Atomistry » Manganese » PDB 117e-1cev » 1cdk
Atomistry »
  Manganese »
    PDB 117e-1cev »
      1cdk »

Manganese in PDB 1cdk: Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C

Enzymatic activity of Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C

All present enzymatic activity of Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C:
2.7.11.11;

Protein crystallography data

The structure of Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C, PDB code: 1cdk was solved by D.Bossemeyer, R.A.Engh, V.Kinzel, H.Ponstingl, R.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 5.00 / 2.00
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 107.610, 80.600, 110.100, 90.00, 88.59, 90.00
R / Rfree (%) 19.7 / n/a

Manganese Binding Sites:

The binding sites of Manganese atom in the Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C (pdb code 1cdk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C, PDB code: 1cdk:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1cdk

Go back to Manganese Binding Sites List in 1cdk
Manganese binding site 1 out of 4 in the Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:18.3
occ:1.00
 O2A A:ANP400 2.0 16.9 1.0
O2G A:ANP400 2.0 18.6 1.0
OD1 A:ASN171 2.1 11.5 1.0
O A:HOH451 2.2 14.5 1.0
OD2 A:ASP184 2.6 16.9 1.0
N3B A:ANP400 2.6 16.9 1.0
PG A:ANP400 2.9 21.6 1.0
CG A:ASN171 3.1 19.6 1.0
CG A:ASP184 3.3 13.7 1.0
PA A:ANP400 3.4 19.0 1.0
ND2 A:ASN171 3.5 15.9 1.0
CB A:ASP184 3.6 13.2 1.0
PB A:ANP400 3.7 20.4 1.0
O1G A:ANP400 3.8 17.3 1.0
CE A:LYS168 3.8 11.5 1.0
MN A:MN402 3.8 16.8 1.0
O3A A:ANP400 3.9 9.4 1.0
O2B A:ANP400 3.9 25.4 1.0
O3G A:ANP400 4.1 8.1 1.0
OD1 A:ASP184 4.2 20.1 1.0
O1A A:ANP400 4.3 18.6 1.0
NZ A:LYS168 4.3 8.6 1.0
OD2 A:ASP166 4.3 23.9 1.0
O3' A:ANP400 4.4 16.7 1.0
O5' A:ANP400 4.5 23.5 1.0
CB A:ASN171 4.5 12.6 1.0
O I:HOH49 4.5 22.1 1.0
C5' A:ANP400 4.7 21.8 1.0
O A:GLU170 4.9 23.5 1.0
C3' A:ANP400 4.9 13.1 1.0
CA A:ASN171 4.9 16.0 1.0
O A:HOH436 4.9 17.1 1.0
O1B A:ANP400 5.0 14.0 1.0

Manganese binding site 2 out of 4 in 1cdk

Go back to Manganese Binding Sites List in 1cdk
Manganese binding site 2 out of 4 in the Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:16.8
occ:1.00
 O1G A:ANP400 1.9 17.3 1.0
OD2 A:ASP184 2.0 16.9 1.0
O2B A:ANP400 2.1 25.4 1.0
OD1 A:ASP184 2.1 20.1 1.0
O A:HOH436 2.2 17.1 1.0
O A:HOH514 2.3 23.0 1.0
CG A:ASP184 2.4 13.7 1.0
PG A:ANP400 3.0 21.6 1.0
PB A:ANP400 3.2 20.4 1.0
N3B A:ANP400 3.3 16.9 1.0
O2G A:ANP400 3.5 18.6 1.0
MN A:MN401 3.8 18.3 1.0
CB A:ASP184 3.9 13.2 1.0
OD2 A:ASP166 4.0 23.9 1.0
CD2 A:PHE54 4.0 18.7 1.0
O1B A:ANP400 4.2 14.0 1.0
O3G A:ANP400 4.3 8.1 1.0
O A:HOH404 4.3 16.3 1.0
O3A A:ANP400 4.4 9.4 1.0
O2A A:ANP400 4.4 16.9 1.0
NZ A:LYS72 4.4 12.2 1.0
CE2 A:PHE54 4.5 13.6 1.0
CA A:GLY186 4.5 12.5 1.0
N A:GLY186 4.6 15.4 1.0
PA A:ANP400 4.7 19.0 1.0
O A:ASP184 4.7 13.2 1.0
CB I:ALA17 4.8 23.5 1.0
O1A A:ANP400 4.8 18.6 1.0
CA A:ASP184 4.8 16.1 1.0

Manganese binding site 3 out of 4 in 1cdk

Go back to Manganese Binding Sites List in 1cdk
Manganese binding site 3 out of 4 in the Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:16.1
occ:1.00
 O2G B:ANP400 2.0 11.2 1.0
O2A B:ANP400 2.0 16.1 1.0
OD1 B:ASN171 2.1 13.6 1.0
O B:HOH449 2.3 19.9 1.0
N3B B:ANP400 2.4 13.1 1.0
OD2 B:ASP184 2.5 20.8 1.0
PG B:ANP400 2.8 19.8 1.0
CG B:ASN171 3.2 16.9 1.0
PA B:ANP400 3.3 17.6 1.0
CG B:ASP184 3.4 15.9 1.0
ND2 B:ASN171 3.6 14.1 1.0
PB B:ANP400 3.6 20.2 1.0
O1G B:ANP400 3.7 20.6 1.0
CB B:ASP184 3.7 14.8 1.0
O3A B:ANP400 3.8 11.9 1.0
MN B:MN402 3.9 19.3 1.0
CE B:LYS168 3.9 7.5 1.0
O2B B:ANP400 3.9 19.4 1.0
O3G B:ANP400 4.0 10.7 1.0
NZ B:LYS168 4.2 11.3 1.0
O1A B:ANP400 4.3 17.7 1.0
OD1 B:ASP184 4.3 16.0 1.0
O J:HOH196 4.4 16.5 1.0
O3' B:ANP400 4.4 21.7 1.0
OD2 B:ASP166 4.4 25.8 1.0
O5' B:ANP400 4.4 22.1 1.0
CB B:ASN171 4.5 7.6 1.0
C5' B:ANP400 4.6 16.3 1.0
O1B B:ANP400 4.9 12.8 1.0
C3' B:ANP400 4.9 11.4 1.0
O B:HOH435 4.9 9.1 1.0
CA B:ASN171 4.9 13.1 1.0

Manganese binding site 4 out of 4 in 1cdk

Go back to Manganese Binding Sites List in 1cdk
Manganese binding site 4 out of 4 in the Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:19.3
occ:1.00
 O1G B:ANP400 1.9 20.6 1.0
OD2 B:ASP184 2.0 20.8 1.0
OD1 B:ASP184 2.1 16.0 1.0
O2B B:ANP400 2.1 19.4 1.0
O B:HOH435 2.3 9.1 1.0
O B:HOH506 2.3 11.2 1.0
CG B:ASP184 2.4 15.9 1.0
PG B:ANP400 3.1 19.8 1.0
PB B:ANP400 3.2 20.2 1.0
N3B B:ANP400 3.3 13.1 1.0
O2G B:ANP400 3.6 11.2 1.0
MN B:MN401 3.9 16.1 1.0
CB B:ASP184 3.9 14.8 1.0
CD2 B:PHE54 4.0 23.4 1.0
OD2 B:ASP166 4.0 25.8 1.0
O1B B:ANP400 4.2 12.8 1.0
O B:HOH404 4.3 15.1 1.0
O3G B:ANP400 4.3 10.7 1.0
O3A B:ANP400 4.3 11.9 1.0
NZ B:LYS72 4.4 16.4 1.0
CE2 B:PHE54 4.5 11.1 1.0
CA B:GLY186 4.5 15.7 1.0
O2A B:ANP400 4.5 16.1 1.0
N B:GLY186 4.6 17.9 1.0
PA B:ANP400 4.7 17.6 1.0
O1A B:ANP400 4.8 17.7 1.0
CA B:ASP184 4.8 24.7 1.0
CB J:ALA17 4.9 19.3 1.0

Reference:

D.Bossemeyer, R.A.Engh, V.Kinzel, H.Ponstingl, R.Huber. Phosphotransferase and Substrate Binding Mechanism of the Camp-Dependent Protein Kinase Catalytic Subunit From Porcine Heart As Deduced From the 2.0 A Structure of the Complex with MN2+ Adenylyl Imidodiphosphate and Inhibitor Peptide Pki(5-24). Embo J. V. 12 849 1993.
ISSN: ISSN 0261-4189
PubMed: 8384554
Page generated: Sat Oct 5 09:52:06 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy