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Potassium in PDB 2nqp: Crystal Structure of Pseudoudirinde Synthase Trua in Complex with Leucyl Trna

Enzymatic activity of Crystal Structure of Pseudoudirinde Synthase Trua in Complex with Leucyl Trna

All present enzymatic activity of Crystal Structure of Pseudoudirinde Synthase Trua in Complex with Leucyl Trna:
5.4.99.12;

Protein crystallography data

The structure of Crystal Structure of Pseudoudirinde Synthase Trua in Complex with Leucyl Trna, PDB code: 2nqp was solved by S.Hur, R.M.Stroud, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.278, 128.585, 159.256, 90.00, 90.00, 90.00
R / Rfree (%) 24.6 / 27.9

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Pseudoudirinde Synthase Trua in Complex with Leucyl Trna (pdb code 2nqp). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Crystal Structure of Pseudoudirinde Synthase Trua in Complex with Leucyl Trna, PDB code: 2nqp:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 2nqp

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Potassium binding site 1 out of 6 in the Crystal Structure of Pseudoudirinde Synthase Trua in Complex with Leucyl Trna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Pseudoudirinde Synthase Trua in Complex with Leucyl Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K77

b:56.4
occ:1.00
 N4 F:C62 2.7 70.2 1.0
C5 F:C62 3.4 73.6 1.0
C4 F:C62 3.4 72.3 1.0
OP1 F:U60 3.5 39.5 1.0
C4 F:C61 4.0 35.2 1.0
N4 F:C61 4.1 35.1 1.0
C5 F:C61 4.1 35.6 1.0
N4 F:C63 4.2 97.1 1.0
OP2 F:C61 4.4 51.2 1.0
N3 F:C61 4.5 37.1 1.0
OP2 F:C62 4.5 71.0 1.0
C6 F:C62 4.6 76.1 1.0
C6 F:C61 4.7 39.0 1.0
P F:U60 4.7 35.7 1.0
N3 F:C62 4.7 73.7 1.0
OP2 F:U60 5.0 35.1 1.0
C2 F:C61 5.0 39.2 1.0

Potassium binding site 2 out of 6 in 2nqp

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Potassium binding site 2 out of 6 in the Crystal Structure of Pseudoudirinde Synthase Trua in Complex with Leucyl Trna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Pseudoudirinde Synthase Trua in Complex with Leucyl Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K78

b:28.7
occ:1.00
 OP1 F:G49 2.6 77.1 1.0
O2' F:G59 2.7 38.8 1.0
O3' F:G59 3.2 35.5 1.0
P F:G49 3.6 78.3 1.0
C2' F:G59 3.8 36.6 1.0
OP2 F:G49 3.8 78.8 1.0
OP1 F:U60 3.8 39.5 1.0
C3' F:G59 3.9 34.9 1.0
C4' F:G59 4.0 35.0 1.0
C3' F:U48 4.2 71.1 1.0
P F:U60 4.2 35.7 1.0
C2' F:U48 4.2 69.7 1.0
O3' F:U48 4.3 75.3 1.0
C1' F:G59 4.6 37.5 1.0
O4' F:G59 4.7 36.1 1.0
O2' F:U48 4.7 71.6 1.0
O5' F:G49 4.9 81.9 1.0
O5' F:U60 5.0 36.7 1.0
C5' F:U60 5.0 40.2 1.0

Potassium binding site 3 out of 6 in 2nqp

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Potassium binding site 3 out of 6 in the Crystal Structure of Pseudoudirinde Synthase Trua in Complex with Leucyl Trna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Pseudoudirinde Synthase Trua in Complex with Leucyl Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K79

b:74.2
occ:1.00
 O4 F:U54 2.8 46.8 1.0
O4 F:U55 3.1 43.5 1.0
OP2 F:A58 3.8 41.4 1.0
C4 F:U54 3.9 46.3 1.0
C4 F:U55 4.0 42.6 1.0
N3 F:U55 4.2 40.1 1.0
C5 F:U54 4.3 49.0 1.0
O6 F:G53 4.8 62.9 1.0
P F:A58 4.8 40.2 1.0

Potassium binding site 4 out of 6 in 2nqp

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Potassium binding site 4 out of 6 in the Crystal Structure of Pseudoudirinde Synthase Trua in Complex with Leucyl Trna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Pseudoudirinde Synthase Trua in Complex with Leucyl Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K271

b:26.7
occ:1.00
 O C:ALA89 3.5 17.3 1.0
CA C:ALA89 3.7 15.4 1.0
C C:ALA89 3.9 15.3 1.0
O5' F:U20 4.0 61.1 1.0
CB C:ALA89 4.3 16.2 1.0
O C:ASN88 4.5 15.3 1.0
C5' F:U20 4.6 68.5 1.0
OP2 F:U20 4.6 56.5 0.7
N C:ALA89 4.8 14.8 1.0
P F:U20 4.9 56.4 0.7

Potassium binding site 5 out of 6 in 2nqp

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Potassium binding site 5 out of 6 in the Crystal Structure of Pseudoudirinde Synthase Trua in Complex with Leucyl Trna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Pseudoudirinde Synthase Trua in Complex with Leucyl Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K80

b:72.4
occ:1.00
 K F:K81 2.8 67.4 1.0
O3' F:U20 2.8 76.2 1.0
O4' F:A20A 3.0 68.8 1.0
O2' F:U20 3.3 86.8 1.0
C4' F:A20A 3.5 67.8 1.0
C3' F:U20 3.7 79.6 1.0
C4' F:U20 3.8 75.5 1.0
P F:A20A 3.8 77.8 1.0
OP2 F:A20A 3.9 81.0 1.0
O4 F:U48 3.9 68.5 1.0
C1' F:A20A 4.0 66.2 1.0
O5' F:A20A 4.0 74.7 1.0
C5' F:A20A 4.1 72.7 1.0
C2' F:U20 4.1 85.2 1.0
O2' F:A20A 4.5 59.8 1.0
C5' F:U20 4.6 68.5 1.0
C2' F:A20A 4.7 62.9 1.0
OP1 F:U20 4.7 54.8 0.7
C2 F:A15 4.7 61.4 1.0
C3' F:A20A 4.7 64.2 1.0
O4' F:U20 4.8 80.8 1.0
O4 F:U60 4.8 36.6 1.0
C1' F:U20 4.9 86.4 1.0

Potassium binding site 6 out of 6 in 2nqp

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Potassium binding site 6 out of 6 in the Crystal Structure of Pseudoudirinde Synthase Trua in Complex with Leucyl Trna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Pseudoudirinde Synthase Trua in Complex with Leucyl Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K81

b:67.4
occ:1.00
 O4 F:U48 2.7 68.5 1.0
OP1 F:G59 2.8 34.1 1.0
K F:K80 2.8 72.4 1.0
O4 F:U60 3.3 36.6 1.0
O2' F:U20 3.4 86.8 1.0
P F:G59 3.6 33.8 1.0
OP2 F:G59 3.6 35.8 1.0
C4 F:U48 3.7 67.9 1.0
C8 F:G59 4.0 39.7 1.0
N7 F:G59 4.0 41.7 1.0
O4' F:A20A 4.0 68.8 1.0
C5 F:U48 4.2 68.9 1.0
OP2 F:A20A 4.3 81.0 1.0
C4 F:U60 4.4 36.1 1.0
O5' F:G59 4.4 32.9 1.0
O3' F:U20 4.6 76.2 1.0
C1' F:A20A 4.8 66.2 1.0
C2' F:U20 4.8 85.2 1.0
N3 F:U48 4.8 66.9 1.0

Reference:

S.Hur, R.M.Stroud. How U38, 39, and 40 of Many Trnas Become the Targets For Pseudouridylation By Trua. Mol.Cell V. 26 189 2007.
ISSN: ISSN 1097-2765
PubMed: 17466622
DOI: 10.1016/J.MOLCEL.2007.02.027
Page generated: Mon Aug 12 06:47:58 2024

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