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Magnesium in PDB 4wb6: Crystal Structure of A L205R Mutant of Human Camp-Dependent Protein Kinase A (Catalytic Alpha Subunit)

Enzymatic activity of Crystal Structure of A L205R Mutant of Human Camp-Dependent Protein Kinase A (Catalytic Alpha Subunit)

All present enzymatic activity of Crystal Structure of A L205R Mutant of Human Camp-Dependent Protein Kinase A (Catalytic Alpha Subunit):
2.7.11.11;

Protein crystallography data

The structure of Crystal Structure of A L205R Mutant of Human Camp-Dependent Protein Kinase A (Catalytic Alpha Subunit), PDB code: 4wb6 was solved by J.Cheung, C.Ginter, M.Cassidy, M.C.Franklin, M.J.Rudolph, W.A.Hendrickson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.49 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.169, 90.193, 90.377, 90.00, 96.12, 90.00
R / Rfree (%) 18.8 / 23.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A L205R Mutant of Human Camp-Dependent Protein Kinase A (Catalytic Alpha Subunit) (pdb code 4wb6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of A L205R Mutant of Human Camp-Dependent Protein Kinase A (Catalytic Alpha Subunit), PDB code: 4wb6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4wb6

Go back to Magnesium Binding Sites List in 4wb6
Magnesium binding site 1 out of 4 in the Crystal Structure of A L205R Mutant of Human Camp-Dependent Protein Kinase A (Catalytic Alpha Subunit)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A L205R Mutant of Human Camp-Dependent Protein Kinase A (Catalytic Alpha Subunit) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:41.9
occ:1.00
 O1G A:ATP401 1.9 47.4 1.0
O1A A:ATP401 2.0 46.8 1.0
O A:HOH523 2.1 46.0 1.0
OD2 A:ASP184 2.2 47.5 1.0
OD1 A:ASN171 2.2 33.1 1.0
O3B A:ATP401 2.5 48.4 1.0
PG A:ATP401 2.8 49.0 1.0
CG A:ASP184 3.3 51.0 1.0
CG A:ASN171 3.3 37.4 1.0
PA A:ATP401 3.4 45.9 1.0
O3G A:ATP401 3.6 56.5 1.0
PB A:ATP401 3.6 42.2 1.0
ND2 A:ASN171 3.7 33.6 1.0
MG A:MG403 3.7 45.7 1.0
CB A:ASP184 3.8 46.2 1.0
O3A A:ATP401 3.8 40.9 1.0
O2B A:ATP401 3.9 48.8 1.0
O2G A:ATP401 4.0 40.3 1.0
CE A:LYS168 4.0 36.9 1.0
NZ A:LYS168 4.2 42.3 1.0
O I:HOH104 4.3 49.9 1.0
OD1 A:ASP184 4.3 48.3 1.0
O3' A:ATP401 4.4 36.5 1.0
O5' A:ATP401 4.4 44.8 1.0
O2A A:ATP401 4.4 48.3 1.0
OD2 A:ASP166 4.5 44.5 1.0
C5' A:ATP401 4.6 43.4 1.0
CB A:ASN171 4.6 41.1 1.0
O1B A:ATP401 4.9 43.6 1.0
C3' A:ATP401 4.9 36.3 1.0
CA A:ASN171 4.9 46.2 1.0
O A:HOH524 4.9 48.2 1.0

Magnesium binding site 2 out of 4 in 4wb6

Go back to Magnesium Binding Sites List in 4wb6
Magnesium binding site 2 out of 4 in the Crystal Structure of A L205R Mutant of Human Camp-Dependent Protein Kinase A (Catalytic Alpha Subunit)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A L205R Mutant of Human Camp-Dependent Protein Kinase A (Catalytic Alpha Subunit) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:45.7
occ:1.00
 O3G A:ATP401 1.9 56.5 1.0
O2B A:ATP401 2.1 48.8 1.0
OD2 A:ASP184 2.1 47.5 1.0
OD1 A:ASP184 2.2 48.3 1.0
O A:HOH524 2.2 48.2 1.0
O A:HOH583 2.4 38.1 1.0
CG A:ASP184 2.5 51.0 1.0
PG A:ATP401 3.0 49.0 1.0
PB A:ATP401 3.2 42.2 1.0
O3B A:ATP401 3.3 48.4 1.0
O1G A:ATP401 3.4 47.4 1.0
MG A:MG402 3.7 41.9 1.0
CB A:ASP184 4.0 46.2 1.0
CD2 A:PHE54 4.0 42.0 1.0
OD2 A:ASP166 4.0 44.5 1.0
O A:HOH574 4.2 54.7 1.0
O1A A:ATP401 4.2 46.8 1.0
CE2 A:PHE54 4.2 40.6 1.0
O1B A:ATP401 4.2 43.6 1.0
O3A A:ATP401 4.3 40.9 1.0
O2G A:ATP401 4.4 40.3 1.0
CA A:GLY186 4.4 45.6 1.0
NZ A:LYS72 4.4 48.3 1.0
N A:GLY186 4.6 42.0 1.0
PA A:ATP401 4.6 45.9 1.0
O2A A:ATP401 4.8 48.3 1.0
CA A:ASP184 4.8 48.4 1.0

Magnesium binding site 3 out of 4 in 4wb6

Go back to Magnesium Binding Sites List in 4wb6
Magnesium binding site 3 out of 4 in the Crystal Structure of A L205R Mutant of Human Camp-Dependent Protein Kinase A (Catalytic Alpha Subunit)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A L205R Mutant of Human Camp-Dependent Protein Kinase A (Catalytic Alpha Subunit) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:47.7
occ:1.00
 O2A B:ATP401 1.9 43.4 1.0
O2G B:ATP401 2.0 49.2 1.0
OD2 B:ASP184 2.1 52.0 1.0
O B:HOH575 2.2 63.2 1.0
OD1 B:ASN171 2.4 51.7 1.0
O3B B:ATP401 2.4 41.9 1.0
PG B:ATP401 2.8 53.9 1.0
CG B:ASP184 3.3 51.8 1.0
PA B:ATP401 3.3 47.4 1.0
CG B:ASN171 3.4 48.6 1.0
PB B:ATP401 3.5 49.5 1.0
O3A B:ATP401 3.7 42.2 1.0
O1G B:ATP401 3.7 53.8 1.0
MG B:MG403 3.7 40.9 1.0
ND2 B:ASN171 3.8 50.3 1.0
CB B:ASP184 3.8 48.5 1.0
O1B B:ATP401 3.8 46.1 1.0
O3G B:ATP401 4.0 51.2 1.0
CE B:LYS168 4.0 49.6 1.0
NZ B:LYS168 4.1 54.5 1.0
OD1 B:ASP184 4.3 54.8 1.0
O1A B:ATP401 4.3 49.0 1.0
O3' B:ATP401 4.3 50.0 1.0
O5' B:ATP401 4.3 49.2 1.0
OD2 B:ASP166 4.4 45.5 1.0
C5' B:ATP401 4.5 51.0 1.0
C3' B:ATP401 4.7 49.4 1.0
O2B B:ATP401 4.8 50.1 1.0
CB B:ASN171 4.8 41.6 1.0
O B:HOH540 4.9 35.4 1.0
O B:GLU170 5.0 44.8 1.0
CA B:GLY52 5.0 53.0 1.0

Magnesium binding site 4 out of 4 in 4wb6

Go back to Magnesium Binding Sites List in 4wb6
Magnesium binding site 4 out of 4 in the Crystal Structure of A L205R Mutant of Human Camp-Dependent Protein Kinase A (Catalytic Alpha Subunit)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A L205R Mutant of Human Camp-Dependent Protein Kinase A (Catalytic Alpha Subunit) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:40.9
occ:1.00
 O1G B:ATP401 2.0 53.8 1.0
OD1 B:ASP184 2.0 54.8 1.0
O1B B:ATP401 2.0 46.1 1.0
O B:HOH540 2.1 35.4 1.0
OD2 B:ASP184 2.2 52.0 1.0
O B:HOH535 2.3 37.7 0.8
CG B:ASP184 2.4 51.8 1.0
PG B:ATP401 3.0 53.9 1.0
PB B:ATP401 3.2 49.5 1.0
O3B B:ATP401 3.3 41.9 1.0
O2G B:ATP401 3.4 49.2 1.0
MG B:MG402 3.7 47.7 1.0
O B:HOH513 3.8 43.8 0.9
OD2 B:ASP166 3.9 45.5 1.0
CB B:ASP184 3.9 48.5 1.0
CD2 B:PHE54 4.1 57.5 1.0
NZ B:LYS72 4.2 44.1 1.0
O2A B:ATP401 4.3 43.4 1.0
O3A B:ATP401 4.3 42.2 1.0
O2B B:ATP401 4.3 50.1 1.0
CA B:GLY186 4.3 47.7 1.0
CE2 B:PHE54 4.3 57.8 1.0
O3G B:ATP401 4.4 51.2 1.0
N B:GLY186 4.4 43.0 1.0
PA B:ATP401 4.5 47.4 1.0
O1A B:ATP401 4.6 49.0 1.0
CA B:ASP184 4.7 48.0 1.0
O B:ASP184 4.7 39.1 1.0
C B:ASP184 4.8 47.7 1.0
ND2 B:ASN171 4.9 50.3 1.0
CG B:ASP166 5.0 45.8 1.0
OD1 B:ASN171 5.0 51.7 1.0

Reference:

J.Cheung, C.Ginter, M.Cassidy, M.C.Franklin, M.J.Rudolph, N.Robine, R.B.Darnell, W.A.Hendrickson. Structural Insights Into Mis-Regulation of Protein Kinase A in Human Tumors. Proc.Natl.Acad.Sci.Usa V. 112 1374 2015.
ISSN: ESSN 1091-6490
PubMed: 25605907
DOI: 10.1073/PNAS.1424206112
Page generated: Tue Aug 20 13:09:59 2024

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