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Potassium in PDB 5hhl: Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group

Protein crystallography data

The structure of Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group, PDB code: 5hhl was solved by C.Zhao, A.M.Pyle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.14 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.830, 119.860, 161.470, 90.00, 92.08, 90.00
R / Rfree (%) 20.1 / 23.8

Potassium Binding Sites:

The binding sites of Potassium atom in the Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group (pdb code 5hhl). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group, PDB code: 5hhl:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 5hhl

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Potassium binding site 1 out of 8 in the Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K301

b:51.5
occ:1.00
 OD1 A:ASP139 2.8 30.7 1.0
O A:CYS228 2.8 27.0 1.0
O A:ILE140 2.8 33.4 1.0
OD1 A:ASP227 2.8 28.9 1.0
O A:HOH477 2.9 33.7 0.7
O A:HOH426 3.5 34.0 1.0
N A:CYS228 3.7 26.5 1.0
O A:HOH496 3.7 81.1 1.0
C A:CYS228 3.7 28.5 1.0
C A:ILE140 3.8 40.7 1.0
O A:HOH477 3.9 33.7 0.3
CG A:ASP227 4.0 34.0 1.0
CG A:ASP139 4.0 34.9 1.0
CG2 A:ILE229 4.0 26.7 1.0
N A:ILE140 4.2 39.7 1.0
O A:HOH489 4.2 28.5 1.0
C A:ASP227 4.3 29.1 1.0
CA A:CYS228 4.3 26.5 1.0
C A:ASP139 4.4 38.9 1.0
CA A:ASP227 4.4 33.7 1.0
CA A:ASP139 4.6 36.6 1.0
N A:ASP141 4.6 30.7 1.0
CA A:ILE140 4.6 40.3 1.0
N A:ILE229 4.6 26.6 1.0
CA A:ASP141 4.7 32.6 1.0
OD2 A:ASP139 4.8 37.3 1.0
CE1 A:TYR272 4.8 26.1 1.0
OD2 A:ASP227 4.8 30.7 1.0
CB A:ASP227 4.9 32.1 1.0
CD1 A:TYR272 4.9 23.8 1.0
O A:ASP139 4.9 37.5 1.0
CB A:ASP139 4.9 40.3 1.0
CA A:ILE229 5.0 26.9 1.0

Potassium binding site 2 out of 8 in 5hhl

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Potassium binding site 2 out of 8 in the Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K301

b:52.4
occ:1.00
 O B:CYS228 2.8 31.1 1.0
OD1 B:ASP139 2.8 59.2 1.0
O B:ILE140 2.8 47.6 1.0
OD1 B:ASP227 2.8 34.0 1.0
O B:HOH414 3.3 30.4 1.0
N B:CYS228 3.6 25.6 1.0
C B:ILE140 3.6 41.1 1.0
C B:CYS228 3.7 32.0 1.0
O B:HOH534 3.7 44.2 1.0
CG B:ASP227 4.0 36.1 1.0
CG B:ASP139 4.0 43.4 1.0
O B:HOH450 4.0 35.1 1.0
N B:ILE140 4.0 43.1 1.0
C B:ASP227 4.2 27.5 1.0
CG2 B:ILE229 4.2 24.8 1.0
CA B:CYS228 4.2 26.1 1.0
CA B:ASP227 4.3 34.4 1.0
C B:ASP139 4.3 30.8 1.0
N B:ASP141 4.3 37.7 1.0
CA B:ASP141 4.5 41.4 1.0
CA B:ILE140 4.5 44.9 1.0
CA B:ASP139 4.6 28.1 1.0
N B:ILE229 4.6 31.1 1.0
OD2 B:ASP139 4.8 57.4 1.0
CB B:ASP227 4.8 35.7 1.0
OD2 B:ASP227 4.8 33.1 1.0
CE1 B:TYR272 4.9 27.5 1.0
O B:ASP139 4.9 34.1 1.0
CB B:ASP139 4.9 31.1 1.0

Potassium binding site 3 out of 8 in 5hhl

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Potassium binding site 3 out of 8 in the Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K301

b:47.0
occ:1.00
 O C:ILE140 2.8 33.7 1.0
OD1 C:ASP227 2.8 29.6 1.0
OD1 C:ASP139 2.8 27.8 1.0
O C:CYS228 2.8 23.7 1.0
O C:HOH487 2.8 34.4 1.0
O C:HOH441 3.4 29.6 1.0
N C:CYS228 3.7 24.7 1.0
C C:CYS228 3.7 25.0 1.0
C C:ILE140 3.8 34.7 1.0
O C:HOH490 3.8 39.3 1.0
CG C:ASP227 3.9 29.0 1.0
CG C:ASP139 4.0 35.0 1.0
CG2 C:ILE229 4.2 30.9 1.0
N C:ILE140 4.2 41.7 1.0
O C:HOH482 4.2 25.9 1.0
C C:ASP227 4.3 25.2 1.0
C C:ASP139 4.4 44.1 1.0
CA C:CYS228 4.4 29.7 1.0
CA C:ASP227 4.4 25.7 1.0
N C:ASP141 4.6 30.8 1.0
CA C:ASP139 4.6 38.0 1.0
CA C:ASP141 4.6 32.6 1.0
CA C:ILE140 4.6 43.3 1.0
N C:ILE229 4.6 24.0 1.0
OD2 C:ASP227 4.7 29.8 1.0
OD2 C:ASP139 4.8 33.4 1.0
CB C:ASP227 4.8 23.7 1.0
CE1 C:TYR272 4.8 35.0 1.0
O C:ASP139 4.8 33.1 1.0
CD1 C:TYR272 4.9 34.1 1.0
CB C:ASP139 4.9 28.5 1.0

Potassium binding site 4 out of 8 in 5hhl

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Potassium binding site 4 out of 8 in the Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K301

b:44.0
occ:1.00
 OD1 D:ASP227 2.7 35.2 1.0
O D:ILE140 2.7 33.4 1.0
OD1 D:ASP139 2.7 27.9 1.0
O D:CYS228 2.8 17.8 1.0
O D:HOH463 3.0 62.3 1.0
O D:HOH440 3.3 29.9 1.0
C D:ILE140 3.7 35.0 1.0
N D:CYS228 3.7 25.4 1.0
C D:CYS228 3.7 23.7 1.0
O D:HOH513 3.8 42.5 1.0
CG D:ASP227 3.9 33.3 1.0
N D:ILE140 4.0 31.7 1.0
CG D:ASP139 4.0 27.4 1.0
CG2 D:ILE229 4.2 25.0 1.0
C D:ASP139 4.2 29.4 1.0
C D:ASP227 4.3 23.1 1.0
CA D:CYS228 4.3 27.8 1.0
CA D:ASP227 4.4 31.4 1.0
CA D:ILE140 4.4 37.5 1.0
CA D:ASP139 4.5 27.0 1.0
N D:ASP141 4.5 32.9 1.0
CA D:ASP141 4.6 36.8 1.0
O D:HOH457 4.6 34.0 1.0
N D:ILE229 4.7 24.4 1.0
OD2 D:ASP227 4.7 34.8 1.0
CB D:ASP227 4.8 30.9 1.0
OD2 D:ASP139 4.8 40.3 1.0
O D:ASP139 4.8 39.9 1.0
CB D:ASP139 4.8 31.0 1.0
CE1 D:TYR272 5.0 22.1 1.0

Potassium binding site 5 out of 8 in 5hhl

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Potassium binding site 5 out of 8 in the Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K301

b:57.7
occ:1.00
 OD1 E:ASP139 2.7 26.4 1.0
O E:CYS228 2.7 27.9 1.0
OD1 E:ASP227 2.8 36.0 1.0
O E:ILE140 2.8 46.0 1.0
O E:HOH464 2.8 43.0 1.0
O E:HOH434 3.4 32.9 1.0
C E:ILE140 3.7 45.0 1.0
N E:CYS228 3.7 22.5 1.0
C E:CYS228 3.7 29.0 1.0
CG E:ASP227 3.9 39.2 1.0
CG E:ASP139 4.0 33.9 1.0
N E:ILE140 4.0 45.8 1.0
O E:HOH479 4.1 49.2 1.0
CG2 E:ILE229 4.2 26.8 1.0
C E:ASP227 4.3 36.9 1.0
CA E:CYS228 4.3 23.4 1.0
C E:ASP139 4.3 40.9 1.0
CA E:ASP227 4.4 32.6 1.0
O E:HOH474 4.4 43.5 1.0
N E:ASP141 4.4 42.7 1.0
CA E:ASP141 4.5 39.3 1.0
CA E:ILE140 4.5 56.4 1.0
CA E:ASP139 4.6 36.0 1.0
N E:ILE229 4.7 34.9 1.0
OD2 E:ASP227 4.7 37.3 1.0
OD2 E:ASP139 4.7 32.0 1.0
CB E:ASP227 4.8 31.0 1.0
O E:ASP139 4.9 41.3 1.0
CB E:ASP139 4.9 28.0 1.0
CE1 E:TYR272 4.9 36.2 1.0

Potassium binding site 6 out of 8 in 5hhl

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Potassium binding site 6 out of 8 in the Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K301

b:51.5
occ:1.00
 OD1 F:ASP139 2.8 35.9 1.0
OD1 F:ASP227 2.8 48.4 1.0
O F:ILE140 2.8 36.7 1.0
O F:CYS228 2.9 27.9 1.0
O F:HOH509 3.3 34.2 1.0
O F:HOH444 3.6 29.9 1.0
C F:ILE140 3.7 42.8 1.0
C F:CYS228 3.8 27.8 1.0
N F:CYS228 3.9 27.8 1.0
CG F:ASP227 3.9 45.3 1.0
CG2 F:ILE229 4.0 27.2 1.0
N F:ILE140 4.0 38.6 1.0
CG F:ASP139 4.0 36.0 1.0
O F:HOH471 4.1 42.5 1.0
C F:ASP139 4.3 36.0 1.0
O F:HOH505 4.3 37.6 1.0
C F:ASP227 4.4 30.7 1.0
CA F:ILE140 4.5 50.1 1.0
CA F:ASP139 4.5 35.6 1.0
CA F:ASP227 4.5 33.9 1.0
CA F:CYS228 4.5 28.0 1.0
N F:ASP141 4.6 38.0 1.0
OD2 F:ASP227 4.7 37.5 1.0
N F:ILE229 4.7 28.8 1.0
CA F:ASP141 4.7 41.5 1.0
OD2 F:ASP139 4.8 36.2 1.0
O F:ASP139 4.8 36.4 1.0
CB F:ASP227 4.9 29.4 1.0
CB F:ASP139 4.9 35.8 1.0
CA F:ILE229 4.9 33.1 1.0
CE1 F:TYR272 5.0 29.6 1.0

Potassium binding site 7 out of 8 in 5hhl

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Potassium binding site 7 out of 8 in the Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K301

b:44.9
occ:1.00
 OD1 G:ASP139 2.7 27.0 1.0
OD1 G:ASP227 2.7 41.3 1.0
O G:ILE140 2.8 36.3 1.0
O G:CYS228 2.8 21.3 1.0
O G:HOH467 3.6 41.6 1.0
O G:HOH431 3.6 31.0 1.0
C G:ILE140 3.7 41.0 1.0
C G:CYS228 3.7 25.4 1.0
N G:CYS228 3.7 32.3 1.0
N G:ILE140 3.8 34.3 1.0
CG G:ASP227 3.9 39.4 1.0
CG G:ASP139 3.9 32.4 1.0
CG2 G:ILE229 4.0 23.4 1.0
C G:ASP139 4.2 31.4 1.0
C G:ASP227 4.3 28.2 1.0
CA G:CYS228 4.3 26.2 1.0
CA G:ILE140 4.4 45.3 1.0
CA G:ASP227 4.4 36.6 1.0
CA G:ASP139 4.4 24.7 1.0
N G:ASP141 4.5 32.4 1.0
N G:ILE229 4.6 29.6 1.0
OD2 G:ASP227 4.6 41.5 1.0
O G:HOH441 4.6 29.9 1.0
CE1 G:TYR272 4.7 29.5 1.0
CA G:ASP141 4.7 32.1 1.0
OD2 G:ASP139 4.8 32.4 1.0
CD1 G:TYR272 4.8 33.5 1.0
CB G:ASP227 4.8 29.9 1.0
CB G:ASP139 4.8 29.8 1.0
O G:ASP139 4.8 32.4 1.0
CA G:ILE229 4.9 25.8 1.0

Potassium binding site 8 out of 8 in 5hhl

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Potassium binding site 8 out of 8 in the Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Reverse Transcriptase Domain of Group II Intron Maturase From Eubacterium Rectale in P21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K301

b:60.9
occ:1.00
 OD1 H:ASP139 2.7 47.0 1.0
OD1 H:ASP227 2.8 38.9 1.0
O H:CYS228 2.8 33.7 1.0
O H:ILE140 2.8 60.6 1.0
O H:HOH420 2.9 49.2 1.0
O H:HOH436 3.4 39.4 1.0
O H:HOH417 3.5 48.8 1.0
C H:ILE140 3.7 53.1 1.0
C H:CYS228 3.7 37.4 1.0
N H:CYS228 3.8 32.4 1.0
CG H:ASP139 3.9 40.7 1.0
CG H:ASP227 4.0 36.8 1.0
CG2 H:ILE229 4.0 27.9 1.0
N H:ILE140 4.0 47.6 1.0
C H:ASP139 4.3 59.5 1.0
C H:ASP227 4.3 43.5 1.0
O H:HOH461 4.3 45.9 1.0
CA H:CYS228 4.4 38.3 1.0
CA H:ASP227 4.5 41.7 1.0
N H:ASP141 4.5 45.9 1.0
CA H:ASP139 4.5 43.5 1.0
CA H:ILE140 4.5 53.2 1.0
CA H:ASP141 4.6 39.5 1.0
N H:ILE229 4.7 48.2 1.0
OD2 H:ASP139 4.7 42.6 1.0
OD2 H:ASP227 4.7 34.1 1.0
CB H:ASP139 4.8 36.8 1.0
CB H:ASP227 4.8 33.5 1.0
CE1 H:TYR272 4.9 44.7 1.0
O H:ASP139 4.9 55.8 1.0
CA H:ILE229 5.0 46.7 1.0

Reference:

C.Zhao, A.M.Pyle. Crystal Structures of A Group II Intron Maturase Reveal A Missing Link in Spliceosome Evolution. Nat.Struct.Mol.Biol. V. 23 558 2016.
ISSN: ESSN 1545-9985
PubMed: 27136328
DOI: 10.1038/NSMB.3224
Page generated: Mon Aug 12 13:49:53 2024

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