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Manganese in PDB 6bg2: Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State

Enzymatic activity of Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State

All present enzymatic activity of Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State:
2.7.11.12;

Protein crystallography data

The structure of Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State, PDB code: 6bg2 was solved by L.Qin, B.Sankaran, C.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.23 / 1.83
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 165.390, 98.500, 116.424, 90.00, 133.47, 90.00
R / Rfree (%) 18.8 / 21.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State (pdb code 6bg2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State, PDB code: 6bg2:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 6bg2

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Manganese binding site 1 out of 8 in the Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn701

b:15.0
occ:1.00
 O1G C:ANP700 2.0 15.1 1.0
O1B C:ANP700 2.0 15.2 1.0
OD2 C:ASP502 2.3 13.1 1.0
O C:HOH1079 2.3 15.8 1.0
OD1 C:ASP502 2.3 13.0 1.0
O C:HOH837 2.4 18.3 1.0
CG C:ASP502 2.6 11.8 1.0
PG C:ANP700 3.2 17.2 1.0
PB C:ANP700 3.3 14.8 1.0
N3B C:ANP700 3.6 15.4 1.0
O2G C:ANP700 3.8 13.7 1.0
MN C:MN702 3.9 13.6 1.0
CD2 C:PHE371 4.0 18.8 1.0
OD2 C:ASP484 4.1 14.7 1.0
O C:HOH930 4.1 22.0 1.0
CB C:ASP502 4.2 13.2 1.0
O2B C:ANP700 4.2 16.5 1.0
NZ C:LYS390 4.2 13.7 1.0
O C:HOH902 4.2 16.1 1.0
O3A C:ANP700 4.4 15.8 1.0
CA C:GLY504 4.4 13.4 1.0
O3G C:ANP700 4.5 15.8 1.0
O C:HOH972 4.6 24.8 1.0
N C:GLY504 4.6 13.1 1.0
O2A C:ANP700 4.6 15.1 1.0
CE2 C:PHE371 4.6 21.9 1.0
PA C:ANP700 4.8 15.4 1.0
CG C:PHE371 4.9 17.6 1.0
O1A C:ANP700 4.9 11.9 1.0
CA C:ASP502 4.9 10.6 1.0

Manganese binding site 2 out of 8 in 6bg2

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Manganese binding site 2 out of 8 in the Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn702

b:13.6
occ:1.00
 O2A C:ANP700 2.1 15.1 1.0
O2G C:ANP700 2.1 13.7 1.0
OD2 C:ASP502 2.2 13.1 1.0
OD1 C:ASN489 2.2 13.4 1.0
O C:HOH936 2.4 19.6 1.0
N3B C:ANP700 2.7 15.4 1.0
PG C:ANP700 2.9 17.2 1.0
CG C:ASP502 3.1 11.8 1.0
CG C:ASN489 3.2 14.0 1.0
PA C:ANP700 3.4 15.4 1.0
CB C:ASP502 3.5 13.2 1.0
ND2 C:ASN489 3.5 12.6 1.0
PB C:ANP700 3.7 14.8 1.0
O1G C:ANP700 3.7 15.1 1.0
O1B C:ANP700 3.9 15.2 1.0
MN C:MN701 3.9 15.0 1.0
O3A C:ANP700 3.9 15.8 1.0
CE C:LYS486 4.1 19.2 1.0
OD1 C:ASP502 4.2 13.0 1.0
O3G C:ANP700 4.2 15.8 1.0
O C:HOH1123 4.3 30.1 1.0
O1A C:ANP700 4.3 11.9 1.0
O3' C:ANP700 4.4 14.9 1.0
NZ C:LYS486 4.4 23.6 1.0
O5' C:ANP700 4.4 12.0 1.0
O C:HOH1068 4.5 38.9 1.0
CB C:ASN489 4.5 10.8 1.0
C5' C:ANP700 4.6 13.2 1.0
OD2 C:ASP484 4.6 14.7 1.0
C3' C:ANP700 4.8 15.0 1.0
CA C:ASN489 4.8 10.5 1.0
O C:GLU488 4.9 15.7 1.0
O C:HOH930 4.9 22.0 1.0
CA C:ASP502 5.0 10.6 1.0

Manganese binding site 3 out of 8 in 6bg2

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Manganese binding site 3 out of 8 in the Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:17.8
occ:1.00
 O1G B:ANP700 2.1 20.8 1.0
O B:HOH832 2.2 15.2 1.0
O1B B:ANP700 2.2 19.5 1.0
OD1 B:ASP502 2.3 17.1 1.0
OD2 B:ASP502 2.3 15.0 1.0
O B:HOH1028 2.3 20.4 1.0
CG B:ASP502 2.6 17.4 1.0
PG B:ANP700 3.2 23.8 1.0
PB B:ANP700 3.3 19.4 1.0
N3B B:ANP700 3.4 19.4 1.0
O2G B:ANP700 3.7 20.7 1.0
MN B:MN702 3.9 16.6 1.0
OD2 B:ASP484 4.0 19.5 1.0
CD1 B:PHE371 4.1 24.8 1.0
CB B:ASP502 4.1 14.5 1.0
O B:HOH954 4.2 23.3 1.0
O2B B:ANP700 4.2 23.9 1.0
O B:HOH853 4.2 18.1 1.0
NZ B:LYS390 4.3 18.5 1.0
O3G B:ANP700 4.4 23.3 1.0
CA B:GLY504 4.4 15.6 1.0
O3A B:ANP700 4.5 17.1 1.0
O2A B:ANP700 4.5 17.9 1.0
N B:GLY504 4.5 14.9 1.0
CE1 B:PHE371 4.7 29.2 1.0
O B:HOH898 4.8 26.4 1.0
PA B:ANP700 4.9 17.1 1.0
CA B:ASP502 4.9 12.7 1.0
CG B:PHE371 4.9 25.6 1.0

Manganese binding site 4 out of 8 in 6bg2

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Manganese binding site 4 out of 8 in the Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn702

b:16.6
occ:1.00
 O2A B:ANP700 2.1 17.9 1.0
OD1 B:ASN489 2.2 15.7 1.0
OD2 B:ASP502 2.2 15.0 1.0
O B:HOH937 2.2 17.4 1.0
O2G B:ANP700 2.3 20.7 1.0
N3B B:ANP700 2.5 19.4 1.0
PG B:ANP700 2.9 23.8 1.0
CG B:ASP502 3.1 17.4 1.0
CG B:ASN489 3.1 17.8 1.0
PA B:ANP700 3.4 17.1 1.0
CB B:ASP502 3.5 14.5 1.0
ND2 B:ASN489 3.5 16.1 1.0
PB B:ANP700 3.6 19.4 1.0
O1G B:ANP700 3.7 20.8 1.0
O3A B:ANP700 3.9 17.1 1.0
O1B B:ANP700 3.9 19.5 1.0
MN B:MN701 3.9 17.8 1.0
O3G B:ANP700 4.1 23.3 1.0
CE B:LYS486 4.1 17.4 1.0
OD1 B:ASP502 4.2 17.1 1.0
O1A B:ANP700 4.3 15.9 1.0
O3' B:ANP700 4.3 19.2 1.0
NZ B:LYS486 4.4 23.4 1.0
O5' B:ANP700 4.4 16.6 1.0
CB B:ASN489 4.5 14.1 1.0
OD2 B:ASP484 4.6 19.5 1.0
C5' B:ANP700 4.6 15.6 1.0
C3' B:ANP700 4.8 16.6 1.0
CA B:ASN489 4.8 14.7 1.0
O B:GLU488 4.9 18.5 1.0
O B:HOH830 4.9 34.4 1.0
O2B B:ANP700 4.9 23.9 1.0
O B:HOH954 4.9 23.3 1.0
CA B:ASP502 4.9 12.7 1.0
O B:HOH832 5.0 15.2 1.0

Manganese binding site 5 out of 8 in 6bg2

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Manganese binding site 5 out of 8 in the Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:60.3
occ:1.00
 O1B A:ANP700 2.2 46.0 1.0
OD1 A:ASP502 2.3 37.5 1.0
MN A:MN702 2.6 73.4 1.0
O1G A:ANP700 2.6 53.9 1.0
O A:HOH825 2.7 38.0 1.0
O2G A:ANP700 3.1 56.3 1.0
O A:HOH828 3.2 37.0 1.0
O1A A:ANP700 3.2 41.7 1.0
CG A:ASP502 3.2 34.5 1.0
PG A:ANP700 3.4 57.3 1.0
PB A:ANP700 3.6 44.1 1.0
OD2 A:ASP502 3.8 37.2 1.0
N3B A:ANP700 4.1 52.0 1.0
O A:HOH1061 4.3 48.7 1.0
PA A:ANP700 4.3 46.0 1.0
CB A:ASP502 4.3 29.8 1.0
O A:HOH1083 4.4 43.0 1.0
O3A A:ANP700 4.4 44.6 1.0
O2B A:ANP700 4.6 41.1 1.0
OD1 A:ASN489 4.7 29.3 1.0
O3G A:ANP700 4.8 58.4 1.0
O2A A:ANP700 5.0 41.1 1.0

Manganese binding site 6 out of 8 in 6bg2

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Manganese binding site 6 out of 8 in the Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn702

b:73.4
occ:1.00
 MN A:MN701 2.6 60.3 1.0
OD1 A:ASP502 2.7 37.5 1.0
O1A A:ANP700 2.7 41.7 1.0
OD1 A:ASN489 2.7 29.3 1.0
O1G A:ANP700 2.9 53.9 1.0
O A:HOH995 3.0 30.8 1.0
CG A:ASP502 3.5 34.5 1.0
O A:HOH913 3.8 39.0 1.0
CB A:ASP502 3.8 29.8 1.0
CG A:ASN489 3.9 26.2 1.0
O1B A:ANP700 3.9 46.0 1.0
O A:HOH828 4.0 37.0 1.0
PA A:ANP700 4.1 46.0 1.0
PG A:ANP700 4.4 57.3 1.0
ND2 A:ASN489 4.4 24.6 1.0
O A:GLU488 4.5 24.9 1.0
OD2 A:ASP502 4.7 37.2 1.0
O2A A:ANP700 4.8 41.1 1.0
O A:HOH825 4.8 38.0 1.0
O A:HOH1061 4.8 48.7 1.0
PB A:ANP700 4.9 44.1 1.0
O2G A:ANP700 4.9 56.3 1.0
CE A:LYS486 4.9 28.8 1.0
O3' A:ANP700 4.9 38.1 1.0
C A:GLU488 4.9 27.5 1.0
O5' A:ANP700 5.0 41.7 1.0

Manganese binding site 7 out of 8 in 6bg2

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Manganese binding site 7 out of 8 in the Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn701

b:16.8
occ:1.00
 O1G D:ANP700 1.9 18.5 1.0
O2B D:ANP700 2.1 15.7 1.0
OD1 D:ASP502 2.2 16.8 1.0
O D:HOH1057 2.3 19.4 1.0
O D:HOH841 2.3 19.9 1.0
OD2 D:ASP502 2.3 13.7 1.0
CG D:ASP502 2.6 14.7 1.0
PG D:ANP700 3.1 20.1 1.0
PB D:ANP700 3.3 18.4 1.0
N3B D:ANP700 3.6 15.8 1.0
O2G D:ANP700 3.7 18.1 1.0
MN D:MN702 3.9 16.5 1.0
CD2 D:PHE371 4.0 23.6 1.0
OD2 D:ASP484 4.0 18.1 1.0
CB D:ASP502 4.1 14.5 1.0
O D:HOH876 4.1 20.4 1.0
O D:HOH998 4.1 17.8 1.0
O1B D:ANP700 4.2 20.9 1.0
NZ D:LYS390 4.2 19.6 1.0
CA D:GLY504 4.4 18.2 1.0
O3A D:ANP700 4.4 15.3 1.0
O3G D:ANP700 4.4 17.5 1.0
O2A D:ANP700 4.5 13.9 1.0
N D:GLY504 4.5 19.5 1.0
CE2 D:PHE371 4.6 28.4 1.0
CG D:PHE371 4.7 23.5 1.0
O D:HOH1054 4.7 26.2 1.0
CB D:PHE371 4.8 21.7 1.0
PA D:ANP700 4.9 15.8 1.0
CA D:ASP502 4.9 14.3 1.0

Manganese binding site 8 out of 8 in 6bg2

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Manganese binding site 8 out of 8 in the Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain in Amp-Pnp Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn702

b:16.5
occ:1.00
 O2A D:ANP700 2.0 13.9 1.0
O2G D:ANP700 2.1 18.1 1.0
OD2 D:ASP502 2.1 13.7 1.0
OD1 D:ASN489 2.2 14.2 1.0
O D:HOH888 2.4 17.0 1.0
N3B D:ANP700 2.6 15.8 1.0
PG D:ANP700 2.9 20.1 1.0
CG D:ASP502 3.1 14.7 1.0
CG D:ASN489 3.2 14.9 1.0
PA D:ANP700 3.4 15.8 1.0
CB D:ASP502 3.5 14.5 1.0
ND2 D:ASN489 3.6 14.0 1.0
PB D:ANP700 3.7 18.4 1.0
O1G D:ANP700 3.7 18.5 1.0
MN D:MN701 3.9 16.8 1.0
O3A D:ANP700 3.9 15.3 1.0
O2B D:ANP700 3.9 15.7 1.0
CE D:LYS486 4.1 19.1 1.0
OD1 D:ASP502 4.2 16.8 1.0
O3G D:ANP700 4.2 17.5 1.0
O3' D:ANP700 4.3 14.2 1.0
O1A D:ANP700 4.3 13.2 1.0
NZ D:LYS486 4.4 19.2 1.0
O5' D:ANP700 4.4 15.1 1.0
OD2 D:ASP484 4.5 18.1 1.0
O D:HOH1142 4.5 34.9 1.0
CB D:ASN489 4.6 15.6 1.0
C5' D:ANP700 4.7 14.9 1.0
C3' D:ANP700 4.8 15.5 1.0
CA D:ASN489 4.8 12.7 1.0
O D:GLU488 4.8 19.4 1.0
CA D:ASP502 5.0 14.3 1.0
O1B D:ANP700 5.0 20.9 1.0

Reference:

L.Qin, B.Sankaran, D.Casteel, C.Kim. Crystal Structure of Cgmp-Dependent Protein Kinase Ialpha (Pkg Ialpha) Catalytic Domain To Be Published.
Page generated: Sun Oct 6 03:54:43 2024

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