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Calcium in PDB 4b5w: Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase R70A Mutant, Hpai, in Complex with Pyruvate

Enzymatic activity of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase R70A Mutant, Hpai, in Complex with Pyruvate

All present enzymatic activity of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase R70A Mutant, Hpai, in Complex with Pyruvate:
4.1.2.20;

Protein crystallography data

The structure of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase R70A Mutant, Hpai, in Complex with Pyruvate, PDB code: 4b5w was solved by M.Coincon, W.Wang, S.Y.K.Seah, J.Sygusch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.49 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.348, 119.144, 140.559, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 18.4

Other elements in 4b5w:

The structure of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase R70A Mutant, Hpai, in Complex with Pyruvate also contains other interesting chemical elements:

Cobalt (Co) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase R70A Mutant, Hpai, in Complex with Pyruvate (pdb code 4b5w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase R70A Mutant, Hpai, in Complex with Pyruvate, PDB code: 4b5w:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4b5w

Go back to Calcium Binding Sites List in 4b5w
Calcium binding site 1 out of 5 in the Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase R70A Mutant, Hpai, in Complex with Pyruvate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase R70A Mutant, Hpai, in Complex with Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1258

b:71.1
occ:1.00
 O A:HOH2243 2.2 51.5 1.0
HZ2 A:LYS137 3.1 70.1 1.0
OD2 A:ASP133 3.3 38.1 1.0
HZ3 A:LYS137 3.3 70.1 1.0
NZ A:LYS137 3.6 58.4 1.0
O A:HOH2242 3.9 45.6 1.0
HZ1 A:LYS137 4.0 70.1 1.0
CG A:ASP133 4.2 32.3 1.0
OD1 A:ASP133 4.4 29.2 1.0
O A:HOH2250 4.5 45.6 1.0
HE3 A:LYS137 4.8 60.0 1.0
CE A:LYS137 4.9 50.0 1.0

Calcium binding site 2 out of 5 in 4b5w

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Calcium binding site 2 out of 5 in the Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase R70A Mutant, Hpai, in Complex with Pyruvate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase R70A Mutant, Hpai, in Complex with Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1254

b:41.3
occ:1.00
 OD2 C:ASP162 2.1 36.0 1.0
O C:HOH2207 2.3 52.2 1.0
O C:HOH2289 2.7 55.8 1.0
CG C:ASP162 2.9 33.7 1.0
OD1 C:ASP162 3.2 33.5 1.0
O C:HOH2233 4.2 43.4 1.0
CB C:ASP162 4.2 24.7 1.0
O C:HOH2205 4.4 30.4 1.0
HB3 C:ASP162 4.4 29.6 1.0
O C:HOH2206 4.4 41.9 1.0
HB2 C:ASP162 4.5 29.6 1.0
O C:PRO158 4.9 22.1 1.0

Calcium binding site 3 out of 5 in 4b5w

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Calcium binding site 3 out of 5 in the Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase R70A Mutant, Hpai, in Complex with Pyruvate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase R70A Mutant, Hpai, in Complex with Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1255

b:22.7
occ:1.00
 O D:HOH2047 2.0 36.1 1.0
O A:HOH2354 2.1 24.8 1.0
O A:HOH2355 2.2 25.4 1.0
O D:HOH2042 2.3 30.8 1.0
OD1 D:ASP37 2.4 15.3 1.0
O D:HOH2043 2.4 29.3 1.0
CG D:ASP37 3.1 15.7 1.0
OD2 D:ASP37 3.3 12.1 1.0
HA A:ALA252 3.7 35.8 1.0
O A:HOH2357 3.9 26.3 1.0
O D:GLY35 4.0 17.6 1.0
O A:HOH2349 4.1 23.5 1.0
O D:HOH2044 4.1 33.9 1.0
O A:GLY251 4.2 22.5 1.0
H D:ASP37 4.3 12.4 1.0
HA D:ASP37 4.4 13.1 1.0
N D:ASP37 4.4 10.4 1.0
O D:HOH2017 4.5 25.2 1.0
CB D:ASP37 4.5 13.1 1.0
CA A:ALA252 4.6 29.8 1.0
CA D:ASP37 4.7 10.9 1.0
C A:GLY251 4.8 27.5 1.0
HA D:PHE36 4.8 12.7 1.0
HB D:ILE16 4.8 14.5 1.0
C D:PHE36 4.9 11.1 1.0
HG2 A:GLN253 4.9 30.0 1.0
N A:ALA252 4.9 28.6 1.0
H A:GLN253 5.0 31.8 1.0
HB3 D:ASP37 5.0 15.8 1.0

Calcium binding site 4 out of 5 in 4b5w

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Calcium binding site 4 out of 5 in the Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase R70A Mutant, Hpai, in Complex with Pyruvate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase R70A Mutant, Hpai, in Complex with Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1257

b:69.6
occ:1.00
 O E:HOH2224 2.4 27.1 1.0
OD1 E:ASP162 2.6 43.0 1.0
O E:HOH2305 2.9 60.5 1.0
CG E:ASP162 3.5 38.1 1.0
OD2 E:ASP162 3.8 37.6 1.0
HB2 E:SER205 3.9 29.3 1.0
O E:HOH2230 4.2 48.1 1.0
HB3 E:LEU161 4.4 24.6 1.0
HA E:ASP162 4.4 24.6 1.0
HB2 E:LEU161 4.4 24.6 1.0
O E:PRO158 4.5 20.2 1.0
HB3 E:SER205 4.7 29.3 1.0
CB E:SER205 4.7 24.4 1.0
O E:HOH2263 4.8 27.6 1.0
CB E:ASP162 4.8 24.7 1.0
HA E:SER205 4.8 27.8 1.0
CB E:LEU161 4.9 20.5 1.0
N E:ASP162 4.9 20.0 1.0
CA E:ASP162 4.9 20.5 1.0
C E:LEU161 4.9 21.7 1.0
O E:LEU161 5.0 30.1 1.0

Calcium binding site 5 out of 5 in 4b5w

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Calcium binding site 5 out of 5 in the Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase R70A Mutant, Hpai, in Complex with Pyruvate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structures of Divalent Metal Dependent Pyruvate Aldolase R70A Mutant, Hpai, in Complex with Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1256

b:25.4
occ:1.00
 OD2 F:ASP140 2.1 29.4 1.0
O F:HOH2163 2.1 37.0 1.0
CG F:ASP140 3.0 30.1 1.0
OD1 F:ASP140 3.3 29.8 1.0
O F:HOH2164 4.3 28.2 1.0
CB F:ASP140 4.3 23.1 1.0
HB3 F:ASP140 4.4 27.7 1.0
HB2 F:ASP140 4.6 27.7 1.0

Reference:

M.Coincon, W.Wang, J.Sygusch, S.Y.K.Seah. Crystal Structure of Reaction Intermediates in Pyruvate Class II Aldolase: Substrate Cleavage, Enolate Stabilization and Substrate Specificity J.Biol.Chem. V. 287 36208 2012.
ISSN: ISSN 0021-9258
PubMed: 22908224
DOI: 10.1074/JBC.M112.400705
Page generated: Sat Jul 13 22:35:47 2024

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