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Calcium in PDB 3hjb: 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae.

Enzymatic activity of 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae.

All present enzymatic activity of 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae.:
5.3.1.9;

Protein crystallography data

The structure of 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae., PDB code: 3hjb was solved by G.Minasov, A.Halavaty, L.Shuvalova, I.Dubrovska, J.Winsor, L.Papazisi, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.88 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 125.661, 75.094, 127.456, 90.00, 90.21, 90.00
R / Rfree (%) 12.7 / 15.1

Other elements in 3hjb:

The structure of 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae. also contains other interesting chemical elements:

Chlorine (Cl) 27 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae. (pdb code 3hjb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae., PDB code: 3hjb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 3hjb

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Calcium binding site 1 out of 10 in the 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca551

b:12.2
occ:0.50
 OE2 A:GLU62 2.4 7.8 1.0
O A:HOH2216 2.4 18.4 1.0
O A:HOH812 2.4 10.5 1.0
O A:HOH2078 2.5 19.8 1.0
OE1 A:GLU62 2.5 7.3 1.0
O A:HOH921 2.6 12.4 1.0
O A:HOH3413 2.7 30.2 1.0
CD A:GLU62 2.8 7.8 1.0
O A:HOH2998 4.2 43.8 1.0
CG A:GLU62 4.3 6.2 1.0
O A:HOH716 4.4 8.2 1.0
O A:HOH1392 4.4 19.4 1.0
ND1 A:HIS19 4.4 5.0 1.0
O A:HOH2847 4.5 31.2 1.0
O A:HOH576 4.6 9.9 1.0
O A:HOH1456 4.6 15.7 1.0
O A:HOH3699 4.8 28.1 1.0

Calcium binding site 2 out of 10 in 3hjb

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Calcium binding site 2 out of 10 in the 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca552

b:20.2
occ:0.50
 O A:HOH3926 2.3 36.0 1.0
O A:HOH2918 2.3 29.0 1.0
O A:HOH2765 2.3 33.5 1.0
O A:HOH1387 2.4 21.2 1.0
OE1 A:GLU168 2.5 9.2 1.0
OE2 A:GLU168 2.6 9.5 1.0
CD A:GLU168 2.9 9.0 1.0
O A:HOH1970 4.1 27.0 1.0
O A:HOH3132 4.3 34.4 1.0
CG A:GLU168 4.3 5.0 1.0
O A:HOH4006 4.4 30.6 1.0
O A:HOH715 4.4 8.2 1.0
OH A:TYR164 4.6 15.8 1.0
NE2 A:HIS344 4.6 8.6 1.0
O A:HOH675 4.7 8.8 1.0
O A:HOH3169 4.7 37.3 1.0
O A:HOH1282 4.8 18.1 1.0
O A:HOH608 4.9 7.9 1.0
CE1 A:TYR164 4.9 9.1 1.0

Calcium binding site 3 out of 10 in 3hjb

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Calcium binding site 3 out of 10 in the 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca553

b:26.9
occ:0.50
 O A:HOH3833 2.2 29.6 1.0
O A:HOH4115 2.2 15.4 0.5
O A:HOH4115 2.4 5.8 0.5
O A:HOH3984 2.5 30.7 1.0
O A:GLU253 2.5 5.6 1.0
O A:HOH3373 2.7 22.4 1.0
OE2 A:GLU253 3.3 26.3 1.0
C A:GLU253 3.6 6.3 1.0
CD A:GLU253 3.8 18.3 1.0
CA A:GLU253 4.1 6.0 1.0
CG A:GLU253 4.4 11.3 1.0
OE1 A:GLU253 4.5 18.9 1.0
OE1 A:GLU234 4.6 32.9 1.0
O A:ALA252 4.7 6.2 1.0
N A:PHE254 4.7 5.3 1.0
O A:HOH3221 4.7 33.0 1.0
NH2 A:ARG224 4.8 7.5 0.5
CB A:GLU253 4.9 7.3 1.0
C A:PHE254 4.9 6.1 1.0
OE2 A:GLU234 4.9 28.8 1.0
N A:GLY255 4.9 5.0 1.0

Calcium binding site 4 out of 10 in 3hjb

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Calcium binding site 4 out of 10 in the 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca554

b:27.4
occ:0.50
 O B:HOH4111 1.3 8.0 0.5
O B:HOH4114 2.2 33.4 1.0
OE2 A:GLU332 2.3 26.0 1.0
O B:GLY330 2.4 9.8 1.0
O A:HOH3970 2.4 3.6 0.5
O B:HOH4111 2.6 31.2 0.5
CA B:CA552 3.0 23.0 0.5
O A:HOH3970 3.3 24.8 0.5
CD A:GLU332 3.4 17.3 1.0
C B:GLY330 3.5 8.2 1.0
OE2 B:GLU332 4.0 22.7 1.0
CG A:GLU332 4.0 9.3 1.0
CG B:GLU332 4.1 8.9 1.0
O B:HOH719 4.1 19.0 1.0
O B:HOH997 4.1 17.4 1.0
O A:HOH1419 4.2 21.1 1.0
O A:HOH717 4.2 13.7 1.0
CA B:GLY330 4.3 8.3 1.0
O A:HOH953 4.3 19.0 1.0
OE1 A:GLU332 4.4 16.9 1.0
CD B:GLU332 4.5 18.2 1.0
N B:ALA331 4.5 6.7 1.0
O A:HOH3971 4.6 28.0 1.0
N B:GLU332 4.7 5.4 1.0
CA B:ALA331 4.7 6.7 1.0
O A:GLY330 4.8 8.9 1.0
C B:ALA331 4.9 5.7 1.0

Calcium binding site 5 out of 10 in 3hjb

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Calcium binding site 5 out of 10 in the 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca551

b:9.8
occ:0.80
 O B:HOH1182 2.3 7.9 1.0
OE2 B:GLU62 2.4 4.9 1.0
OE1 B:GLU62 2.5 5.7 1.0
O B:HOH651 2.5 5.1 1.0
O B:HOH638 2.5 5.6 1.0
CD B:GLU62 2.8 5.9 1.0
O B:HOH1355 4.2 11.6 1.0
OG B:SER22 4.3 4.8 1.0
CG B:GLU62 4.3 5.8 1.0
ND1 B:HIS19 4.3 2.6 1.0
O B:HOH649 4.3 7.5 1.0
O B:HOH627 4.4 6.0 1.0
O B:HOH1500 4.6 16.4 1.0
CA B:HIS19 4.9 2.3 1.0
CB B:HIS19 5.0 2.6 1.0

Calcium binding site 6 out of 10 in 3hjb

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Calcium binding site 6 out of 10 in the 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca552

b:23.0
occ:0.50
 O A:HOH3970 1.3 3.6 0.5
O A:HOH3971 2.1 28.0 1.0
OE2 B:GLU332 2.2 22.7 1.0
O A:GLY330 2.4 8.9 1.0
O B:HOH4111 2.4 8.0 0.5
O A:HOH3970 2.6 24.8 0.5
CA A:CA554 3.0 27.4 0.5
CD B:GLU332 3.3 18.2 1.0
O B:HOH4111 3.4 31.2 0.5
C A:GLY330 3.5 7.6 1.0
O A:HOH829 3.8 19.3 1.0
CG B:GLU332 3.9 8.9 1.0
O A:HOH663 4.1 13.8 1.0
O B:HOH1259 4.2 18.3 1.0
OE2 A:GLU332 4.2 26.0 1.0
O B:HOH997 4.2 17.4 1.0
O A:HOH1419 4.2 21.1 1.0
CG A:GLU332 4.3 9.3 1.0
CA A:GLY330 4.3 6.7 1.0
OE1 B:GLU332 4.3 17.9 1.0
N A:ALA331 4.5 5.8 1.0
O B:HOH3539 4.6 41.1 1.0
CA A:ALA331 4.6 4.9 1.0
CD A:GLU332 4.7 17.3 1.0
N A:GLU332 4.7 5.0 1.0
O B:HOH4114 4.7 33.4 1.0
O B:GLY330 4.9 9.8 1.0
C A:ALA331 4.9 5.4 1.0

Calcium binding site 7 out of 10 in 3hjb

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Calcium binding site 7 out of 10 in the 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca551

b:10.0
occ:0.80
 OE2 C:GLU62 2.4 4.8 1.0
O C:HOH1246 2.4 7.9 1.0
OE1 C:GLU62 2.4 4.8 1.0
O C:HOH734 2.5 6.1 1.0
O C:HOH617 2.5 6.2 1.0
CD C:GLU62 2.8 4.6 1.0
CG C:GLU62 4.3 4.7 1.0
OG C:SER22 4.3 4.4 1.0
O C:HOH655 4.3 8.4 1.0
ND1 C:HIS19 4.3 3.1 1.0
O C:HOH667 4.4 6.9 1.0
O C:HOH1427 4.5 12.8 1.0
CA C:HIS19 4.9 3.1 1.0
CB C:HIS19 5.0 3.4 1.0

Calcium binding site 8 out of 10 in 3hjb

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Calcium binding site 8 out of 10 in the 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca551

b:17.9
occ:0.80
 O D:HOH2011 2.4 15.6 1.0
O D:HOH2302 2.4 21.1 1.0
OE2 D:GLU62 2.4 9.5 1.0
OE1 D:GLU62 2.5 9.3 1.0
O D:HOH811 2.5 9.1 1.0
O D:HOH830 2.6 9.7 1.0
CD D:GLU62 2.8 8.7 1.0
CG D:GLU62 4.3 7.8 1.0
O D:HOH703 4.4 6.4 1.0
O D:HOH3652 4.4 40.8 1.0
ND1 D:HIS19 4.4 4.3 1.0
O D:HOH1340 4.5 15.2 1.0
O D:HOH1351 4.6 14.3 1.0
O D:HOH691 4.6 9.2 1.0
O D:HOH3680 4.8 31.6 1.0

Calcium binding site 9 out of 10 in 3hjb

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Calcium binding site 9 out of 10 in the 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca552

b:18.9
occ:0.50
 O D:HOH3927 2.1 18.4 0.5
O D:HOH3928 2.3 31.3 1.0
O D:HOH2839 2.4 37.6 1.0
O D:HOH1444 2.4 23.1 1.0
OE1 D:GLU168 2.5 9.6 1.0
OE2 D:GLU168 2.6 10.3 1.0
CD D:GLU168 2.9 9.4 1.0
O D:HOH1506 3.0 14.8 0.5
O D:HOH2954 4.2 29.7 1.0
O D:HOH3783 4.3 37.9 1.0
CG D:GLU168 4.3 6.0 1.0
O D:HOH1506 4.4 11.8 0.5
O D:HOH615 4.4 9.9 1.0
OH D:TYR164 4.6 17.6 1.0
O D:HOH3523 4.6 41.6 0.5
NE2 D:HIS344 4.6 8.4 1.0
O D:HOH709 4.7 10.2 1.0
O D:HOH1157 4.7 13.2 0.8
O D:HOH3523 4.9 27.8 0.5
O D:HOH624 4.9 9.5 1.0
CE1 D:TYR164 5.0 9.7 1.0

Calcium binding site 10 out of 10 in 3hjb

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Calcium binding site 10 out of 10 in the 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca553

b:27.5
occ:0.50
 O D:HOH3930 2.1 10.5 0.5
O D:HOH3337 2.2 31.8 1.0
O D:HOH3881 2.4 7.1 0.5
O D:GLU253 2.5 6.2 1.0
O D:HOH3881 2.6 25.6 0.5
O D:HOH2802 2.6 24.7 1.0
O D:HOH3985 2.7 31.3 1.0
OE2 D:GLU253 3.1 27.3 1.0
C D:GLU253 3.6 7.0 1.0
CD D:GLU253 3.7 20.0 1.0
CA D:GLU253 4.1 6.5 1.0
CG D:GLU253 4.3 12.9 1.0
OE1 D:GLU253 4.4 22.1 1.0
N D:PHE254 4.7 5.6 1.0
OE1 D:GLU234 4.7 28.0 1.0
O D:ALA252 4.8 6.5 1.0
CB D:GLU253 4.8 7.2 1.0
O D:HOH3463 4.8 35.2 1.0
NH2 D:ARG224 4.8 5.7 0.5
C D:PHE254 4.9 6.4 1.0
OE2 D:GLU234 5.0 27.8 1.0
N D:GLY255 5.0 6.3 1.0

Reference:

G.Minasov, A.Halavaty, L.Shuvalova, I.Dubrovska, J.Winsor, L.Papazisi, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 1.5 Angstrom Crystal Structure of Glucose-6-Phosphate Isomerase From Vibrio Cholerae. To Be Published.
Page generated: Sat Jul 13 11:04:50 2024

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