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Calcium in PDB 3m6y: Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution.

Enzymatic activity of Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution.

All present enzymatic activity of Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution.:
4.1.3.16;

Protein crystallography data

The structure of Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution., PDB code: 3m6y was solved by E.V.Filippova, G.Minasov, L.Shuvalova, O.Kiryukhina, S.Clancy, A.Joachimiak, F.W.Anderson, Midwest Center For Structural Genomics(Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 88.05 / 1.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.679, 106.187, 88.205, 90.00, 90.95, 90.00
R / Rfree (%) 15.2 / 18

Other elements in 3m6y:

The structure of Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution. also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution. (pdb code 3m6y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution., PDB code: 3m6y:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3m6y

Go back to Calcium Binding Sites List in 3m6y
Calcium binding site 1 out of 6 in the Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca252

b:8.5
occ:0.90
 O A:HOH1188 2.4 11.1 1.0
O A:HOH385 2.4 11.0 1.0
OXT A:ALA251 2.5 14.7 1.0
O A:ALA251 2.5 12.5 1.0
C A:ALA251 2.8 13.5 1.0
O A:HOH390 4.3 17.6 1.0
O A:HOH355 4.3 17.8 1.0
O A:HOH700 4.3 16.6 0.5
CA A:ALA251 4.3 13.5 1.0
O A:HOH303 4.7 9.5 1.0
O A:HOH700 4.8 17.4 0.5

Calcium binding site 2 out of 6 in 3m6y

Go back to Calcium Binding Sites List in 3m6y
Calcium binding site 2 out of 6 in the Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca253

b:12.5
occ:0.50
 CA A:CA253 0.0 12.5 0.5
CA A:CA253 1.8 18.0 0.5
O A:HOH657 2.0 35.7 1.0
O A:HOH851 2.3 27.2 1.0
O A:HOH659 2.4 35.2 1.0
OD1 A:ASN211 2.4 15.3 1.0
O A:HOH692 2.6 26.4 1.0
O A:HOH736 2.7 31.8 1.0
CG A:ASN211 3.4 12.5 1.0
ND2 A:ASN211 3.8 16.5 1.0
O A:HOH447 3.9 21.1 1.0
O A:HOH330 4.1 26.1 1.0
O A:HOH340 4.3 19.1 1.0
O A:HOH424 4.3 16.9 1.0
O A:HOH700 4.5 16.6 0.5
O A:HOH700 4.6 17.4 0.5
CB A:ASN211 4.7 8.9 1.0
O A:TYR250 4.8 15.6 1.0
O A:HOH1117 4.8 34.9 1.0

Calcium binding site 3 out of 6 in 3m6y

Go back to Calcium Binding Sites List in 3m6y
Calcium binding site 3 out of 6 in the Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca253

b:18.0
occ:0.50
 CA A:CA253 0.0 18.0 0.5
CA A:CA253 1.8 12.5 0.5
O A:HOH692 2.2 26.4 1.0
O A:HOH736 2.4 31.8 1.0
OD1 A:ASN211 2.5 15.3 1.0
O A:HOH330 2.6 26.1 1.0
O A:HOH340 2.7 19.1 1.0
O A:HOH659 3.0 35.2 1.0
O A:HOH851 3.4 27.2 1.0
CG A:ASN211 3.5 12.5 1.0
O A:HOH657 3.6 35.7 1.0
ND2 A:ASN211 3.8 16.5 1.0
O A:HOH424 4.1 16.9 1.0
OE1 A:GLU213 4.2 15.4 1.0
NH2 A:ARG12 4.2 11.5 1.0
NH1 A:ARG12 4.5 12.0 1.0
CZ A:ARG12 4.6 11.0 1.0
O A:TYR250 4.7 15.6 1.0
CB A:ASN211 4.8 8.9 1.0
O A:ASN211 4.9 9.0 1.0

Calcium binding site 4 out of 6 in 3m6y

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Calcium binding site 4 out of 6 in the Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca252

b:17.4
occ:0.90
 OXT B:ALA251 2.3 21.4 1.0
O B:HOH998 2.3 25.4 1.0
O B:ALA251 2.4 19.4 1.0
C B:ALA251 2.8 20.3 1.0
CA B:ALA251 4.3 18.8 1.0
O B:HOH354 4.4 23.6 1.0
O B:HOH313 4.6 19.9 1.0
O B:HOH555 4.8 32.5 1.0

Calcium binding site 5 out of 6 in 3m6y

Go back to Calcium Binding Sites List in 3m6y
Calcium binding site 5 out of 6 in the Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca253

b:14.9
occ:0.50
 CA B:CA253 0.0 14.9 0.5
CA B:CA253 2.5 34.0 0.5
OE2 B:GLU109 2.5 35.2 1.0
OE1 B:GLU109 2.6 30.3 1.0
CD B:GLU109 2.9 31.2 1.0
O B:HOH1156 4.4 39.3 1.0
CG B:GLU109 4.5 25.1 1.0
O B:HOH1133 5.0 27.5 1.0

Calcium binding site 6 out of 6 in 3m6y

Go back to Calcium Binding Sites List in 3m6y
Calcium binding site 6 out of 6 in the Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca253

b:34.0
occ:0.50
 CA B:CA253 0.0 34.0 0.5
CA B:CA253 2.5 14.9 0.5
OE1 B:GLU109 3.4 30.3 1.0
O B:HOH1133 4.1 27.5 1.0
CD B:GLU109 4.2 31.2 1.0
OE2 B:GLU109 4.3 35.2 1.0

Reference:

E.V.Filippova, G.Minasov, L.Shuvalova, O.Kiryukhina, S.Clancy, A.Joachimiak, W.F.Anderson. Structure of 4-Hydroxy-2-Oxoglutarate Aldolase From Bacillus Cereus at 1.45 A Resolution. To Be Published.
Page generated: Sat Jul 13 13:28:23 2024

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