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Calcium in PDB 1y7o: The Structure of Streptococcus Pneumoniae A153P Clpp

Enzymatic activity of The Structure of Streptococcus Pneumoniae A153P Clpp

All present enzymatic activity of The Structure of Streptococcus Pneumoniae A153P Clpp:
3.4.21.92;

Protein crystallography data

The structure of The Structure of Streptococcus Pneumoniae A153P Clpp, PDB code: 1y7o was solved by M.S.Kimber, A.Gribun, R.Ching, R.Sprangers, K.M.Fiebig, W.A.Houry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.50 / 2.51
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.650, 105.650, 236.192, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 24.8

Calcium Binding Sites:

The binding sites of Calcium atom in the The Structure of Streptococcus Pneumoniae A153P Clpp (pdb code 1y7o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the The Structure of Streptococcus Pneumoniae A153P Clpp, PDB code: 1y7o:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1y7o

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Calcium binding site 1 out of 8 in the The Structure of Streptococcus Pneumoniae A153P Clpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of Streptococcus Pneumoniae A153P Clpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:60.8
occ:1.00
 O A:MSE79 2.2 18.9 1.0
O A:ALA84 2.4 21.9 1.0
O A:ILE82 2.7 21.3 1.0
C A:MSE79 3.4 19.8 1.0
C A:ALA84 3.6 22.0 1.0
CG1 A:ILE82 3.6 20.5 1.0
C A:ILE82 3.8 21.7 1.0
O A:ASN80 3.9 21.3 1.0
O A:LYS83 4.1 23.7 1.0
CA A:ASN80 4.1 20.3 1.0
C A:ASN80 4.1 20.6 1.0
CG2 A:VAL86 4.2 21.1 1.0
N A:ASN80 4.2 20.0 1.0
C A:LYS83 4.2 23.4 1.0
CA A:ASP85 4.3 22.0 1.0
N A:VAL86 4.3 21.8 1.0
N A:ASP85 4.3 21.8 1.0
N A:ALA84 4.4 22.8 1.0
CA A:ILE82 4.6 21.2 1.0
CA A:MSE79 4.6 19.7 1.0
CD1 A:ILE82 4.6 20.8 1.0
CA A:ALA84 4.6 22.5 1.0
N A:ILE82 4.6 20.8 1.0
OG B:SER194 4.6 40.4 1.0
C A:ASP85 4.6 21.9 1.0
CB A:ILE82 4.7 20.9 1.0
N A:LYS83 4.7 22.7 1.0
CA A:LYS83 4.9 23.8 1.0
N A:PHE81 5.0 20.9 1.0

Calcium binding site 2 out of 8 in 1y7o

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Calcium binding site 2 out of 8 in the The Structure of Streptococcus Pneumoniae A153P Clpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of Streptococcus Pneumoniae A153P Clpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1004

b:52.0
occ:1.00
 O B:HOH1032 2.3 22.3 1.0
O B:MSE79 2.4 16.0 1.0
O B:ILE82 2.5 19.0 1.0
O B:ALA84 2.5 17.2 1.0
C B:ALA84 3.5 17.2 1.0
C B:MSE79 3.6 16.5 1.0
C B:ILE82 3.6 18.9 1.0
CG1 B:ILE82 3.9 17.6 1.0
CG2 B:VAL86 3.9 15.3 1.0
N B:VAL86 4.2 16.6 1.0
C B:LYS83 4.2 18.5 1.0
CA B:ASN80 4.2 17.0 1.0
O B:ASN80 4.2 18.3 1.0
N B:ASP85 4.3 16.4 1.0
O B:LYS83 4.3 18.8 1.0
CA B:ASP85 4.3 17.0 1.0
C B:ASN80 4.3 17.5 1.0
N B:ASN80 4.4 16.7 1.0
N B:ALA84 4.4 17.6 1.0
N B:LYS83 4.5 19.1 1.0
OG C:SER194 4.6 34.0 1.0
CA B:ILE82 4.6 18.4 1.0
CA B:ALA84 4.6 17.6 1.0
N B:ILE82 4.6 18.0 1.0
CA B:LYS83 4.6 19.3 1.0
CA B:MSE79 4.6 16.6 1.0
C B:ASP85 4.6 16.6 1.0
CB B:VAL86 4.7 15.5 1.0
CB B:ILE82 4.8 18.2 1.0
CD1 B:ILE82 4.9 18.7 1.0

Calcium binding site 3 out of 8 in 1y7o

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Calcium binding site 3 out of 8 in the The Structure of Streptococcus Pneumoniae A153P Clpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structure of Streptococcus Pneumoniae A153P Clpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1002

b:56.8
occ:1.00
 O C:ALA84 2.5 22.2 1.0
O C:MSE79 2.5 20.6 1.0
O C:ILE82 2.7 26.1 1.0
OG D:SER194 2.9 46.9 1.0
CB D:SER194 3.4 47.1 1.0
C C:ALA84 3.6 22.4 1.0
O C:HOH1033 3.6 31.2 1.0
C C:MSE79 3.7 21.0 1.0
C C:ILE82 3.8 25.5 1.0
O C:HOH1012 3.9 34.8 1.0
CG1 C:ILE82 4.0 25.9 1.0
CA C:ASP85 4.0 21.0 1.0
CG2 C:VAL86 4.1 18.1 1.0
N C:ASP85 4.2 21.6 1.0
N C:VAL86 4.2 19.4 1.0
C C:LYS83 4.3 24.3 1.0
O C:LYS83 4.4 24.2 1.0
C C:ASP85 4.4 20.2 1.0
CA C:ASN80 4.4 22.6 1.0
N C:ALA84 4.5 23.2 1.0
N C:ASN80 4.5 22.1 1.0
O C:ASN80 4.6 23.9 1.0
C C:ASN80 4.6 23.4 1.0
CA C:ALA84 4.7 22.8 1.0
CA C:MSE79 4.7 20.5 1.0
CA C:ILE82 4.7 25.3 1.0
N C:LYS83 4.7 25.8 1.0
OD1 C:ASP85 4.8 26.2 1.0
CA C:LYS83 4.8 25.4 1.0
N C:ILE82 4.8 25.2 1.0
CD1 C:ILE82 4.9 25.4 1.0
CB C:ILE82 4.9 25.7 1.0
CA D:SER194 4.9 47.0 1.0
CB C:VAL86 4.9 18.1 1.0

Calcium binding site 4 out of 8 in 1y7o

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Calcium binding site 4 out of 8 in the The Structure of Streptococcus Pneumoniae A153P Clpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structure of Streptococcus Pneumoniae A153P Clpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1006

b:35.3
occ:1.00
 O C:GLU156 2.3 17.7 1.0
C C:GLU156 3.3 17.7 1.0
CA C:GLU156 3.8 18.6 1.0
O C:HOH1019 4.4 39.6 1.0
CB C:GLU156 4.5 18.9 1.0
N C:ASN157 4.5 17.7 1.0
O C:ALA155 4.6 18.5 1.0
N C:GLY159 4.7 18.0 1.0
CA C:GLY159 4.9 18.6 1.0

Calcium binding site 5 out of 8 in 1y7o

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Calcium binding site 5 out of 8 in the The Structure of Streptococcus Pneumoniae A153P Clpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Structure of Streptococcus Pneumoniae A153P Clpp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1007

b:60.2
occ:1.00
 O E:MSE79 2.5 27.2 1.0
O E:ALA84 2.5 33.5 1.0
O E:ILE82 2.6 32.8 1.0
C E:ALA84 3.5 33.8 1.0
C E:ILE82 3.6 32.6 1.0
C E:MSE79 3.7 27.8 1.0
CG1 E:ILE82 3.8 31.5 1.0
CG2 E:VAL86 4.0 31.0 1.0
CA E:ASP85 4.1 33.5 1.0
C E:LYS83 4.1 34.1 1.0
O E:LYS83 4.2 33.8 1.0
N E:ASP85 4.2 33.7 1.0
N E:VAL86 4.2 32.0 1.0
N E:ALA84 4.3 34.2 1.0
C E:ASP85 4.4 32.8 1.0
OG F:SER194 4.4 52.6 1.0
CA E:ILE82 4.5 31.9 1.0
CD1 E:ILE82 4.5 31.7 1.0
N E:LYS83 4.5 33.6 1.0
O E:ASN80 4.5 29.1 1.0
CA E:ALA84 4.6 34.0 1.0
N E:ILE82 4.6 31.6 1.0
CA E:MSE79 4.6 28.1 1.0
CA E:ASN80 4.6 28.7 1.0
N E:ASN80 4.6 28.2 1.0
CB E:ILE82 4.7 31.6 1.0
CA E:LYS83 4.7 34.5 1.0
C E:ASN80 4.7 29.3 1.0
CB E:VAL86 4.7 31.7 1.0

Calcium binding site 6 out of 8 in 1y7o

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Calcium binding site 6 out of 8 in the The Structure of Streptococcus Pneumoniae A153P Clpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Structure of Streptococcus Pneumoniae A153P Clpp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1003

b:62.0
occ:1.00
 OD1 F:ASP85 2.6 26.8 1.0
OD2 F:ASP85 2.9 26.7 1.0
CG F:ASP85 3.1 25.2 1.0
O F:HOH1015 3.2 52.3 1.0
CB F:ASP85 4.5 25.8 1.0
NZ F:LYS109 4.8 31.1 1.0

Calcium binding site 7 out of 8 in 1y7o

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Calcium binding site 7 out of 8 in the The Structure of Streptococcus Pneumoniae A153P Clpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Structure of Streptococcus Pneumoniae A153P Clpp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1008

b:59.3
occ:1.00
 O F:MSE79 2.3 23.3 1.0
O F:ILE82 2.5 28.3 1.0
O F:ALA84 2.5 26.4 1.0
O F:HOH1010 2.6 22.7 1.0
C F:MSE79 3.5 23.2 1.0
C F:ALA84 3.6 26.3 1.0
CG1 F:ILE82 3.6 26.3 1.0
C F:ILE82 3.6 27.8 1.0
CG2 F:VAL86 4.0 25.4 1.0
O F:ASN80 4.1 24.2 1.0
O F:LYS83 4.1 28.3 1.0
CA F:ASP85 4.2 25.5 1.0
N F:VAL86 4.2 25.2 1.0
C F:LYS83 4.2 28.1 1.0
C F:ASN80 4.2 24.4 1.0
N F:ASP85 4.3 25.8 1.0
CA F:ASN80 4.3 23.8 1.0
N F:ASN80 4.3 23.8 1.0
N F:ILE82 4.3 26.5 1.0
CA F:ILE82 4.4 26.7 1.0
N F:ALA84 4.4 27.4 1.0
O G:ASN193 4.5 42.3 1.0
CA F:MSE79 4.5 22.8 1.0
C F:ASP85 4.5 25.1 1.0
CA F:ALA84 4.6 27.0 1.0
CB F:ILE82 4.6 26.2 1.0
N F:LYS83 4.7 28.7 1.0
CD1 F:ILE82 4.7 26.0 1.0
CA F:LYS83 4.8 28.9 1.0
CB F:VAL86 4.8 25.2 1.0
N F:PHE81 5.0 25.1 1.0

Calcium binding site 8 out of 8 in 1y7o

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Calcium binding site 8 out of 8 in the The Structure of Streptococcus Pneumoniae A153P Clpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Structure of Streptococcus Pneumoniae A153P Clpp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca1005

b:53.9
occ:1.00
 O G:ALA84 2.5 28.8 1.0
O G:MSE79 2.8 25.2 1.0
O G:HOH1011 2.9 18.4 1.0
O G:ILE82 2.9 27.2 1.0
C G:ALA84 3.3 28.5 1.0
O G:LYS83 3.4 29.8 1.0
C G:LYS83 3.8 29.1 1.0
N G:ASP85 3.8 28.0 1.0
C G:ILE82 3.9 27.5 1.0
CA G:ASP85 3.9 27.6 1.0
CG1 G:ILE82 4.0 26.0 1.0
C G:MSE79 4.0 25.0 1.0
N G:ALA84 4.1 28.7 1.0
CG2 G:VAL86 4.3 24.8 1.0
N G:VAL86 4.4 25.3 1.0
CA G:ALA84 4.4 28.6 1.0
C G:ASP85 4.5 26.2 1.0
CA G:LYS83 4.5 29.4 1.0
N G:LYS83 4.6 28.4 1.0
CD1 G:ILE82 4.6 25.4 1.0
OD1 G:ASP85 4.7 31.3 1.0
CA G:ASN80 4.8 25.0 1.0
O G:ASN80 4.8 25.5 1.0
C G:ASN80 4.8 25.6 1.0
CA G:ILE82 4.8 26.8 1.0
N G:ASN80 4.9 24.6 1.0
CB G:ILE82 5.0 26.3 1.0
CA G:MSE79 5.0 25.0 1.0
N G:ILE82 5.0 26.9 1.0

Reference:

A.Gribun, M.S.Kimber, R.Ching, R.Sprangers, K.M.Fiebig, W.A.Houry. The Clpp Double Ring Tetradecameric Protease Exhibits Plastic Ring-Ring Interactions, and the N Termini of Its Subunits Form Flexible Loops That Are Essential For Clpxp and Clpap Complex Formation. J.Biol.Chem. V. 280 16185 2005.
ISSN: ISSN 0021-9258
PubMed: 15701650
DOI: 10.1074/JBC.M414124200
Page generated: Fri Jul 12 08:01:16 2024

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