Magnesium 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:

Potassium (K) 11 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp, PDB code: 7rut:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 7rut

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Magnesium binding site 1 out of 9 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg301

b:71.6
occ:1.00
 O D:HOH441 3.1 47.5 1.0
O2A E:ATP303 3.3 24.5 1.0
K D:K303 3.5 25.2 1.0
CG1 E:ILE58 4.0 29.0 1.0
OD1 D:ASP218 4.0 27.0 1.0
O E:HOH484 4.1 42.8 1.0
PA E:ATP303 4.2 21.5 1.0
CD1 E:ILE58 4.3 29.5 1.0
O1A E:ATP303 4.4 20.7 1.0
O5' E:ATP303 4.6 21.4 1.0
O E:ILE58 4.6 28.4 1.0
C5' E:ATP303 4.7 22.8 1.0
O E:HOH407 4.7 42.6 1.0
CG D:ASP218 4.9 25.7 1.0
O E:HOH468 5.0 32.3 1.0

Magnesium binding site 2 out of 9 in 7rut

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Magnesium binding site 2 out of 9 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg301

b:19.0
occ:1.00
 O2B B:ATP304 2.0 18.3 1.0
O1A B:ATP304 2.0 22.4 1.0
OD1 C:ASN214 2.0 17.9 1.0
O C:HOH441 2.1 21.7 1.0
O2G B:ATP304 2.1 22.4 1.0
O C:HOH454 2.1 20.9 1.0
PB B:ATP304 3.1 19.8 1.0
CG C:ASN214 3.2 19.8 1.0
PA B:ATP304 3.3 20.7 1.0
PG B:ATP304 3.3 21.8 1.0
O3A B:ATP304 3.5 20.2 1.0
O3B B:ATP304 3.6 19.6 1.0
O C:HOH465 3.7 23.3 1.0
ND2 C:ASN214 3.7 20.5 1.0
NZ B:LYS78 3.8 20.9 1.0
K C:K303 4.0 25.9 1.0
O3G B:ATP304 4.1 23.5 1.0
O C:HOH419 4.1 24.1 1.0
O C:ASN214 4.2 19.1 1.0
O2A B:ATP304 4.2 24.4 1.0
O5' B:ATP304 4.3 20.9 1.0
OD1 C:ASP218 4.4 27.3 1.0
N7 B:ATP304 4.4 19.1 1.0
CB C:ASN214 4.4 19.1 1.0
O1G B:ATP304 4.5 23.4 1.0
O1B B:ATP304 4.5 19.9 1.0
OE1 C:GLU193 4.5 22.8 1.0
OG C:SER217 4.5 19.1 0.6
CA C:ASN214 4.6 17.3 1.0
C8 B:ATP304 4.7 20.3 1.0
C C:ASN214 4.7 17.2 1.0
CE B:LYS78 4.8 19.3 1.0
OE2 C:GLU193 4.9 22.8 1.0
OD2 C:ASP218 4.9 25.6 1.0
CG C:ASP218 5.0 24.3 1.0

Magnesium binding site 3 out of 9 in 7rut

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Magnesium binding site 3 out of 9 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg302

b:57.3
occ:1.00
 O F:HOH420 2.4 53.2 1.0
K F:K303 3.3 24.5 1.0
OD1 F:ASP218 3.5 25.2 1.0
O2A C:ATP305 3.6 23.0 1.0
CG1 C:ILE58 3.8 33.4 1.0
CD1 C:ILE58 3.8 34.5 1.0
PA C:ATP305 4.3 19.6 1.0
O1A C:ATP305 4.3 19.5 1.0
CG F:ASP218 4.5 24.8 1.0
O C:HOH467 4.6 27.2 1.0
O5' C:ATP305 4.7 20.2 1.0
O C:ILE58 4.8 27.1 1.0
O F:HOH492 4.9 48.1 1.0
C5' C:ATP305 4.9 20.2 1.0
OD2 F:ASP218 5.0 25.8 1.0

Magnesium binding site 4 out of 9 in 7rut

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Magnesium binding site 4 out of 9 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg301

b:18.5
occ:1.00
 O1A C:ATP305 2.0 19.5 1.0
O2B C:ATP305 2.0 18.2 1.0
OD1 F:ASN214 2.0 17.7 1.0
O2G C:ATP305 2.1 19.1 1.0
O F:HOH429 2.1 20.3 1.0
O F:HOH451 2.2 19.7 1.0
CG F:ASN214 3.1 17.4 1.0
PB C:ATP305 3.1 18.8 1.0
PA C:ATP305 3.2 19.6 1.0
PG C:ATP305 3.3 20.2 1.0
O3A C:ATP305 3.5 18.0 1.0
O3B C:ATP305 3.5 18.7 1.0
O C:HOH467 3.6 27.2 1.0
ND2 F:ASN214 3.7 17.5 1.0
NZ C:LYS78 3.9 23.8 1.0
K F:K303 4.0 24.5 1.0
O3G C:ATP305 4.1 19.9 1.0
O F:HOH410 4.1 22.0 1.0
O F:ASN214 4.2 18.4 1.0
O2A C:ATP305 4.2 23.0 1.0
OD1 F:ASP218 4.3 25.2 1.0
O5' C:ATP305 4.3 20.2 1.0
OG F:SER217 4.4 19.8 0.4
O1G C:ATP305 4.4 21.7 1.0
CB F:ASN214 4.4 17.1 1.0
N7 C:ATP305 4.5 19.9 1.0
O1B C:ATP305 4.5 19.6 1.0
CA F:ASN214 4.6 17.4 1.0
O C:HOH472 4.6 46.3 1.0
C F:ASN214 4.7 18.5 1.0
OE1 F:GLU193 4.7 23.5 1.0
C8 C:ATP305 4.7 19.3 1.0
OD2 F:ASP218 4.8 25.8 1.0
CE C:LYS78 4.9 21.4 1.0
CG F:ASP218 4.9 24.8 1.0

Magnesium binding site 5 out of 9 in 7rut

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Magnesium binding site 5 out of 9 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
F:Mg302

b:50.6
occ:1.00
 O B:HOH442 2.5 46.8 1.0
K B:K302 3.2 23.4 1.0
CG1 F:ILE58 3.3 34.0 1.0
CD1 F:ILE58 3.4 35.7 1.0
O2A F:ATP304 3.5 23.9 1.0
OD1 B:ASP218 3.5 24.9 1.0
O F:HOH498 3.8 46.8 1.0
PA F:ATP304 4.3 20.7 1.0
O1A F:ATP304 4.4 20.5 1.0
CG B:ASP218 4.4 24.1 1.0
O F:ILE58 4.4 24.5 1.0
CB F:ILE58 4.8 30.8 1.0
OD2 B:ASP218 4.8 23.6 1.0
O5' F:ATP304 4.9 21.2 1.0
O B:HOH481 5.0 30.2 1.0
O F:HOH435 5.0 34.7 1.0

Magnesium binding site 6 out of 9 in 7rut

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Magnesium binding site 6 out of 9 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg301

b:18.2
occ:1.00
 O2B F:ATP304 2.0 19.1 1.0
O B:HOH437 2.0 19.9 1.0
O1A F:ATP304 2.0 20.5 1.0
OD1 B:ASN214 2.1 18.7 1.0
O1G F:ATP304 2.1 19.7 1.0
O B:HOH467 2.2 21.5 1.0
PB F:ATP304 3.1 20.4 1.0
CG B:ASN214 3.2 18.4 1.0
PA F:ATP304 3.3 20.7 1.0
PG F:ATP304 3.3 20.1 1.0
O3A F:ATP304 3.5 20.6 1.0
O3B F:ATP304 3.5 19.3 1.0
ND2 B:ASN214 3.7 20.8 1.0
O B:HOH481 3.8 30.2 1.0
NZ F:LYS78 3.9 23.9 1.0
K B:K302 3.9 23.4 1.0
O3G F:ATP304 4.1 20.2 1.0
O B:HOH432 4.1 22.6 1.0
O B:ASN214 4.2 17.9 1.0
OD1 B:ASP218 4.3 24.9 1.0
O2A F:ATP304 4.3 23.9 1.0
O5' F:ATP304 4.3 21.2 1.0
OG B:SER217 4.4 22.3 0.5
CB B:ASN214 4.4 16.1 1.0
O2G F:ATP304 4.4 23.1 1.0
N7 F:ATP304 4.5 19.7 1.0
O1B F:ATP304 4.5 22.4 1.0
CA B:ASN214 4.6 17.2 1.0
OE1 B:GLU193 4.7 30.0 1.0
C B:ASN214 4.7 17.3 1.0
C8 F:ATP304 4.7 21.1 1.0
CE F:LYS78 4.9 23.6 1.0
CG B:ASP218 4.9 24.1 1.0
OD2 B:ASP218 4.9 23.6 1.0

Magnesium binding site 7 out of 9 in 7rut

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Magnesium binding site 7 out of 9 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg502

b:20.0
occ:1.00
 O2B A:ATP505 2.0 21.1 1.0
O2A A:ATP505 2.0 21.9 1.0
O3G A:ATP505 2.1 23.1 1.0
PB A:ATP505 3.1 22.0 1.0
PA A:ATP505 3.3 22.3 1.0
PG A:ATP505 3.3 23.3 1.0
O3A A:ATP505 3.5 21.9 1.0
O3B A:ATP505 3.6 21.6 1.0
O A:HOH677 3.7 24.5 1.0
NZ A:LYS78 3.9 24.4 1.0
K A:K503 4.0 26.5 1.0
O2G A:ATP505 4.0 23.6 1.0
O5' A:ATP505 4.3 22.6 1.0
O1A A:ATP505 4.3 24.7 1.0
N7 A:ATP505 4.4 20.1 1.0
O1B A:ATP505 4.5 23.2 1.0
O1G A:ATP505 4.5 25.4 1.0
C8 A:ATP505 4.7 21.5 1.0
CE A:LYS78 4.8 23.4 1.0

Magnesium binding site 8 out of 9 in 7rut

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Magnesium binding site 8 out of 9 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
D:Mg301

b:18.7
occ:1.00
 O2B E:ATP303 2.0 18.7 1.0
OD1 D:ASN214 2.0 19.2 1.0
O D:HOH450 2.1 20.7 1.0
O1A E:ATP303 2.1 20.7 1.0
O1G E:ATP303 2.1 21.2 1.0
O D:HOH466 2.1 22.4 1.0
PB E:ATP303 3.1 20.2 1.0
CG D:ASN214 3.2 19.4 1.0
PA E:ATP303 3.3 21.5 1.0
PG E:ATP303 3.3 20.9 1.0
O3A E:ATP303 3.5 20.2 1.0
O3B E:ATP303 3.6 20.5 1.0
ND2 D:ASN214 3.7 18.7 1.0
O E:HOH468 3.8 32.3 1.0
NZ E:LYS78 3.9 25.0 1.0
K D:K303 4.0 25.2 1.0
O2G E:ATP303 4.1 22.3 1.0
O D:HOH437 4.1 23.4 1.0
O D:ASN214 4.2 19.4 1.0
O5' E:ATP303 4.3 21.4 1.0
O2A E:ATP303 4.4 24.5 1.0
OD1 D:ASP218 4.4 27.0 1.0
OG D:SER217 4.4 21.7 0.5
CB D:ASN214 4.4 18.5 1.0
N7 E:ATP303 4.5 19.5 1.0
O3G E:ATP303 4.5 22.7 1.0
O1B E:ATP303 4.5 21.8 1.0
CA D:ASN214 4.6 18.6 1.0
C D:ASN214 4.7 18.7 1.0
OE1 D:GLU193 4.7 25.5 1.0
C8 E:ATP303 4.7 22.4 1.0
O D:HOH404 4.9 30.5 1.0
CE E:LYS78 4.9 22.0 1.0
OD2 D:ASP218 4.9 25.4 1.0
CG D:ASP218 5.0 25.7 1.0

Magnesium binding site 9 out of 9 in 7rut

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Magnesium binding site 9 out of 9 in the Structure of Human Atp:Cobalamin Adenosyltransferase R190C Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg302

b:19.6
occ:1.00
 O1A D:ATP306 2.0 21.2 1.0
O1G D:ATP306 2.0 20.4 1.0
O1B D:ATP306 2.0 19.1 1.0
PB D:ATP306 3.1 20.1 1.0
PA D:ATP306 3.3 20.8 1.0
PG D:ATP306 3.3 20.6 1.0
O3A D:ATP306 3.5 21.2 1.0
O3B D:ATP306 3.5 21.2 1.0
O D:HOH481 3.6 30.7 1.0
NZ D:LYS78 3.9 23.8 1.0
O2G D:ATP306 4.0 20.6 1.0
O2A D:ATP306 4.3 25.2 1.0
O5' D:ATP306 4.3 21.0 1.0
O3G D:ATP306 4.5 22.4 1.0
N7 D:ATP306 4.5 21.2 1.0
O2B D:ATP306 4.5 21.8 1.0
C8 D:ATP306 4.7 22.4 1.0
CE D:LYS78 4.8 22.1 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: Thu Oct 3 08:06:45 2024

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