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Calcium in PDB 4em6: The Structure of Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis

Enzymatic activity of The Structure of Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis

All present enzymatic activity of The Structure of Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis:
5.3.1.9;

Protein crystallography data

The structure of The Structure of Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis, PDB code: 4em6 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 95.07 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 71.590, 72.730, 115.250, 95.42, 91.54, 110.06
R / Rfree (%) 13.1 / 16.9

Other elements in 4em6:

The structure of The Structure of Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Structure of Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis (pdb code 4em6). 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 Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis, PDB code: 4em6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4em6

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Calcium binding site 1 out of 8 in the The Structure of Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis


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 Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca602

b:27.2
occ:1.00
 O D:HOH1245 2.3 19.6 1.0
O D:HOH1288 2.3 9.0 1.0
O D:HOH1216 2.4 21.3 1.0
O D:GLY327 2.4 5.6 1.0
O D:HOH822 2.5 15.7 1.0
O B:HOH1139 2.5 18.2 1.0
O D:HOH1260 2.7 27.5 1.0
C D:GLY327 3.6 5.8 1.0
O D:HOH1040 4.1 10.0 1.0
N D:GLY329 4.3 4.4 1.0
O D:HOH1106 4.3 15.1 1.0
O B:HOH881 4.4 7.6 1.0
CA D:GLY327 4.4 6.5 1.0
O B:HOH718 4.5 2.0 1.0
O D:HOH1163 4.5 16.4 1.0
O D:HOH816 4.5 7.5 1.0
O D:HOH741 4.6 2.1 1.0
N D:TYR328 4.6 4.7 1.0
O B:HOH1099 4.6 12.5 1.0
O D:HOH890 4.7 17.8 1.0
CA D:TYR328 4.7 4.9 1.0
O B:HOH741 4.7 8.7 1.0
O D:HOH1266 4.7 31.2 1.0
C D:TYR328 4.8 4.2 1.0
CA D:GLY329 4.9 4.4 1.0

Calcium binding site 2 out of 8 in 4em6

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Calcium binding site 2 out of 8 in the The Structure of Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis


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 Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:22.7
occ:1.00
 O A:HOH1351 2.4 10.6 1.0
O A:GLY531 2.5 13.9 1.0
O A:HOH1352 2.5 6.8 1.0
O A:HOH1354 2.5 8.7 1.0
O A:HOH1353 2.6 11.0 1.0
O A:HOH1355 2.6 9.0 1.0
O A:HOH1356 2.6 7.5 1.0
C A:GLY531 3.5 15.5 1.0
O A:ARG532 4.1 9.2 1.0
O A:HOH1361 4.3 17.2 1.0
C A:ARG532 4.3 9.5 1.0
CA A:GLY531 4.3 18.9 1.0
N A:ARG532 4.4 12.2 1.0
CA A:ARG532 4.5 10.5 1.0
O C:HOH968 4.6 10.1 1.0
N A:ASP533 4.8 8.7 1.0
O C:HOH862 4.9 8.9 1.0
O C:HOH880 4.9 2.0 1.0
CB C:SER32 4.9 10.1 1.0
O C:HOH879 4.9 7.2 1.0
O A:HOH1359 5.0 15.8 1.0

Calcium binding site 3 out of 8 in 4em6

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Calcium binding site 3 out of 8 in the The Structure of Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis


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 Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:15.7
occ:1.00
 O B:GLY531 2.3 16.2 1.0
O B:HOH792 2.4 13.2 1.0
O B:HOH858 2.4 12.0 1.0
O D:HOH844 2.5 4.8 1.0
C B:GLY531 3.4 15.9 1.0
CA B:ARG532 4.2 10.6 1.0
N B:ARG532 4.3 12.6 1.0
O D:HOH884 4.4 2.7 1.0
CA B:GLY531 4.4 18.3 1.0
NZ D:LYS432 4.4 9.2 1.0
O D:HOH985 4.6 5.7 1.0
CE D:LYS432 4.7 12.4 1.0
C B:ARG532 4.7 9.9 1.0
O D:HOH774 4.9 4.1 1.0
O D:HOH984 5.0 8.5 1.0

Calcium binding site 4 out of 8 in 4em6

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Calcium binding site 4 out of 8 in the The Structure of Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis


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 Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:35.0
occ:1.00
 O B:HOH1351 2.2 20.5 1.0
O B:ALA169 2.4 6.4 1.0
O B:HIS172 2.4 13.7 1.0
O D:HOH1256 2.6 25.9 1.0
O B:HOH1360 2.9 27.4 1.0
C B:ALA169 3.5 6.7 1.0
C B:HIS172 3.6 14.4 1.0
O D:HOH864 4.0 8.0 1.0
N B:HIS172 4.2 10.9 1.0
CA B:PRO170 4.3 8.4 1.0
CA B:ALA169 4.3 6.6 1.0
N B:PRO170 4.4 7.2 1.0
CA B:HIS172 4.4 11.8 1.0
C B:PRO170 4.5 8.8 1.0
CB B:HIS172 4.6 11.6 1.0
CB B:ALA169 4.6 6.3 1.0
N B:ASP173 4.6 17.0 1.0
O D:HOH1176 4.8 16.2 1.0
CA B:ASP173 4.8 18.4 1.0
O B:HOH1177 4.8 27.3 1.0
O B:PRO170 4.9 7.5 1.0
N B:TYR171 4.9 8.7 1.0

Calcium binding site 5 out of 8 in 4em6

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Calcium binding site 5 out of 8 in the The Structure of Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis


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 Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca603

b:18.7
occ:0.50
 O C:ALA33 2.2 10.5 1.0
O C:HOH1261 2.5 24.1 1.0
O C:HOH1304 2.5 21.2 1.0
C C:ALA33 3.3 10.6 1.0
CA C:ALA33 3.9 10.3 1.0
N C:ASP34 4.4 9.4 1.0
CB C:ALA33 4.5 10.7 1.0
O C:SER32 4.7 10.8 1.0
CA C:ASP34 4.9 10.4 1.0
CD C:PRO35 5.0 11.4 1.0

Calcium binding site 6 out of 8 in 4em6

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Calcium binding site 6 out of 8 in the The Structure of Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis


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 Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca604

b:42.4
occ:1.00
 O C:HOH1307 2.4 16.8 1.0
O C:HOH1306 2.4 10.9 1.0
O C:HOH1305 2.4 2.8 1.0
O C:HOH1309 2.6 13.2 1.0
O C:ASP362 2.7 11.2 1.0
C C:ASP362 3.7 11.1 1.0
NH1 A:ARG455 3.9 12.5 1.0
CA C:GLY363 3.9 10.7 1.0
O A:HOH912 4.1 7.2 1.0
NZ C:LYS364 4.1 19.3 1.0
O C:HOH1308 4.2 13.8 1.0
O C:GLY363 4.2 11.2 1.0
N C:GLY363 4.2 10.7 1.0
C C:GLY363 4.3 11.1 1.0
CE C:LYS364 4.4 18.8 1.0
CG A:PRO458 4.6 9.6 1.0
O A:HOH955 4.6 6.9 1.0
CD A:ARG455 4.7 10.7 1.0
CZ A:ARG455 4.7 10.6 1.0
O A:ARG455 4.7 8.7 1.0
O C:HOH732 4.7 2.0 1.0
O A:GLU454 4.8 8.5 1.0
O A:HOH898 4.8 13.6 1.0
CD C:LYS364 4.8 16.0 1.0
CA C:ASP362 4.8 11.6 1.0
CA A:ARG455 5.0 9.0 1.0
NE A:ARG455 5.0 10.5 1.0

Calcium binding site 7 out of 8 in 4em6

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Calcium binding site 7 out of 8 in the The Structure of Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis


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 Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca605

b:30.4
occ:1.00
 O C:HOH1296 2.3 22.2 1.0
O C:HOH1314 2.4 17.2 1.0
O C:ALA169 2.4 6.1 1.0
O C:HOH1188 2.5 16.5 1.0
O C:HIS172 2.5 12.4 1.0
O C:HOH1315 2.8 28.4 1.0
C C:ALA169 3.5 6.1 1.0
C C:HIS172 3.7 13.3 1.0
O A:HOH768 3.9 7.0 1.0
CA C:ALA169 4.2 5.3 1.0
N C:HIS172 4.3 9.6 1.0
CB C:HIS172 4.3 9.8 1.0
CA C:HIS172 4.4 10.5 1.0
N C:PRO170 4.4 5.8 1.0
CB C:ALA169 4.5 5.5 1.0
CA C:PRO170 4.5 6.4 1.0
O A:HOH1236 4.5 17.0 1.0
O A:HOH1062 4.7 10.7 1.0
O C:HOH1284 4.7 30.9 1.0
C C:PRO170 4.8 7.0 1.0
O C:HOH1159 4.8 16.1 1.0
N C:ASP173 4.8 16.5 1.0
CG C:HIS172 4.9 8.7 1.0

Calcium binding site 8 out of 8 in 4em6

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Calcium binding site 8 out of 8 in the The Structure of Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis


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 Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca608

b:30.7
occ:1.00
 O C:HOH932 2.3 7.4 1.0
O C:GLY327 2.3 7.9 1.0
O C:HOH1287 2.5 26.0 1.0
O C:HOH1009 2.6 16.4 1.0
C C:GLY327 3.5 8.2 1.0
O C:HOH1150 4.1 14.5 1.0
N C:GLY329 4.3 5.5 1.0
CA C:GLY327 4.3 9.0 1.0
O A:HOH740 4.3 2.0 1.0
O A:HOH839 4.4 10.7 1.0
O C:HOH746 4.5 3.7 1.0
N C:TYR328 4.5 6.6 1.0
O C:HOH1210 4.6 19.2 1.0
O C:HOH773 4.6 5.2 1.0
CA C:TYR328 4.7 6.6 1.0
O A:HOH911 4.7 10.4 1.0
O C:HOH939 4.7 14.8 1.0
C C:TYR328 4.8 5.8 1.0
CA C:GLY329 4.9 5.5 1.0

Reference:

M.C.Clifton, T.E.Edwards, Seattle Structural Genomics Center For Infectious Disease(Ssgcid). The Structure of Glucose-6-Phosphate Isomerase (Gpi) From Brucella Melitensis To Be Published.
Page generated: Sun Jul 14 00:01:32 2024

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