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Potassium in PDB 1jbs: Crystal Structure of Ribotoxin Restrictocin and A 29-Mer Srd Rna Analog

Protein crystallography data

The structure of Crystal Structure of Ribotoxin Restrictocin and A 29-Mer Srd Rna Analog, PDB code: 1jbs was solved by X.Yang, T.Gerczei, L.Glover, C.C.Correll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.80 / 1.97
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.511, 101.863, 41.092, 90.00, 92.97, 90.00
R / Rfree (%) 21.3 / 25.7

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Ribotoxin Restrictocin and A 29-Mer Srd Rna Analog (pdb code 1jbs). 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 Ribotoxin Restrictocin and A 29-Mer Srd Rna Analog, PDB code: 1jbs:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 1jbs

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Potassium binding site 1 out of 6 in the Crystal Structure of Ribotoxin Restrictocin and A 29-Mer Srd Rna Analog


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 Ribotoxin Restrictocin and A 29-Mer Srd Rna Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K404

b:29.4
occ:1.00
 N7 C:OMG24 2.6 31.2 1.0
O C:HOH422 2.7 32.3 1.0
O C:HOH425 2.8 30.4 1.0
O6 C:OMG24 2.9 27.4 1.0
O C:HOH417 2.9 29.2 1.0
O C:HOH414 3.0 25.0 1.0
O C:HOH436 3.3 32.3 1.0
C5 C:OMG24 3.3 31.4 1.0
C6 C:OMG24 3.4 29.0 1.0
C8 C:OMG24 3.8 32.1 1.0
O C:HOH418 4.0 26.5 1.0
C5 C:C23 4.3 32.5 1.0
OP2 C:C23 4.4 33.4 1.0
C4 C:OMG24 4.6 31.5 1.0
O C:HOH454 4.6 38.5 1.0
O C:HOH466 4.7 48.5 1.0
O6 C:OMG25 4.7 33.6 1.0
N1 C:OMG24 4.7 29.4 1.0
N7 C:OMG25 4.8 34.1 1.0
N4 C:C23 4.8 34.8 1.0
N9 C:OMG24 4.8 33.3 1.0
C4 C:C23 4.9 32.4 1.0
C6 C:C23 4.9 32.0 1.0
O C:HOH423 4.9 29.2 1.0
O C:HOH452 5.0 37.1 1.0

Potassium binding site 2 out of 6 in 1jbs

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Potassium binding site 2 out of 6 in the Crystal Structure of Ribotoxin Restrictocin and A 29-Mer Srd Rna Analog


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 Ribotoxin Restrictocin and A 29-Mer Srd Rna Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K405

b:33.2
occ:1.00
 O C:HOH428 2.5 34.6 1.0
O4 C:U7 2.7 27.9 1.0
O C:HOH408 2.8 23.5 1.0
O C:HOH410 2.8 26.4 1.0
O C:HOH436 2.9 32.3 1.0
O C:HOH452 3.0 37.1 1.0
O C:HOH418 3.5 26.5 1.0
O C:HOH451 3.5 38.0 1.0
C4 C:U7 3.8 28.1 1.0
O C:HOH431 3.8 32.6 1.0
N4 C:OMC6 3.8 23.2 1.0
O C:HOH413 4.1 26.2 1.0
N3 C:U7 4.2 27.1 1.0
OP2 C:A21 4.3 33.9 1.0
O C:HOH421 4.3 29.3 1.0
O C:HOH430 4.4 31.2 1.0
N3 C:C8 4.5 28.5 1.0
N4 C:C8 4.7 25.2 1.0
C4 C:OMC6 4.7 25.3 1.0
O C:HOH420 4.7 28.5 1.0
OP1 C:A21 4.8 33.8 1.0
P C:A21 4.9 34.0 1.0
O6 C:OMG24 4.9 27.4 1.0
OP2 C:C22 5.0 30.4 1.0

Potassium binding site 3 out of 6 in 1jbs

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Potassium binding site 3 out of 6 in the Crystal Structure of Ribotoxin Restrictocin and A 29-Mer Srd Rna Analog


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 Ribotoxin Restrictocin and A 29-Mer Srd Rna Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K406

b:38.1
occ:1.00
 O C:HOH435 2.7 35.3 1.0
O6 C:G14 2.7 31.0 1.0
O A:HOH216 2.8 35.0 1.0
O C:HOH446 3.1 37.6 1.0
C6 C:G14 3.9 32.8 1.0
N4 C:C13 3.9 33.3 1.0
N6 C:A15 4.3 28.0 1.0
OD2 A:ASP40 4.5 31.8 1.0
N7 C:G14 4.6 33.7 1.0
NZ A:LYS42 4.6 42.4 1.0
OP2 C:U11 4.7 31.0 1.0
C5 C:G14 4.7 33.1 1.0
O6 C:G18 4.7 31.7 1.0
OD1 A:ASP40 4.8 32.7 1.0
O A:HOH205 4.8 36.4 1.0
O A:ASP40 4.8 32.9 1.0
O C:HOH412 4.8 26.0 1.0
CG A:ASP40 4.8 34.5 1.0
N1 C:G14 5.0 31.9 1.0
C4 C:C13 5.0 34.6 1.0

Potassium binding site 4 out of 6 in 1jbs

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Potassium binding site 4 out of 6 in the Crystal Structure of Ribotoxin Restrictocin and A 29-Mer Srd Rna Analog


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 Ribotoxin Restrictocin and A 29-Mer Srd Rna Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K401

b:25.4
occ:1.00
 O D:HOH407 2.7 21.0 1.0
O D:HOH411 2.7 22.0 1.0
O6 D:OMG24 2.7 19.6 1.0
N7 D:OMG24 2.8 18.0 1.0
O D:HOH439 2.9 27.5 1.0
O D:HOH440 3.1 28.4 1.0
O D:HOH420 3.2 22.4 1.0
C6 D:OMG24 3.3 17.9 1.0
C5 D:OMG24 3.4 18.3 1.0
O D:HOH493 3.6 50.2 1.0
C8 D:OMG24 4.0 21.9 1.0
C5 D:C23 4.2 25.7 1.0
O D:HOH409 4.2 20.0 1.0
OP2 D:C23 4.4 30.2 1.0
O D:HOH451 4.5 30.1 1.0
O6 D:OMG25 4.5 21.2 1.0
C4 D:OMG24 4.7 17.1 1.0
N1 D:OMG24 4.7 16.9 1.0
O D:HOH432 4.7 27.0 1.0
N7 D:OMG25 4.8 22.0 1.0
N4 D:C23 4.8 22.9 1.0
C4 D:C23 4.8 25.6 1.0
C6 D:C23 4.8 27.2 1.0
O D:HOH448 4.9 32.4 1.0
N4 D:OMC6 5.0 11.6 1.0
N9 D:OMG24 5.0 20.9 1.0

Potassium binding site 5 out of 6 in 1jbs

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Potassium binding site 5 out of 6 in the Crystal Structure of Ribotoxin Restrictocin and A 29-Mer Srd Rna Analog


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 Ribotoxin Restrictocin and A 29-Mer Srd Rna Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K402

b:25.7
occ:1.00
 O D:HOH404 2.6 14.7 1.0
O D:HOH468 2.7 33.4 1.0
O4 D:U7 2.7 18.0 1.0
O D:HOH414 2.8 22.2 1.0
O D:HOH456 3.1 31.6 1.0
O D:HOH420 3.2 22.4 1.0
O D:HOH431 3.2 25.9 1.0
O D:HOH409 3.3 20.0 1.0
C4 D:U7 3.8 18.3 1.0
O D:HOH424 3.8 26.6 1.0
O D:HOH405 4.1 18.8 1.0
N4 D:OMC6 4.1 11.6 1.0
O D:HOH428 4.1 27.2 1.0
N3 D:U7 4.2 19.4 1.0
OP2 D:A21 4.3 30.5 1.0
N3 D:C8 4.5 20.6 1.0
O D:HOH417 4.6 24.5 1.0
N4 D:C8 4.7 17.1 1.0
O D:HOH481 4.7 38.7 1.0
OP1 D:A21 4.8 31.2 1.0
OP2 D:C22 4.8 31.0 1.0
O D:HOH410 4.9 20.4 1.0
P D:A21 4.9 30.6 1.0
C4 D:OMC6 4.9 16.7 1.0

Potassium binding site 6 out of 6 in 1jbs

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Potassium binding site 6 out of 6 in the Crystal Structure of Ribotoxin Restrictocin and A 29-Mer Srd Rna Analog


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 Ribotoxin Restrictocin and A 29-Mer Srd Rna Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K403

b:26.4
occ:1.00
 O6 D:G14 2.7 25.5 1.0
O D:HOH446 2.7 28.3 1.0
O B:HOH172 2.7 28.9 1.0
O B:HOH200 2.9 38.1 1.0
O B:HOH179 2.9 35.7 1.0
O D:HOH460 3.0 31.5 1.0
O D:HOH416 3.0 23.9 1.0
O D:HOH430 3.2 26.1 1.0
C6 D:G14 3.8 28.5 1.0
N4 D:C13 4.1 22.5 1.0
N6 D:A15 4.1 30.9 1.0
O B:HOH233 4.2 43.5 1.0
N7 D:G14 4.4 27.8 1.0
O D:HOH466 4.4 29.9 1.0
OD2 B:ASP40 4.4 28.9 1.0
C5 D:G14 4.5 28.1 1.0
O B:HOH178 4.5 31.7 1.0
O D:HOH426 4.7 25.8 1.0
O6 D:G18 4.8 24.9 1.0
OP2 D:U11 4.8 27.3 1.0
OD1 B:ASP40 4.9 31.6 1.0
CG B:ASP40 4.9 28.1 1.0
O B:ASP40 4.9 27.9 1.0
C6 D:A15 4.9 30.6 1.0
N1 D:G14 4.9 27.8 1.0

Reference:

X.Yang, T.Gerczei, L.T.Glover, C.C.Correll. Crystal Structures of Restrictocin-Inhibitor Complexes with Implications For Rna Recognition and Base Flipping. Nat.Struct.Biol. V. 8 968 2001.
ISSN: ISSN 1072-8368
PubMed: 11685244
DOI: 10.1038/NSB1101-968
Page generated: Mon Aug 12 04:36:48 2024

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