites List in 3wfr
Magnesium binding site 2 out of 4 in the Trna Processing Enzyme Complex 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Trna Processing Enzyme Complex 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg603

b:81.2
occ:1.00
OP1 B:C74 2.0 83.2 0.5
OD2 F:ASP58 2.1 74.4 1.0
OD1 F:ASP60 2.3 78.9 1.0
O1 F:POP602 2.5 0.7 0.5
O2B F:CTP601 2.5 0.7 0.5
O1A F:CTP601 2.7 81.6 0.5
OD2 F:ASP60 2.7 92.6 1.0
CG F:ASP60 2.8 83.8 1.0
CG F:ASP58 2.9 81.2 1.0
O1G F:CTP601 3.3 0.0 0.5
O4 F:POP602 3.4 0.1 0.5
P B:C74 3.5 94.3 0.5
PB F:CTP601 3.5 0.5 0.5
O F:ASP58 3.5 70.8 1.0
PA F:CTP601 3.6 93.5 0.5
CB F:ASP58 3.6 79.7 1.0
P1 F:POP602 3.7 0.0 0.5
OD1 F:ASP58 3.7 88.4 1.0
O3A F:CTP601 3.8 0.6 0.5
O3B F:CTP601 3.8 0.2 0.5
C F:ASP58 3.9 72.8 1.0
O2 F:POP602 3.9 0.2 0.5
O5' F:CTP601 3.9 67.6 0.5
O3' B:A73 4.0 95.8 0.5
C5' F:CTP601 4.1 81.5 0.5
PG F:CTP601 4.2 0.4 0.5
O5 F:POP602 4.2 0.2 0.5
C5' B:C74 4.2 96.8 0.5
P2 F:POP602 4.2 0.8 0.5
O3' B:A73 4.3 95.2 0.5
O5' B:C74 4.3 84.1 0.5
CB F:ASP60 4.3 81.2 1.0
CA F:ASP58 4.4 76.9 1.0
N F:VAL59 4.4 70.7 1.0
C F:VAL59 4.4 75.6 1.0
O F:POP602 4.5 0.3 0.5
O F:VAL59 4.5 80.0 1.0
OP2 B:C74 4.5 82.1 0.5
OD2 F:ASP112 4.6 80.3 1.0
N F:ASP60 4.7 77.0 1.0
CA F:VAL59 4.7 71.4 1.0
O2G F:CTP601 4.8 0.1 0.5
N F:GLY42 4.8 75.7 1.0
O3 F:POP602 4.9 0.6 0.5
O1B F:CTP601 4.9 0.0 0.5
O2' B:A73 5.0 97.9 0.5

Magnesium binding site 3 out of 4 in 3wfr

Go back to Magnesium Binding Sites List in 3wfr
Magnesium binding site 3 out of 4 in the Trna Processing Enzyme Complex 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Trna Processing Enzyme Complex 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg603

b:76.4
occ:1.00
OP1 C:C75 2.1 48.7 0.5
OD2 G:ASP58 2.1 0.6 1.0
O1A G:CTP601 2.2 49.4 0.5
OD1 G:ASP60 2.4 85.5 1.0
OD2 G:ASP60 2.5 78.2 1.0
O2B G:CTP601 2.7 81.6 0.5
CG G:ASP60 2.8 78.9 1.0
O G:POP602 2.8 90.2 0.5
O6 G:POP602 2.9 82.0 0.5
CG G:ASP58 3.0 1.0 1.0
PA G:CTP601 3.3 70.3 0.5
O1G G:CTP601 3.3 98.1 0.5
P C:C75 3.5 83.3 0.5
P2 G:POP602 3.5 79.1 0.5
C5' C:C75 3.5 67.9 0.5
O5' G:CTP601 3.5 67.8 0.5
PB G:CTP601 3.5 79.9 0.5
O3A G:CTP601 3.6 63.8 0.5
OD1 G:ASP58 3.7 0.3 1.0
C5' G:CTP601 3.7 68.6 0.5
CB G:ASP58 3.8 0.9 1.0
O3B G:CTP601 3.8 85.8 0.5
O G:ASP58 3.8 84.9 1.0
O5' C:C75 3.9 69.0 0.5
O3' C:C74 4.1 84.5 0.5
O3' C:C74 4.1 84.6 0.5
PG G:CTP601 4.1 97.9 0.5
P1 G:POP602 4.2 95.4 0.5
C G:ASP58 4.2 86.0 1.0
O3 G:POP602 4.3 99.8 0.5
CB G:ASP60 4.3 72.6 1.0
O5 G:POP602 4.4 74.3 0.5
OD2 G:ASP112 4.5 73.7 1.0
O4 G:POP602 4.6 83.4 0.5
O2A G:CTP601 4.6 75.9 0.5
OP2 C:C75 4.6 80.9 0.5
CA G:ASP58 4.7 90.3 1.0
O2G G:CTP601 4.7 97.7 0.5
C4' C:C75 4.8 65.2 0.5
N G:VAL59 4.8 76.9 1.0
O1 G:POP602 4.9 97.6 0.5
C G:VAL59 4.9 65.2 1.0
N G:GLY42 4.9 79.5 1.0
N G:ASP60 4.9 65.3 1.0
O1B G:CTP601 5.0 82.4 0.5

Magnesium binding site 4 out of 4 in 3wfr

Go back to Magnesium Binding Sites List in 3wfr
Magnesium binding site 4 out of 4 in the Trna Processing Enzyme Complex 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Trna Processing Enzyme Complex 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg603

b:55.3
occ:1.00
O2B H:CTP601 2.0 80.2 0.5
OD2 H:ASP58 2.1 59.2 1.0
OP1 D:C75 2.1 63.2 0.5
OD1 H:ASP60 2.3 70.1 1.0
O1A H:CTP601 2.3 47.1 0.5
O1 H:POP602 2.3 80.8 0.5
OD2 H:ASP60 2.9 58.8 1.0
CG H:ASP60 3.0 63.3 1.0
CG H:ASP58 3.0 66.8 1.0
PB H:CTP601 3.2 80.6 0.5
PA H:CTP601 3.3 48.5 0.5
O4 H:POP602 3.4 0.9 0.5
O1G H:CTP601 3.4 0.5 0.5
O5' H:CTP601 3.5 52.9 0.5
P D:C75 3.5 66.8 0.5
O3A H:CTP601 3.6 66.1 0.5
P1 H:POP602 3.7 82.1 0.5
O3B H:CTP601 3.7 36.1 0.5
C5' H:CTP601 3.7 53.9 0.5
CB H:ASP58 3.8 67.4 1.0
OD1 H:ASP58 3.8 76.7 1.0
C5' D:C75 3.8 74.4 0.5
O H:ASP58 3.9 69.6 1.0
O5 H:POP602 4.0 0.8 0.5
O2 H:POP602 4.0 75.9 0.5
PG H:CTP601 4.0 0.1 0.5
O3' D:C74 4.1 62.1 0.5
P2 H:POP602 4.1 0.5 0.5
O5' D:C75 4.2 73.0 0.5
C H:ASP58 4.2 62.0 1.0
O2G H:CTP601 4.3 0.8 0.5
O H:POP602 4.4 37.0 0.5
CB H:ASP60 4.4 59.4 1.0
N H:GLY42 4.5 61.4 1.0
O1B H:CTP601 4.5 85.4 0.5
O3' D:C74 4.6 63.7 0.5
OP2 D:C75 4.6 67.8 0.5
OD2 H:ASP112 4.6 0.6 1.0
CA H:ASP58 4.6 62.1 1.0
CA H:GLY42 4.7 59.1 1.0
O2A H:CTP601 4.7 48.5 0.5
O3 H:POP602 4.7 86.8 0.5
N H:VAL59 4.8 56.8 1.0
O2' D:C74 4.8 81.6 0.5
N H:ASP60 4.9 70.3 1.0

Reference:

S.Yamashita, D.Takeshita, K.Tomita. Translocation and Rotation of Trna During Template-Independent Rna Polymerization By Trna Nucleotidyltransferase Structure V. 22 315 2014.
ISSN: ISSN 0969-2126
PubMed: 24389024
DOI: 10.1016/J.STR.2013.12.002
Page generated: Thu Aug 15 13:24:02 2024

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