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Magnesium in PDB 8se1: Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation

Enzymatic activity of Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation

All present enzymatic activity of Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation:
2.7.11.13;

Protein crystallography data

The structure of Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation, PDB code: 8se1 was solved by A.T.Q.Cong, T.L.Witter, E.S.Bruinsma, S.Jayaraman, M.B.Dugan, J.R.Hawse, M.P.Goetz, M.J.Schellenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.75 / 3.32
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 130.556, 89.098, 160.714, 90, 107.05, 90
R / Rfree (%) 19.9 / 25.6

Other elements in 8se1:

The structure of Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation also contains other interesting chemical elements:

Zinc (Zn) 10 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation (pdb code 8se1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation, PDB code: 8se1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8se1

Go back to Magnesium Binding Sites List in 8se1
Magnesium binding site 1 out of 6 in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg707

b:29.8
occ:1.00
 OD1 A:ASN471 2.0 51.0 1.0
OD2 A:ASP484 2.1 67.3 1.0
O A:HOH805 2.1 25.8 1.0
O3G A:ANP706 2.2 32.4 1.0
O1A A:ANP706 2.3 34.9 1.0
N3B A:ANP706 2.3 36.2 1.0
PG A:ANP706 2.7 34.7 1.0
CG A:ASN471 2.9 43.5 1.0
CG A:ASP484 3.1 64.6 1.0
ND2 A:ASN471 3.1 41.5 1.0
CB A:ASP484 3.6 53.0 1.0
PB A:ANP706 3.7 36.3 1.0
PA A:ANP706 3.7 35.2 1.0
O1G A:ANP706 3.7 36.2 1.0
MG A:MG708 3.7 48.0 1.0
CE A:LYS468 3.8 34.5 1.0
O2G A:ANP706 4.0 36.1 1.0
O2B A:ANP706 4.0 42.8 1.0
NZ A:LYS468 4.1 49.0 1.0
OD1 A:ASP484 4.1 68.2 1.0
O A:HOH833 4.2 16.3 1.0
O3A A:ANP706 4.2 35.4 1.0
C5' A:ANP706 4.3 38.8 1.0
CB A:ASN471 4.3 41.5 1.0
O5' A:ANP706 4.5 35.1 1.0
O2A A:ANP706 4.7 33.3 1.0
CB A:ASP470 4.7 48.0 1.0
O A:HOH801 4.7 48.1 1.0
OD2 A:ASP466 4.7 59.0 1.0
CA A:ASN471 4.8 43.3 1.0
O A:ASP470 4.8 49.0 1.0
O3' A:ANP706 4.8 41.5 1.0
C A:ASP470 4.8 47.0 1.0
O1B A:ANP706 4.9 35.7 1.0
N A:ASN471 4.9 45.4 1.0
C3' A:ANP706 5.0 40.0 1.0

Magnesium binding site 2 out of 6 in 8se1

Go back to Magnesium Binding Sites List in 8se1
Magnesium binding site 2 out of 6 in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg708

b:48.0
occ:1.00
 O2B A:ANP706 1.9 42.8 1.0
O A:HOH801 2.0 48.1 1.0
OD2 A:ASP484 2.1 67.3 1.0
OD1 A:ASP484 2.1 68.2 1.0
O1G A:ANP706 2.1 36.2 1.0
O A:HOH807 2.2 64.7 1.0
CG A:ASP484 2.3 64.6 1.0
PG A:ANP706 3.0 34.7 1.0
PB A:ANP706 3.1 36.3 1.0
N3B A:ANP706 3.3 36.2 1.0
O3G A:ANP706 3.5 32.4 1.0
OD2 A:ASP466 3.6 59.0 1.0
MG A:MG707 3.7 29.8 1.0
CB A:ASP484 3.8 53.0 1.0
O A:HOH832 4.0 42.2 1.0
O1A A:ANP706 4.0 34.9 1.0
O1B A:ANP706 4.1 35.7 1.0
O3A A:ANP706 4.1 35.4 1.0
NZ A:LYS371 4.3 36.3 1.0
O2G A:ANP706 4.4 36.1 1.0
O A:ASP484 4.5 38.4 1.0
PA A:ANP706 4.6 35.2 1.0
CB A:ALA25 4.6 73.3 1.0
CA A:ASP484 4.6 44.0 1.0
O A:HOH829 4.6 3.9 1.0
ND2 A:ASN471 4.6 41.5 1.0
N A:GLY486 4.7 45.4 1.0
C A:ASP484 4.7 36.6 1.0
CG A:ASP466 4.8 57.8 1.0
CA A:GLY486 4.8 48.1 1.0
CE A:MET487 4.9 57.9 1.0
O2A A:ANP706 4.9 33.3 1.0

Magnesium binding site 3 out of 6 in 8se1

Go back to Magnesium Binding Sites List in 8se1
Magnesium binding site 3 out of 6 in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg709

b:74.2
occ:1.00
 OD2 A:ASP246 1.8 154.9 1.0
OD2 A:ASP187 1.9 169.8 1.0
OD1 A:ASP248 2.0 198.8 1.0
OD1 A:ASP187 2.1 168.2 1.0
OD2 A:ASP248 2.2 193.6 1.0
CG A:ASP187 2.2 165.0 1.0
CG A:ASP248 2.3 194.4 1.0
CG A:ASP246 2.5 147.7 1.0
OD1 A:ASP246 2.7 153.0 1.0
O A:TRP247 3.3 180.1 1.0
CB A:ASP187 3.7 156.3 1.0
CB A:ASP248 3.8 191.1 1.0
C A:TRP247 3.9 167.0 1.0
CB A:ASP246 3.9 136.8 1.0
OD1 A:ASP193 3.9 122.0 1.0
C A:ASP246 4.2 134.3 1.0
O A:ASP246 4.2 139.2 1.0
N A:ASP248 4.3 184.3 1.0
CA A:ASP248 4.4 189.9 1.0
N A:TRP247 4.4 132.1 1.0
CA A:ASP187 4.5 147.4 1.0
CG A:ASP193 4.5 119.9 1.0
CB A:ASP193 4.6 116.4 1.0
O A:HOH806 4.6 32.6 1.0
CA A:ASP246 4.6 132.3 1.0
N A:ASP193 4.6 122.3 1.0
N A:ASP187 4.7 138.8 1.0
CA A:TRP247 4.8 144.2 1.0
C A:MET186 4.9 128.9 1.0
O A:MET186 4.9 128.5 1.0
CB A:MET186 5.0 118.5 1.0

Magnesium binding site 4 out of 6 in 8se1

Go back to Magnesium Binding Sites List in 8se1
Magnesium binding site 4 out of 6 in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg707

b:23.9
occ:1.00
 OD2 B:ASP484 2.0 56.0 1.0
O1A B:ANP706 2.1 29.7 1.0
O B:HOH813 2.1 20.0 1.0
OD1 B:ASN471 2.1 50.0 1.0
O3G B:ANP706 2.3 35.7 1.0
N3B B:ANP706 2.5 33.1 1.0
PG B:ANP706 2.9 36.0 1.0
CG B:ASP484 2.9 54.5 1.0
CG B:ASN471 3.1 43.4 1.0
CB B:ASP484 3.4 48.5 1.0
ND2 B:ASN471 3.5 42.2 1.0
PA B:ANP706 3.5 36.2 1.0
O1G B:ANP706 3.6 34.8 1.0
PB B:ANP706 3.7 34.7 1.0
MG B:MG708 3.8 32.9 1.0
O2B B:ANP706 3.8 36.6 1.0
CE B:LYS468 3.9 42.9 1.0
OD1 B:ASP484 4.0 57.1 1.0
C5' B:ANP706 4.0 41.1 1.0
O3A B:ANP706 4.1 33.5 1.0
NZ B:LYS468 4.2 45.1 1.0
O5' B:ANP706 4.2 38.7 1.0
O2G B:ANP706 4.3 41.8 1.0
CB B:ASN471 4.4 40.5 1.0
O2A B:ANP706 4.5 38.4 1.0
OD2 B:ASP466 4.6 54.4 1.0
O3' B:ANP706 4.7 40.1 1.0
C3' B:ANP706 4.7 40.2 1.0
CA B:ASN471 4.8 40.0 1.0
O B:ASP470 4.8 40.5 1.0
O B:HOH801 4.9 30.2 1.0
CA B:ASP484 4.9 41.3 1.0
C B:ASP470 4.9 41.3 1.0
O1B B:ANP706 4.9 34.4 1.0
N B:ASN471 5.0 40.0 1.0
CB B:ASP470 5.0 42.9 1.0
C4' B:ANP706 5.0 40.1 1.0

Magnesium binding site 5 out of 6 in 8se1

Go back to Magnesium Binding Sites List in 8se1
Magnesium binding site 5 out of 6 in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg708

b:32.9
occ:1.00
 O2B B:ANP706 2.0 36.6 1.0
OD1 B:ASP484 2.0 57.1 1.0
O1G B:ANP706 2.0 34.8 1.0
OD2 B:ASP484 2.1 56.0 1.0
O B:HOH801 2.1 30.2 1.0
O B:HOH809 2.2 39.5 1.0
CG B:ASP484 2.3 54.5 1.0
PG B:ANP706 3.2 36.0 1.0
PB B:ANP706 3.3 34.7 1.0
OD2 B:ASP466 3.4 54.4 1.0
N3B B:ANP706 3.6 33.1 1.0
O3G B:ANP706 3.7 35.7 1.0
MG B:MG707 3.8 23.9 1.0
CB B:ASP484 3.8 48.5 1.0
O1A B:ANP706 4.0 29.7 1.0
O1B B:ANP706 4.2 34.4 1.0
O3A B:ANP706 4.3 33.5 1.0
O B:ASP484 4.4 32.5 1.0
O2G B:ANP706 4.5 41.8 1.0
N B:GLY486 4.5 34.3 1.0
NZ B:LYS371 4.5 40.1 1.0
CG B:ASP466 4.6 54.6 1.0
CA B:ASP484 4.6 41.3 1.0
CA B:GLY486 4.6 36.5 1.0
C B:ASP484 4.6 34.4 1.0
PA B:ANP706 4.7 36.2 1.0
ND2 B:ASN471 4.8 42.2 1.0
C B:GLY486 4.8 40.5 1.0

Magnesium binding site 6 out of 6 in 8se1

Go back to Magnesium Binding Sites List in 8se1
Magnesium binding site 6 out of 6 in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg709

b:33.7
occ:1.00
 OD1 B:ASP248 2.0 83.1 1.0
OD2 B:ASP187 2.3 89.8 1.0
OD2 B:ASP246 2.3 59.4 1.0
OD1 B:ASP246 2.5 56.3 1.0
OD1 B:ASP187 2.6 89.9 1.0
CG B:ASP187 2.7 86.5 1.0
CG B:ASP248 2.7 84.2 1.0
OD2 B:ASP248 2.7 83.4 1.0
CG B:ASP246 2.7 55.5 1.0
OD2 B:ASP193 3.7 61.9 1.0
O B:TRP247 3.8 67.9 1.0
CB B:ASP187 4.0 75.0 1.0
CB B:ASP248 4.1 85.2 1.0
CG B:ASP193 4.2 59.3 1.0
O B:HOH804 4.2 5.6 1.0
CB B:ASP246 4.3 50.0 1.0
N B:ASP193 4.3 50.9 1.0
CB B:MET186 4.5 45.9 1.0
C B:TRP247 4.5 70.3 1.0
CB B:ASP193 4.6 45.7 1.0
N B:ASP187 4.7 54.0 1.0
CA B:ASP248 4.7 84.2 1.0
C B:MET186 4.7 50.2 1.0
CA B:SER192 4.8 44.6 1.0
CA B:ASP187 4.8 62.1 1.0
C B:ASP246 4.8 49.7 1.0
O B:MET186 4.8 53.5 1.0
N B:ASP248 4.9 75.9 1.0
O B:ASP246 4.9 51.1 1.0
OD1 B:ASP193 4.9 58.3 1.0

Reference:

A.T.Q.Cong, T.L.Witter, E.S.Bruinsma, S.S.Bhattacharya, S.Jayaraman, M.B.Dugan, J.Paluncic, M.J.Kuffel, J.Farmakes, J.Alvey, X.Wu, A.P.Fields, A.Pandey, J.R.Hawse, M.P.Goetz, M.J.Schellenberg. Molecular Basis of Allosteric Regulation and Pharmaceutical Targeting of Protein Kinase C B To Be Published.
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