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Potassium in PDB 7rut: Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp

Enzymatic activity of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp

All present enzymatic activity of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp:
2.5.1.17;

Protein crystallography data

The structure of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp, PDB code: 7rut was solved by R.Mascarenhas, H.Gouda, M.Koutmos, R.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.49 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.151, 75.769, 95.844, 90, 91.3, 90
R / Rfree (%) 15 / 18.5

Other elements in 7rut:

The structure of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp also contains other interesting chemical elements:

Magnesium (Mg) 9 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Potassium atom in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp (pdb code 7rut). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 11 binding sites of Potassium where determined in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp, PDB code: 7rut:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 11 in 7rut

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Potassium binding site 1 out of 11 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K302

b:40.1
occ:1.00
 OE2 E:GLU84 2.7 29.6 1.0
NH2 E:ARG191 2.9 17.7 1.0
OG1 E:THR88 3.0 21.7 1.0
NE E:ARG195 3.2 20.2 1.0
K D:K304 3.3 24.5 1.0
NH2 E:ARG195 3.4 19.7 1.0
CD E:ARG191 3.5 17.4 1.0
CG E:ARG191 3.6 16.2 1.0
CZ E:ARG195 3.7 20.2 1.0
CD E:GLU84 3.9 23.8 1.0
CG2 E:THR88 4.0 21.5 1.0
CD D:ARG191 4.0 16.0 1.0
CZ E:ARG191 4.0 17.7 1.0
NH2 D:ARG195 4.0 19.9 1.0
CB E:THR88 4.1 19.7 1.0
NE E:ARG191 4.2 17.7 1.0
CG E:ARG195 4.2 19.3 1.0
CD E:ARG195 4.2 19.1 1.0
NE D:ARG191 4.6 17.2 1.0
OE1 E:GLU84 4.6 26.5 1.0
O E:HOH426 4.7 21.5 1.0
NH2 D:ARG194 4.7 16.5 1.0
CG E:GLU84 4.7 18.5 1.0
NH1 E:ARG195 4.9 20.5 1.0
OE1 E:GLU91 4.9 20.8 1.0

Potassium binding site 2 out of 11 in 7rut

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Potassium binding site 2 out of 11 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K303

b:25.9
occ:1.00
 O B:ILE58 2.7 29.3 1.0
O B:HOH499 2.8 47.3 1.0
O2G B:ATP304 2.8 22.4 1.0
OD1 C:ASP218 2.9 27.3 1.0
O2A B:ATP304 2.9 24.4 1.0
OD2 C:ASP218 2.9 25.6 1.0
O1G B:ATP304 3.0 23.4 1.0
CG C:ASP218 3.2 24.3 1.0
O1A B:ATP304 3.4 22.4 1.0
PG B:ATP304 3.5 21.8 1.0
O B:HOH417 3.6 37.6 1.0
PA B:ATP304 3.6 20.7 1.0
O C:HOH441 3.7 21.7 1.0
C B:ILE58 3.8 29.6 1.0
O B:HOH496 3.9 40.3 1.0
MG C:MG301 4.0 19.0 1.0
O C:HOH419 4.1 24.1 1.0
CG1 B:ILE58 4.1 36.9 1.0
O3B B:ATP304 4.2 19.6 1.0
CA B:TYR59 4.2 28.0 1.0
N B:TYR59 4.4 29.2 1.0
O3A B:ATP304 4.5 20.2 1.0
N B:THR60 4.7 26.1 1.0
CB C:ASP218 4.7 22.9 1.0
O C:HOH468 4.7 53.6 1.0
CA B:ILE58 4.8 32.8 1.0
O3G B:ATP304 4.9 23.5 1.0
PB B:ATP304 4.9 19.8 1.0
CD1 B:ILE58 4.9 37.5 1.0
O5' B:ATP304 5.0 20.9 1.0

Potassium binding site 3 out of 11 in 7rut

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Potassium binding site 3 out of 11 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K304

b:54.5
occ:1.00
 NZ B:LYS177 3.0 44.7 1.0
CE C:LYS177 3.3 48.2 1.0
NZ C:LYS177 3.3 49.9 1.0
CE B:LYS177 3.8 44.4 1.0
CZ C:PHE98 4.2 30.8 1.0
CZ B:PHE98 4.2 32.3 1.0
CZ F:PHE98 4.3 32.3 1.0
CD2 F:LEU102 4.4 30.8 1.0
CD2 B:LEU102 4.5 32.3 1.0
CD F:LYS177 4.5 45.0 1.0
CD2 C:LEU102 4.5 32.2 1.0
CD C:LYS177 4.6 45.3 1.0
CE2 C:PHE98 4.8 30.5 1.0
CE2 B:PHE98 4.8 31.2 1.0
NZ F:LYS177 4.9 50.4 1.0
CE2 F:PHE98 4.9 31.5 1.0

Potassium binding site 4 out of 11 in 7rut

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Potassium binding site 4 out of 11 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K303

b:24.5
occ:1.00
 O C:ILE58 2.7 27.1 1.0
O2G C:ATP305 2.8 19.1 1.0
OD2 F:ASP218 2.9 25.8 1.0
OD1 F:ASP218 2.9 25.2 1.0
O2A C:ATP305 3.0 23.0 1.0
O1G C:ATP305 3.0 21.7 1.0
CG F:ASP218 3.2 24.8 1.0
MG C:MG302 3.3 57.3 1.0
O C:HOH413 3.3 40.2 1.0
O1A C:ATP305 3.3 19.5 1.0
PG C:ATP305 3.5 20.2 1.0
PA C:ATP305 3.6 19.6 1.0
C C:ILE58 3.7 27.6 1.0
O F:HOH429 3.8 20.3 1.0
MG F:MG301 4.0 18.5 1.0
CG1 C:ILE58 4.1 33.4 1.0
O F:HOH410 4.1 22.0 1.0
O F:HOH420 4.1 53.2 1.0
O3B C:ATP305 4.2 18.7 1.0
CA C:TYR59 4.2 26.1 1.0
N C:TYR59 4.4 25.7 1.0
O3A C:ATP305 4.5 18.0 1.0
N C:THR60 4.6 25.0 1.0
CB F:ASP218 4.7 21.5 1.0
CA C:ILE58 4.8 30.4 1.0
O3G C:ATP305 4.8 19.9 1.0
PB C:ATP305 4.9 18.8 1.0
CD1 C:ILE58 5.0 34.5 1.0
CB C:ILE58 5.0 30.6 1.0
O5' C:ATP305 5.0 20.2 1.0

Potassium binding site 5 out of 11 in 7rut

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Potassium binding site 5 out of 11 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K302

b:23.4
occ:1.00
 O F:ILE58 2.7 24.5 1.0
O1G F:ATP304 2.8 19.7 1.0
OD1 B:ASP218 2.8 24.9 1.0
OD2 B:ASP218 2.8 23.6 1.0
O2A F:ATP304 3.0 23.9 1.0
O2G F:ATP304 3.0 23.1 1.0
MG F:MG302 3.2 50.6 1.0
CG B:ASP218 3.2 24.1 1.0
O1A F:ATP304 3.3 20.5 1.0
O F:HOH435 3.4 34.7 1.0
PG F:ATP304 3.5 20.1 1.0
PA F:ATP304 3.6 20.7 1.0
C F:ILE58 3.7 24.2 1.0
O B:HOH437 3.8 19.9 1.0
O F:HOH498 3.9 46.8 1.0
MG B:MG301 3.9 18.2 1.0
CG1 F:ILE58 4.1 34.0 1.0
O B:HOH432 4.1 22.6 1.0
O3B F:ATP304 4.2 19.3 1.0
O B:HOH442 4.2 46.8 1.0
CA F:TYR59 4.3 23.8 1.0
N F:TYR59 4.4 24.5 1.0
O3A F:ATP304 4.4 20.6 1.0
N F:THR60 4.7 24.8 1.0
CB B:ASP218 4.7 22.7 1.0
CA F:ILE58 4.8 26.6 1.0
O3G F:ATP304 4.8 20.2 1.0
PB F:ATP304 4.9 20.4 1.0
CD1 F:ILE58 4.9 35.7 1.0
CB F:ILE58 4.9 30.8 1.0
O5' F:ATP304 5.0 21.2 1.0
O2B F:ATP304 5.0 19.1 1.0

Potassium binding site 6 out of 11 in 7rut

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Potassium binding site 6 out of 11 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K303

b:24.5
occ:1.00
 NH2 F:ARG195 3.2 21.4 1.0
NH2 B:ARG195 3.3 19.6 1.0
O F:HOH479 3.3 23.1 1.0
O C:HOH450 3.3 22.9 1.0
NH2 C:ARG195 3.3 18.7 1.0
O B:HOH452 3.4 26.3 1.0
CD B:ARG191 4.0 17.2 1.0
CD C:ARG191 4.1 18.2 1.0
CD F:ARG191 4.1 16.3 1.0
NH2 B:ARG191 4.3 17.9 1.0
OE2 B:GLU84 4.4 27.1 1.0
CZ F:ARG195 4.4 20.1 1.0
CZ B:ARG195 4.4 19.2 1.0
NH2 F:ARG191 4.4 17.6 1.0
OE2 F:GLU84 4.4 28.7 1.0
OE2 C:GLU84 4.5 27.2 1.0
NH2 C:ARG191 4.5 18.9 1.0
CZ C:ARG195 4.5 19.1 1.0
NE B:ARG191 4.6 17.6 1.0
O B:HOH506 4.7 54.1 1.0
NE F:ARG195 4.7 19.4 1.0
NE C:ARG191 4.7 17.3 1.0
CZ B:ARG191 4.7 17.1 1.0
NE B:ARG195 4.7 19.8 1.0
NE F:ARG191 4.7 16.4 1.0
O F:HOH517 4.8 55.3 1.0
NE C:ARG195 4.8 19.9 1.0
CZ F:ARG191 4.8 16.7 1.0
CZ C:ARG191 4.9 17.8 1.0
CG B:ARG191 5.0 16.9 1.0

Potassium binding site 7 out of 11 in 7rut

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Potassium binding site 7 out of 11 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:26.5
occ:1.00
 O A:ILE58 2.7 30.2 1.0
O3G A:ATP505 2.9 23.1 1.0
O1A A:ATP505 3.0 24.7 1.0
O1G A:ATP505 3.1 25.4 1.0
C3 A:GOL501 3.2 66.8 1.0
O2A A:ATP505 3.3 21.9 1.0
PG A:ATP505 3.5 23.3 1.0
PA A:ATP505 3.6 22.3 1.0
O3 A:GOL501 3.7 67.5 1.0
O A:HOH644 3.7 37.7 1.0
C A:ILE58 3.8 31.8 1.0
O A:HOH688 3.9 52.8 1.0
MG A:MG502 4.0 20.0 1.0
CG1 A:ILE58 4.1 37.2 1.0
CA A:TYR59 4.2 32.1 1.0
O3B A:ATP505 4.2 21.6 1.0
C2 A:GOL501 4.3 67.2 1.0
N A:TYR59 4.4 31.4 1.0
O3A A:ATP505 4.5 21.9 1.0
O2 A:GOL501 4.5 67.0 1.0
N A:THR60 4.6 30.1 1.0
CA A:ILE58 4.8 34.1 1.0
O2G A:ATP505 4.9 23.6 1.0
PB A:ATP505 4.9 22.0 1.0
O5' A:ATP505 5.0 22.6 1.0
CD1 A:ILE58 5.0 38.0 1.0

Potassium binding site 8 out of 11 in 7rut

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Potassium binding site 8 out of 11 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K504

b:24.6
occ:1.00
 OD2 A:ASP218 2.8 25.1 1.0
OD1 A:ASP218 2.9 23.9 1.0
CG A:ASP218 3.2 23.9 1.0
O A:HOH624 3.7 20.4 1.0
O A:HOH630 4.1 24.0 1.0
O A:HOH666 4.6 43.5 1.0
CB A:ASP218 4.7 21.3 1.0

Potassium binding site 9 out of 11 in 7rut

Go back to Potassium Binding Sites List in 7rut
Potassium binding site 9 out of 11 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K303

b:25.2
occ:1.00
 O E:ILE58 2.6 28.4 1.0
O1G E:ATP303 2.9 21.2 1.0
OD1 D:ASP218 2.9 27.0 1.0
OD2 D:ASP218 2.9 25.4 1.0
O2A E:ATP303 3.0 24.5 1.0
O3G E:ATP303 3.1 22.7 1.0
CG D:ASP218 3.2 25.7 1.0
O1A E:ATP303 3.3 20.7 1.0
O E:HOH407 3.4 42.6 1.0
MG E:MG301 3.5 71.6 1.0
PG E:ATP303 3.5 20.9 1.0
PA E:ATP303 3.6 21.5 1.0
O D:HOH450 3.7 20.7 1.0
C E:ILE58 3.7 28.6 1.0
O E:HOH484 4.0 42.8 1.0
MG D:MG301 4.0 18.7 1.0
O D:HOH437 4.2 23.4 1.0
CA E:TYR59 4.2 28.4 1.0
O3B E:ATP303 4.2 20.5 1.0
CG1 E:ILE58 4.2 29.0 1.0
N E:TYR59 4.4 27.7 1.0
O D:HOH441 4.4 47.5 1.0
O3A E:ATP303 4.5 20.2 1.0
N E:THR60 4.6 28.1 1.0
CB D:ASP218 4.7 22.8 1.0
CA E:ILE58 4.8 28.4 1.0
O2G E:ATP303 4.8 22.3 1.0
PB E:ATP303 4.9 20.2 1.0

Potassium binding site 10 out of 11 in 7rut

Go back to Potassium Binding Sites List in 7rut
Potassium binding site 10 out of 11 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K304

b:24.5
occ:1.00
 NH2 D:ARG195 3.3 19.9 1.0
K E:K302 3.3 40.1 1.0
NH2 E:ARG195 3.3 19.7 1.0
O D:HOH473 3.4 24.4 1.0
CD E:ARG191 4.1 17.4 1.0
CD D:ARG191 4.1 16.0 1.0
NH2 E:ARG191 4.4 17.7 1.0
OE2 D:GLU84 4.4 27.2 1.0
CZ D:ARG195 4.4 19.1 1.0
OE2 E:GLU84 4.4 29.6 1.0
NH2 D:ARG191 4.5 18.6 1.0
CZ E:ARG195 4.5 20.2 1.0
NE E:ARG191 4.7 17.7 1.0
NE D:ARG195 4.7 19.5 1.0
NE D:ARG191 4.7 17.2 1.0
CZ E:ARG191 4.8 17.7 1.0
NE E:ARG195 4.8 20.2 1.0
CZ D:ARG191 4.9 16.9 1.0
O D:HOH515 5.0 54.4 1.0

Reference:

H.Gouda, R.Mascarenhas, S.Pillay, M.Ruetz, M.Koutmos, R.Banerjee. Patient Mutations in Human Atp:Cob(I)Alamin Adenosyltransferase Differentially Affect Its Catalytic Versus Chaperone Functions. J.Biol.Chem. 01373 2021.
ISSN: ESSN 1083-351X
PubMed: 34757128
DOI: 10.1016/J.JBC.2021.101373
Page generated: Mon Aug 12 20:56:33 2024

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