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Calcium in PDB 6u7l: 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli.

Enzymatic activity of 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli.

All present enzymatic activity of 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli.:
4.2.1.42;

Protein crystallography data

The structure of 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli., PDB code: 6u7l was solved by G.Minasov, L.Shuvalova, Z.Wawrzak, I.Dubrovska, O.Kiryukhina, M.Endres, K.J.F.Satchell, 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) 29.23 / 2.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.462, 167.574, 117.065, 90.00, 103.97, 90.00
R / Rfree (%) 20.7 / 24.1

Other elements in 6u7l:

The structure of 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli. also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli. (pdb code 6u7l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli., PDB code: 6u7l:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 6u7l

Go back to Calcium Binding Sites List in 6u7l
Calcium binding site 1 out of 9 in the 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:62.1
occ:1.00
 OD1 A:ASP419 2.3 60.7 1.0
OE2 A:GLU321 2.3 65.3 1.0
O A:HOH720 2.3 51.6 1.0
O A:CYS288 2.3 64.9 1.0
O A:ALA417 2.3 66.1 1.0
OE1 A:GLN287 2.3 56.6 1.0
CG A:ASP419 3.5 58.5 1.0
CD A:GLN287 3.5 53.5 1.0
CD A:GLU321 3.5 62.4 1.0
C A:ALA417 3.6 63.1 1.0
C A:CYS288 3.6 61.0 1.0
CA A:ASP419 3.7 58.1 1.0
N A:ASP419 3.8 57.7 1.0
CB A:ASP419 4.2 57.9 1.0
CG A:GLN287 4.2 55.6 1.0
N A:CYS288 4.2 62.2 1.0
CA A:ALA417 4.3 59.9 1.0
CB A:GLN287 4.3 54.5 1.0
CG A:GLU321 4.4 62.4 1.0
C A:SER418 4.4 61.1 1.0
OD2 A:ASP419 4.4 59.4 1.0
OE1 A:GLU321 4.4 65.7 1.0
NE2 A:GLN287 4.4 52.7 1.0
N A:GLY289 4.5 62.5 1.0
CA A:CYS288 4.5 62.3 1.0
CA A:GLY289 4.5 65.8 1.0
N A:SER418 4.6 63.8 1.0
CB A:ALA417 4.7 61.2 1.0
CB A:CYS422 4.8 53.6 1.0
CE2 A:PHE436 4.8 47.6 1.0
O A:GLY289 4.9 78.9 1.0
CA A:SER418 4.9 62.1 1.0
O A:SER418 5.0 64.3 1.0
C A:GLN287 5.0 59.2 1.0

Calcium binding site 2 out of 9 in 6u7l

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Calcium binding site 2 out of 9 in the 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:92.1
occ:1.00
 O A:HOH735 2.3 73.4 1.0
O A:GLN507 2.3 63.5 1.0
O D:HOH720 3.2 93.8 1.0
C A:GLN507 3.5 52.6 1.0
CA A:GLN507 4.0 49.1 1.0
OE1 D:GLU256 4.2 59.4 1.0
OG D:SER253 4.4 57.3 1.0
CE3 A:TRP508 4.6 79.7 1.0
CB A:GLN507 4.6 47.0 1.0
N A:TRP508 4.6 52.6 1.0
CZ3 A:TRP508 4.7 88.2 1.0
O A:ASP506 4.9 46.4 1.0
CA A:TRP508 4.9 49.4 1.0

Calcium binding site 3 out of 9 in 6u7l

Go back to Calcium Binding Sites List in 6u7l
Calcium binding site 3 out of 9 in the 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:63.4
occ:0.50
 O A:GLU479 2.3 75.0 1.0
C A:GLU479 3.5 71.9 1.0
CA A:GLU479 4.2 76.3 1.0
CG A:GLU479 4.3 91.3 1.0
N A:GLU480 4.6 66.5 1.0
OE1 A:GLU484 4.8 79.3 1.0
CB A:GLU479 4.8 79.8 1.0
CA A:GLU480 4.9 63.9 1.0
CG A:GLU480 5.0 64.6 1.0

Calcium binding site 4 out of 9 in 6u7l

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Calcium binding site 4 out of 9 in the 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:69.3
occ:1.00
 O B:HOH710 2.3 69.4 1.0
OE2 B:GLU321 2.3 76.9 1.0
OD1 B:ASP419 2.3 75.5 1.0
O B:CYS288 2.3 77.0 1.0
OE1 B:GLN287 2.3 65.1 1.0
O B:ALA417 2.3 80.8 1.0
CG B:ASP419 3.5 69.4 1.0
CD B:GLN287 3.5 64.0 1.0
CD B:GLU321 3.5 74.9 1.0
C B:ALA417 3.6 76.2 1.0
C B:CYS288 3.6 76.2 1.0
CA B:ASP419 3.7 64.3 1.0
N B:ASP419 3.7 64.7 1.0
CB B:ASP419 4.1 65.9 1.0
N B:CYS288 4.2 71.2 1.0
CG B:GLN287 4.2 64.6 1.0
OH A:TYR177 4.2 0.5 1.0
CA B:ALA417 4.3 73.7 1.0
CB B:GLN287 4.3 64.4 1.0
C B:SER418 4.3 65.7 1.0
CG B:GLU321 4.4 76.1 1.0
OD2 B:ASP419 4.4 74.0 1.0
OE1 B:GLU321 4.4 81.8 1.0
NE2 B:GLN287 4.4 60.5 1.0
CA B:CYS288 4.5 76.3 1.0
N B:GLY289 4.5 77.9 1.0
CA B:GLY289 4.6 79.3 1.0
N B:SER418 4.6 73.1 1.0
CB B:ALA417 4.7 77.7 1.0
CB B:CYS422 4.7 62.7 1.0
CE2 B:PHE436 4.8 54.8 1.0
CZ A:TYR177 4.9 0.1 1.0
CA B:SER418 4.9 69.5 1.0
O B:GLY289 4.9 85.9 1.0
O B:SER418 4.9 67.0 1.0
C B:GLN287 5.0 65.8 1.0

Calcium binding site 5 out of 9 in 6u7l

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Calcium binding site 5 out of 9 in the 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:0.1
occ:1.00
 O B:GLU479 2.3 0.8 1.0
C B:GLU479 3.6 98.9 1.0
OE1 B:GLU484 4.3 90.0 1.0
CA B:GLU479 4.5 0.6 1.0
N B:GLU480 4.5 92.4 1.0
CG B:GLU479 4.5 0.6 1.0
CA B:GLU480 4.6 88.2 1.0
CG B:GLU480 4.7 89.4 1.0
OE2 B:GLU484 4.7 97.4 1.0
CD B:GLU484 4.9 91.5 1.0

Calcium binding site 6 out of 9 in 6u7l

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Calcium binding site 6 out of 9 in the 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:52.0
occ:1.00
 OE2 C:GLU321 2.3 58.4 1.0
O C:HOH708 2.3 47.6 1.0
OD1 C:ASP419 2.3 52.9 1.0
O C:ALA417 2.3 61.1 1.0
O C:CYS288 2.3 63.7 1.0
OE1 C:GLN287 2.3 59.3 1.0
CG C:ASP419 3.5 50.4 1.0
CD C:GLN287 3.5 52.0 1.0
C C:ALA417 3.5 57.2 1.0
CD C:GLU321 3.5 60.6 1.0
C C:CYS288 3.6 59.4 1.0
CA C:ASP419 3.7 50.5 1.0
N C:ASP419 3.7 51.3 1.0
CB C:ASP419 4.1 49.3 1.0
N C:CYS288 4.2 58.4 1.0
CG C:GLN287 4.2 50.9 1.0
CA C:ALA417 4.2 56.8 1.0
CB C:GLN287 4.3 51.1 1.0
C C:SER418 4.3 53.2 1.0
CG C:GLU321 4.4 57.4 1.0
OD2 C:ASP419 4.4 54.7 1.0
OE1 C:GLU321 4.4 65.8 1.0
NE2 C:GLN287 4.4 50.7 1.0
N C:GLY289 4.5 62.3 1.0
CA C:CYS288 4.5 60.3 1.0
CA C:GLY289 4.6 63.3 1.0
N C:SER418 4.6 58.7 1.0
CB C:ALA417 4.6 58.8 1.0
OH D:TYR177 4.7 0.9 1.0
CB C:CYS422 4.7 53.7 1.0
CE2 C:PHE436 4.8 45.0 1.0
O C:GLY289 4.8 68.7 1.0
CA C:SER418 4.9 58.8 1.0
O C:SER418 4.9 52.5 1.0
C C:GLN287 5.0 53.9 1.0

Calcium binding site 7 out of 9 in 6u7l

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Calcium binding site 7 out of 9 in the 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca602

b:99.3
occ:1.00
 O C:HOH705 2.3 93.4 1.0
O C:HOH746 2.3 91.2 1.0
O C:HOH743 2.3 85.9 1.0
O C:HOH749 2.3 80.8 1.0
O C:GLU479 2.3 84.0 1.0
C C:GLU479 3.5 67.2 1.0
OE1 C:GLU484 3.8 56.8 1.0
OE2 C:GLU484 4.3 60.8 1.0
N C:GLU480 4.3 64.6 1.0
CA C:GLU480 4.3 59.6 1.0
CA C:GLU479 4.4 67.7 1.0
CD C:GLU484 4.5 55.6 1.0
O C:GLY478 4.8 63.6 1.0
CG C:GLU480 4.9 63.8 1.0

Calcium binding site 8 out of 9 in 6u7l

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Calcium binding site 8 out of 9 in the 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:65.6
occ:1.00
 O D:HOH702 2.3 77.1 1.0
O D:ALA417 2.3 72.9 1.0
O D:CYS288 2.3 82.0 1.0
OE2 D:GLU321 2.3 73.8 1.0
OD1 D:ASP419 2.3 69.5 1.0
OE1 D:GLN287 2.3 66.7 1.0
CG D:ASP419 3.5 65.0 1.0
CD D:GLN287 3.5 61.8 1.0
C D:ALA417 3.5 70.0 1.0
CD D:GLU321 3.6 72.4 1.0
C D:CYS288 3.6 80.8 1.0
CA D:ASP419 3.7 63.1 1.0
N D:ASP419 3.7 64.8 1.0
CB D:ASP419 4.1 64.3 1.0
N D:CYS288 4.2 74.1 1.0
CG D:GLN287 4.2 63.1 1.0
CA D:ALA417 4.2 68.5 1.0
CB D:GLN287 4.3 63.0 1.0
C D:SER418 4.3 66.5 1.0
CG D:GLU321 4.4 70.3 1.0
OD2 D:ASP419 4.4 69.6 1.0
NE2 D:GLN287 4.4 62.6 1.0
OE1 D:GLU321 4.4 82.0 1.0
N D:GLY289 4.5 85.3 1.0
CA D:CYS288 4.5 80.2 1.0
CA D:GLY289 4.5 91.0 1.0
N D:SER418 4.6 70.7 1.0
CB D:ALA417 4.7 71.2 1.0
CB D:CYS422 4.7 58.8 1.0
CE2 D:PHE436 4.8 53.9 1.0
O D:GLY289 4.8 94.5 1.0
CA D:SER418 4.9 69.3 1.0
O D:SER418 4.9 68.7 1.0
C D:ASP419 5.0 61.3 1.0
C D:GLN287 5.0 63.1 1.0

Calcium binding site 9 out of 9 in 6u7l

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Calcium binding site 9 out of 9 in the 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca602

b:0.3
occ:1.00
 O D:HOH732 2.3 80.7 1.0
O D:HOH709 2.3 68.9 1.0
O D:GLU479 2.3 87.0 1.0
O D:HOH723 2.3 75.9 1.0
C D:GLU479 3.5 81.8 1.0
CA D:GLU479 4.2 87.6 1.0
N D:GLU480 4.6 78.1 1.0
CB D:GLU479 4.8 88.2 1.0
OE1 D:GLU484 4.8 79.3 1.0
CA D:GLU480 4.9 76.5 1.0
CG D:GLU480 4.9 81.3 1.0

Reference:

G.Minasov, L.Shuvalova, Z.Wawrzak, I.Dubrovska, O.Kiryukhina, M.Endres, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid). 2.75 Angstrom Crystal Structure of Galactarate Dehydratase From Escherichia Coli. To Be Published.
Page generated: Tue Jul 16 15:47:12 2024

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