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Calcium in PDB 1t6m: X-Ray Structure of the R70D Pi-Plc Enzyme: Insight Into the Role of Calcium and Surrounding Amino Acids on Active Site Geometry and Catalysis.

Enzymatic activity of X-Ray Structure of the R70D Pi-Plc Enzyme: Insight Into the Role of Calcium and Surrounding Amino Acids on Active Site Geometry and Catalysis.

All present enzymatic activity of X-Ray Structure of the R70D Pi-Plc Enzyme: Insight Into the Role of Calcium and Surrounding Amino Acids on Active Site Geometry and Catalysis.:
4.6.1.13;

Protein crystallography data

The structure of X-Ray Structure of the R70D Pi-Plc Enzyme: Insight Into the Role of Calcium and Surrounding Amino Acids on Active Site Geometry and Catalysis., PDB code: 1t6m was solved by D.Apiyo, L.Zhao, M.-D.Tsai, T.L.Selby, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.30 / 2.11
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 91.221, 147.725, 96.562, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 24

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of the R70D Pi-Plc Enzyme: Insight Into the Role of Calcium and Surrounding Amino Acids on Active Site Geometry and Catalysis. (pdb code 1t6m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the X-Ray Structure of the R70D Pi-Plc Enzyme: Insight Into the Role of Calcium and Surrounding Amino Acids on Active Site Geometry and Catalysis., PDB code: 1t6m:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1t6m

Go back to Calcium Binding Sites List in 1t6m
Calcium binding site 1 out of 4 in the X-Ray Structure of the R70D Pi-Plc Enzyme: Insight Into the Role of Calcium and Surrounding Amino Acids on Active Site Geometry and Catalysis.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of the R70D Pi-Plc Enzyme: Insight Into the Role of Calcium and Surrounding Amino Acids on Active Site Geometry and Catalysis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:14.7
occ:1.00
 OD2 A:ASP228 2.0 23.4 1.0
CD2 A:HIS231 2.0 24.8 1.0
O A:HOH546 2.3 38.6 1.0
CG A:HIS231 2.9 26.5 1.0
CG A:ASP228 3.0 24.0 1.0
NE2 A:HIS231 3.1 27.4 1.0
CB A:HIS231 3.3 25.6 1.0
OD1 A:ASP228 3.4 24.8 1.0
OD1 A:ASN230 3.4 5.9 1.0
OD1 A:ASN225 3.9 45.9 1.0
ND1 A:HIS231 4.1 25.8 1.0
CE1 A:HIS231 4.2 26.4 1.0
ND2 A:ASN197 4.3 33.3 1.0
CB A:ASP228 4.3 24.2 1.0
CG A:ASN230 4.5 20.1 1.0
CA A:HIS231 4.6 25.8 1.0
OH A:TYR233 4.7 24.0 1.0

Calcium binding site 2 out of 4 in 1t6m

Go back to Calcium Binding Sites List in 1t6m
Calcium binding site 2 out of 4 in the X-Ray Structure of the R70D Pi-Plc Enzyme: Insight Into the Role of Calcium and Surrounding Amino Acids on Active Site Geometry and Catalysis.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of the R70D Pi-Plc Enzyme: Insight Into the Role of Calcium and Surrounding Amino Acids on Active Site Geometry and Catalysis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:14.4
occ:1.00
 OD2 A:ASP37 2.1 23.2 1.0
OD1 A:ASP73 2.2 21.2 1.0
O A:HOH503 2.9 18.1 1.0
O A:HOH549 2.9 48.6 1.0
CG A:ASP37 3.1 22.2 1.0
CG A:ASP73 3.2 22.1 1.0
O A:HOH505 3.4 4.3 1.0
OD1 A:ASP37 3.4 28.4 1.0
OD2 A:ASP73 3.5 23.0 1.0
OD2 A:ASP71 3.9 20.5 1.0
O A:HOH504 3.9 8.2 1.0
O A:HOH530 4.0 17.4 1.0
OE2 A:GLU121 4.3 25.1 1.0
OE1 A:GLU121 4.3 27.8 1.0
OD1 A:ASP71 4.3 22.1 1.0
CB A:ASP37 4.4 20.9 1.0
CG A:ASP71 4.4 22.2 1.0
CB A:ASP73 4.5 20.7 1.0
CD A:GLU121 4.5 26.9 1.0
NE2 A:HIS36 4.6 20.3 1.0
CE1 A:HIS86 4.7 29.0 1.0
ND1 A:HIS86 4.7 28.6 1.0
NZ A:LYS119 4.8 41.5 1.0
CA A:ASP37 4.8 16.9 1.0

Calcium binding site 3 out of 4 in 1t6m

Go back to Calcium Binding Sites List in 1t6m
Calcium binding site 3 out of 4 in the X-Ray Structure of the R70D Pi-Plc Enzyme: Insight Into the Role of Calcium and Surrounding Amino Acids on Active Site Geometry and Catalysis.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of the R70D Pi-Plc Enzyme: Insight Into the Role of Calcium and Surrounding Amino Acids on Active Site Geometry and Catalysis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:25.9
occ:1.00
 OD2 B:ASP73 2.1 33.8 1.0
OD1 B:ASP37 2.1 22.3 1.0
O B:HOH554 3.0 37.1 1.0
CG B:ASP73 3.0 25.7 1.0
CG B:ASP37 3.1 20.4 1.0
O B:HOH509 3.2 26.7 1.0
OD1 B:ASP73 3.4 30.6 1.0
OD2 B:ASP37 3.4 25.6 1.0
O B:HOH526 3.6 33.5 1.0
CE1 B:HIS86 3.8 41.1 1.0
OD1 B:ASP71 3.9 26.0 1.0
ND1 B:HIS86 4.0 40.7 1.0
O B:HOH529 4.0 18.0 1.0
OE1 B:GLU121 4.1 22.8 1.0
OE2 B:GLU121 4.2 25.1 1.0
CB B:ASP73 4.4 22.7 1.0
CB B:ASP37 4.4 16.9 1.0
CD B:GLU121 4.4 24.3 1.0
NE2 B:HIS36 4.5 19.2 1.0
CG B:ASP71 4.7 21.7 1.0
OD2 B:ASP71 4.8 25.0 1.0
CA B:ASP37 4.8 16.0 1.0
NE2 B:HIS86 4.9 42.5 1.0
CD2 B:HIS36 5.0 14.3 1.0

Calcium binding site 4 out of 4 in 1t6m

Go back to Calcium Binding Sites List in 1t6m
Calcium binding site 4 out of 4 in the X-Ray Structure of the R70D Pi-Plc Enzyme: Insight Into the Role of Calcium and Surrounding Amino Acids on Active Site Geometry and Catalysis.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of the R70D Pi-Plc Enzyme: Insight Into the Role of Calcium and Surrounding Amino Acids on Active Site Geometry and Catalysis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:25.8
occ:1.00
 OD1 B:ASN230 2.1 35.0 1.0
OD1 B:ASP228 2.1 23.0 1.0
CG B:ASP228 3.1 25.4 1.0
CG B:ASN230 3.1 33.5 1.0
OD2 B:ASP228 3.4 25.1 1.0
ND2 B:ASN230 3.6 38.9 1.0
O B:HOH584 4.4 34.1 1.0
N B:ASN230 4.4 19.0 1.0
CB B:ASP228 4.4 25.8 1.0
CB B:ASN230 4.4 31.6 1.0
C B:ASN230 4.5 18.7 1.0
CB B:HIS231 4.5 14.7 1.0
CA B:ASN230 4.7 19.4 1.0
ND2 B:ASN197 4.7 43.1 1.0
CA B:ASP228 4.7 18.3 1.0
O B:ASN230 4.7 18.1 1.0
N B:HIS231 4.7 16.7 1.0
C B:ASP228 4.9 18.0 1.0
N B:LEU229 5.0 21.2 1.0

Reference:

D.Apiyo, L.Zhao, M.-D.Tsai, T.L.Selby. X-Ray Structure of the R69D Phosphatidylinositol-Specific Phospholipase C Enzyme: Insight Into the Role of Calcium and Surrounding Amino Acids in Active Site Geometry and Catalysis. Biochemistry V. 44 9980 2005.
ISSN: ISSN 0006-2960
PubMed: 16042375
DOI: 10.1021/BI047896V
Page generated: Thu Jul 11 22:57:24 2024

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