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Potassium in PDB 3w1i: Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela

Enzymatic activity of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela

All present enzymatic activity of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela:
2.9.1.1;

Protein crystallography data

The structure of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela, PDB code: 3w1i was solved by Y.Itoh, S.Sekine, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.94 / 3.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.825, 280.936, 97.645, 90.00, 113.45, 90.00
R / Rfree (%) 17.4 / 23.5

Other elements in 3w1i:

The structure of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela also contains other interesting chemical elements:

Platinum (Pt) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela (pdb code 3w1i). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela, PDB code: 3w1i:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in 3w1i

Go back to Potassium Binding Sites List in 3w1i
Potassium binding site 1 out of 5 in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela


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 the N-Terminal Truncated Selenocysteine Synthase Sela within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K2001

b:0.3
occ:1.00
 OD1 B:ASN140 3.0 82.4 1.0
OD1 B:ASP317 3.4 0.8 1.0
OD1 A:ASN140 3.5 86.4 1.0
OD2 A:ASP317 3.7 0.8 1.0
CG B:ASP317 3.8 0.8 1.0
CG A:ASP317 3.9 1.0 1.0
CB A:ASP317 4.0 0.5 1.0
N B:ASP317 4.0 99.9 1.0
CG B:ASN140 4.1 90.6 1.0
CG2 B:THR320 4.3 93.8 1.0
CB B:ASP317 4.3 0.2 1.0
OG1 B:THR320 4.3 95.0 1.0
OD2 B:ASP317 4.4 0.5 1.0
O B:ASN140 4.5 82.2 1.0
CG A:ASN140 4.5 80.2 1.0
N A:ASP317 4.6 94.8 1.0
CA B:ILE316 4.6 81.6 1.0
CA B:ASN140 4.6 74.3 1.0
NE2 B:GLN291 4.6 80.7 1.0
CB B:ASN140 4.6 85.3 1.0
OD1 A:ASP317 4.6 0.2 1.0
CA B:ASP317 4.8 0.4 1.0
C B:ILE316 4.9 89.1 1.0
CB B:ILE316 4.9 75.8 1.0
CA A:ASP317 5.0 98.3 1.0
CB B:THR320 5.0 89.5 1.0

Potassium binding site 2 out of 5 in 3w1i

Go back to Potassium Binding Sites List in 3w1i
Potassium binding site 2 out of 5 in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela


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 the N-Terminal Truncated Selenocysteine Synthase Sela within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K501

b:0.6
occ:1.00
 OD1 D:ASN140 3.2 93.9 1.0
OD1 C:ASN140 3.4 0.1 1.0
OD1 C:ASP317 3.5 0.1 1.0
OD1 D:ASP317 3.5 0.8 1.0
CG C:ASP317 4.0 0.9 1.0
CG D:ASP317 4.1 0.3 1.0
CG D:ASN140 4.2 81.4 1.0
OG1 D:THR320 4.2 0.6 1.0
CB C:ASP317 4.2 0.8 1.0
N C:ASP317 4.3 83.8 1.0
CG C:ASN140 4.3 81.0 1.0
N D:ASP317 4.3 91.5 1.0
NE2 D:GLN291 4.4 80.5 1.0
CB D:ASP317 4.5 0.4 1.0
CG2 D:THR320 4.5 0.6 1.0
O D:ASN140 4.5 87.0 1.0
CA D:ASN140 4.7 77.6 1.0
OD2 C:ASP317 4.8 0.3 1.0
OD2 D:ASP317 4.8 0.8 1.0
CB D:ASN140 4.9 79.1 1.0
OG1 C:THR320 4.9 0.3 1.0
ND2 C:ASN140 4.9 69.2 1.0
CA C:ASP317 4.9 91.1 1.0
CA D:ILE316 4.9 86.7 1.0
CB D:THR320 5.0 0.3 1.0
ND2 D:ASN140 5.0 77.5 1.0

Potassium binding site 3 out of 5 in 3w1i

Go back to Potassium Binding Sites List in 3w1i
Potassium binding site 3 out of 5 in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela


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 the N-Terminal Truncated Selenocysteine Synthase Sela within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K501

b:0.5
occ:1.00
 OD1 F:ASP317 2.8 0.8 1.0
OD1 E:ASP317 3.2 94.6 1.0
OD1 F:ASN140 3.2 90.8 1.0
OD1 E:ASN140 3.4 85.5 1.0
CG F:ASP317 3.8 0.9 1.0
CB F:ASP317 4.0 0.6 1.0
CG E:ASP317 4.1 0.4 1.0
N E:ASP317 4.2 93.2 1.0
CB E:ASP317 4.3 0.7 1.0
CG F:ASN140 4.3 82.5 1.0
CG2 E:THR320 4.3 99.8 1.0
N F:ASP317 4.4 86.0 1.0
CG E:ASN140 4.4 86.5 1.0
OG1 E:THR320 4.5 0.6 1.0
O E:ASN140 4.7 82.6 1.0
CA E:ILE316 4.7 69.1 1.0
CB E:ASN140 4.8 67.1 1.0
CA E:ASN140 4.8 73.0 1.0
OG1 F:THR320 4.8 81.7 1.0
CA F:ASP317 4.9 99.6 1.0
CA E:ASP317 4.9 95.6 1.0
OD2 F:ASP317 4.9 99.5 1.0
C E:ILE316 5.0 74.7 1.0

Potassium binding site 4 out of 5 in 3w1i

Go back to Potassium Binding Sites List in 3w1i
Potassium binding site 4 out of 5 in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela


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 the N-Terminal Truncated Selenocysteine Synthase Sela within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K501

b:0.7
occ:1.00
 OD1 H:ASN140 3.2 83.2 1.0
OD1 G:ASN140 3.3 97.8 1.0
OD1 H:ASP317 3.4 0.8 1.0
CG H:ASP317 3.6 0.9 1.0
OD1 G:ASP317 3.8 0.1 1.0
CB H:ASP317 4.1 0.2 1.0
CG G:ASP317 4.1 0.4 1.0
OD2 H:ASP317 4.1 0.3 1.0
N G:ASP317 4.2 0.7 1.0
OG1 G:THR320 4.2 0.3 1.0
N H:ASP317 4.3 0.9 1.0
CB G:ASP317 4.3 0.1 1.0
CG H:ASN140 4.4 81.1 1.0
CG G:ASN140 4.4 0.4 1.0
NE2 H:GLN291 4.5 98.2 1.0
NE2 G:GLN291 4.7 94.7 1.0
CG2 G:THR320 4.7 0.6 1.0
OD2 G:ASP317 4.8 0.6 1.0
CA H:ASP317 4.8 0.5 1.0
CA G:ILE316 4.9 90.0 1.0
CG2 H:THR320 4.9 0.7 1.0
CB G:ASN140 4.9 99.6 1.0
CA G:ASP317 4.9 0.0 1.0
OG1 H:THR320 4.9 79.7 1.0
O G:ASN140 5.0 0.2 1.0
CA G:ASN140 5.0 90.6 1.0

Potassium binding site 5 out of 5 in 3w1i

Go back to Potassium Binding Sites List in 3w1i
Potassium binding site 5 out of 5 in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela


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 the N-Terminal Truncated Selenocysteine Synthase Sela within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K501

b:0.2
occ:1.00
 OD1 J:ASP317 3.1 0.2 1.0
OD2 I:ASP317 3.3 0.3 1.0
OD1 J:ASN140 3.6 99.5 1.0
OD1 I:ASN140 3.7 97.7 1.0
N J:ASP317 3.9 0.1 1.0
CG J:ASP317 3.9 0.5 1.0
OG1 J:THR320 3.9 0.4 1.0
CG I:ASP317 4.0 0.1 1.0
CB J:ASP317 4.0 0.5 1.0
CG2 J:THR320 4.2 0.6 1.0
CB I:ASP317 4.3 0.3 1.0
CA J:ILE316 4.5 0.1 1.0
CA J:ASP317 4.6 0.7 1.0
CG J:ASN140 4.6 95.8 1.0
N I:ASP317 4.7 92.3 1.0
CB J:THR320 4.7 0.7 1.0
C J:ILE316 4.7 0.6 1.0
CG I:ASN140 4.7 92.1 1.0
O J:ASN140 4.7 96.8 1.0
CG2 I:THR320 4.8 0.8 1.0
CB J:ILE316 4.8 0.6 1.0
CG2 J:ILE316 4.8 1.0 1.0
CA J:ASN140 4.8 92.8 1.0
OD1 I:ASP317 4.9 0.8 1.0
CB J:ASN140 4.9 84.3 1.0
NE2 J:GLN291 5.0 82.0 1.0

Reference:

Y.Itoh, M.J.Brocker, S.Sekine, G.Hammond, S.Suetsugu, D.Soll, S.Yokoyama. Decameric Sela-Trna(Sec) Ring Structure Reveals Mechanism of Bacterial Selenocysteine Formation Science V. 340 75 2013.
ISSN: ISSN 0036-8075
PubMed: 23559248
DOI: 10.1126/SCIENCE.1229521
Page generated: Mon Aug 12 09:50:12 2024

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