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Sodium in PDB 5ibx: 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae

Enzymatic activity of 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae

All present enzymatic activity of 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae:
5.3.1.1;

Protein crystallography data

The structure of 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae, PDB code: 5ibx was solved by G.Minasov, L.Shuvalova, I.Dubrovska, K.Flores, S.Shatsman, K.Kwon, 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) 29.69 / 1.65
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 78.845, 84.351, 92.463, 75.43, 65.97, 62.03
R / Rfree (%) 19.6 / 23.2

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Sodium atom in the 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae (pdb code 5ibx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 13 binding sites of Sodium where determined in the 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae, PDB code: 5ibx:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 13 in 5ibx

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Sodium binding site 1 out of 13 in the 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:19.8
occ:1.00
 O A:HOH606 2.3 22.3 1.0
O A:VAL229 2.3 18.3 1.0
O A:MET224 2.4 19.6 1.0
O A:HOH453 2.4 23.9 1.0
O A:HOH618 2.4 40.9 1.0
O A:CME226 2.5 20.2 1.0
C A:VAL229 3.5 18.0 1.0
C A:MET224 3.5 20.6 1.0
C A:CME226 3.7 20.6 1.0
O A:HOH600 3.7 39.6 1.0
C A:ALA225 4.0 19.7 1.0
N A:CME226 4.1 19.5 1.0
N A:VAL229 4.1 18.2 1.0
O A:PRO227 4.2 21.0 1.0
CA A:ALA225 4.3 19.8 1.0
CA A:VAL229 4.3 18.1 1.0
C A:PRO227 4.3 20.2 1.0
O A:HOH639 4.3 20.2 0.4
O A:ALA225 4.3 20.4 1.0
N A:ALA225 4.4 19.5 1.0
N A:ASP230 4.5 18.4 1.0
CA A:PRO227 4.5 21.3 1.0
CA A:MET224 4.5 20.7 1.0
N A:PRO227 4.5 21.1 1.0
OD1 A:ASP230 4.5 19.4 1.0
CB A:VAL229 4.6 18.6 1.0
CA A:CME226 4.6 20.4 1.0
CA A:ASP230 4.7 19.1 1.0
N A:ASP228 4.9 19.8 1.0
O A:HOH545 5.0 37.0 1.0

Sodium binding site 2 out of 13 in 5ibx

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Sodium binding site 2 out of 13 in the 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:21.6
occ:1.00
 O B:HOH637 2.2 25.4 1.0
O B:HOH645 2.3 28.1 1.0
O B:VAL229 2.4 18.9 1.0
O B:HOH445 2.5 21.6 1.0
O B:MET224 2.5 24.1 1.0
O B:CME226 2.7 23.1 1.0
C B:VAL229 3.6 19.4 1.0
C B:MET224 3.7 23.6 1.0
C B:CME226 3.8 23.0 1.0
O B:HOH714 3.8 45.7 1.0
O B:HOH650 4.2 31.6 1.0
N B:VAL229 4.2 19.5 1.0
O B:HOH505 4.2 20.5 1.0
O B:PRO227 4.3 21.3 1.0
C B:ALA225 4.3 24.6 1.0
N B:CME226 4.3 23.9 1.0
C B:PRO227 4.3 21.7 1.0
CA B:VAL229 4.4 19.1 1.0
CA B:PRO227 4.4 22.5 1.0
CE B:MET224 4.5 24.3 1.0
N B:PRO227 4.5 22.7 1.0
CA B:MET224 4.5 23.7 1.0
N B:ASP230 4.5 18.4 1.0
OD1 B:ASP230 4.5 19.0 1.0
O B:HOH681 4.6 27.1 1.0
N B:ALA225 4.6 24.0 1.0
O B:ALA225 4.6 25.4 1.0
CA B:ALA225 4.7 24.5 1.0
CA B:ASP230 4.7 18.6 1.0
CA B:CME226 4.7 24.5 1.0
CB B:VAL229 4.7 19.9 1.0
O B:HOH717 4.9 42.9 1.0
N B:ASP228 4.9 20.4 1.0

Sodium binding site 3 out of 13 in 5ibx

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Sodium binding site 3 out of 13 in the 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:25.4
occ:1.00
 O B:HOH659 2.3 25.4 1.0
O B:HOH629 2.3 29.6 1.0
O C:HOH577 2.3 23.2 1.0
O C:HOH599 2.4 27.6 1.0
O B:ASP198 2.4 17.3 1.0
O C:HOH511 2.5 13.6 1.0
C B:ASP198 3.5 17.2 1.0
CA B:ASP198 3.9 17.6 1.0
ND1 C:HIS104 4.1 17.4 1.0
CB B:ASP198 4.2 17.8 1.0
O C:ASP101 4.2 16.1 1.0
O B:HOH715 4.2 34.0 1.0
O C:HOH659 4.3 26.4 1.0
CE1 C:HIS104 4.3 17.0 1.0
O C:HOH644 4.4 24.9 1.0
O B:HOH560 4.4 28.3 1.0
OD1 C:ASP101 4.5 15.7 1.0
N B:PHE199 4.7 16.3 1.0
CG B:ASP198 5.0 19.2 1.0
C C:ASP101 5.0 14.3 1.0
CA C:ASP101 5.0 14.6 1.0

Sodium binding site 4 out of 13 in 5ibx

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Sodium binding site 4 out of 13 in the 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:21.5
occ:1.00
 O C:MET224 2.3 26.9 1.0
O C:VAL229 2.3 21.8 1.0
O C:HOH509 2.4 21.5 1.0
O C:HOH595 2.5 24.3 1.0
O C:HOH619 2.5 21.9 1.0
O C:CYS226 2.5 24.3 1.0
C C:MET224 3.5 27.3 1.0
C C:VAL229 3.5 21.1 1.0
C C:CYS226 3.6 25.8 1.0
O C:PRO227 4.1 25.6 1.0
C C:ALA225 4.1 27.4 1.0
N C:VAL229 4.1 22.1 1.0
N C:CYS226 4.1 27.6 1.0
C C:PRO227 4.2 25.8 1.0
CA C:VAL229 4.3 21.0 1.0
CA C:PRO227 4.3 27.1 1.0
CA C:MET224 4.3 26.2 1.0
O C:ALA225 4.3 27.9 1.0
N C:PRO227 4.4 26.7 1.0
O C:HOH495 4.4 27.9 1.0
N C:ALA225 4.4 25.4 1.0
CA C:CYS226 4.5 26.7 1.0
N C:ASP230 4.5 20.7 1.0
CA C:ALA225 4.5 27.1 1.0
CE C:MET224 4.6 26.3 1.0
CB C:VAL229 4.6 21.3 1.0
OD1 C:ASP230 4.7 22.3 1.0
O C:HOH666 4.7 28.3 1.0
CA C:ASP230 4.7 21.4 1.0
N C:ASP228 4.8 24.6 1.0
O C:HOH679 4.9 27.7 0.5
O C:TYR223 4.9 24.4 1.0

Sodium binding site 5 out of 13 in 5ibx

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Sodium binding site 5 out of 13 in the 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:18.7
occ:1.00
 O C:HOH660 2.2 20.5 1.0
O C:HOH469 2.3 22.7 1.0
O C:HOH524 2.3 27.5 1.0
O C:GLY88 2.5 17.8 1.0
O C:HOH652 2.5 22.9 1.0
O C:HOH684 2.7 26.9 1.0
C C:GLY88 3.5 17.6 1.0
CA C:GLY88 3.8 18.0 1.0
O C:HOH715 3.9 27.8 1.0
OD1 C:ASP90 4.2 22.8 1.0
CD2 C:LEU52 4.3 17.4 1.0
O C:HOH439 4.4 25.5 1.0
OD2 C:ASP90 4.4 20.9 1.0
O C:HOH429 4.5 20.3 1.0
O C:HOH468 4.6 27.1 1.0
CG C:ASP90 4.6 21.0 1.0
N C:THR89 4.7 16.8 1.0
O C:HOH486 4.7 25.7 1.0
O C:HOH574 4.8 33.2 1.0

Sodium binding site 6 out of 13 in 5ibx

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Sodium binding site 6 out of 13 in the 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na303

b:31.4
occ:1.00
 O C:HOH615 2.2 18.4 0.6
O C:HOH608 2.2 35.9 1.0
O C:ALA172 2.4 16.1 1.0
O E:ALA197 2.5 18.6 1.0
O E:HOH415 2.6 16.5 1.0
O C:LYS177 3.0 18.0 1.0
C C:ALA172 3.4 15.2 1.0
C E:ALA197 3.6 17.3 1.0
O C:HOH615 3.7 16.2 0.4
O C:HOH593 3.8 23.7 1.0
O C:HOH522 3.9 23.9 1.0
O E:HOH614 4.0 36.5 1.0
C C:LYS177 4.1 18.2 1.0
OG C:SER178 4.2 27.2 1.0
N C:ILE173 4.3 14.4 1.0
CA C:SER178 4.3 20.7 1.0
CA C:ILE173 4.3 14.9 1.0
CA C:ALA172 4.3 14.7 1.0
CA E:ALA197 4.4 17.2 1.0
CB C:ALA172 4.4 15.2 1.0
N E:ASP198 4.5 16.1 1.0
CB E:ALA197 4.5 17.4 1.0
OD1 E:ASP198 4.6 17.2 1.0
CA E:ASP198 4.6 16.5 1.0
N C:GLY174 4.7 15.5 1.0
N C:SER178 4.7 19.5 1.0
O C:HOH605 4.8 34.3 1.0
CB C:SER178 4.9 24.6 1.0
O E:HOH500 4.9 34.9 1.0

Sodium binding site 7 out of 13 in 5ibx

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Sodium binding site 7 out of 13 in the 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na304

b:23.1
occ:1.00
 O C:HOH653 2.2 33.1 1.0
O C:HOH550 2.3 15.8 0.5
O C:HOH498 2.4 26.6 1.0
O C:HOH622 2.4 31.0 1.0
O C:HOH540 2.5 27.4 1.0
O C:HOH718 2.5 33.6 1.0
O C:HOH648 3.8 45.6 1.0
O C:HOH682 4.2 23.5 1.0
O C:HOH693 4.2 25.1 1.0
O C:HOH635 4.2 27.6 1.0
O E:HOH629 4.2 19.9 1.0
O E:HOH672 4.2 21.0 1.0
O C:HOH637 4.2 23.3 1.0
O C:GLY174 4.4 15.7 1.0
O C:HOH553 4.4 19.5 1.0
O C:HOH725 4.6 36.8 1.0
O C:ILE173 4.7 16.3 1.0
O E:HOH619 4.7 21.9 1.0
O C:HOH714 4.7 28.9 1.0
O C:HOH641 4.8 28.3 1.0
OD2 C:ASP101 5.0 17.0 1.0

Sodium binding site 8 out of 13 in 5ibx

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Sodium binding site 8 out of 13 in the 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:18.2
occ:1.00
 O D:HOH622 2.3 22.3 1.0
O D:VAL229 2.3 15.3 1.0
O D:MET224 2.3 19.7 1.0
O D:HOH496 2.4 19.8 1.0
O D:HOH624 2.5 32.5 1.0
O D:CME226 2.5 19.9 1.0
C D:VAL229 3.5 15.9 1.0
C D:MET224 3.5 19.8 1.0
C D:CME226 3.7 21.0 1.0
O D:HOH610 3.9 31.3 1.0
N D:VAL229 4.1 17.1 1.0
C D:ALA225 4.1 20.4 1.0
N D:CME226 4.2 19.9 1.0
O D:PRO227 4.2 19.6 1.0
CA D:VAL229 4.2 16.1 1.0
CA D:ALA225 4.3 20.0 1.0
C D:PRO227 4.3 20.1 1.0
N D:ALA225 4.3 19.2 1.0
O D:HOH492 4.4 22.2 1.0
CA D:PRO227 4.5 21.3 1.0
CA D:MET224 4.5 19.1 1.0
O D:ALA225 4.5 21.8 1.0
N D:ASP230 4.5 15.3 1.0
CB D:VAL229 4.5 16.6 1.0
O D:HOH673 4.5 34.4 1.0
OD1 D:ASP230 4.5 17.8 1.0
N D:PRO227 4.5 21.2 1.0
O D:HOH690 4.6 42.7 1.0
CA D:CME226 4.6 21.4 1.0
CA D:ASP230 4.7 16.1 1.0
N D:ASP228 4.9 19.7 1.0

Sodium binding site 9 out of 13 in 5ibx

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Sodium binding site 9 out of 13 in the 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na301

b:19.3
occ:1.00
 O E:VAL229 2.3 17.8 1.0
O E:HOH618 2.3 20.7 1.0
O E:MET224 2.3 19.1 1.0
O E:HOH616 2.4 34.5 1.0
O E:CME226 2.4 21.1 1.0
O E:HOH434 2.6 20.8 1.0
C E:VAL229 3.5 18.0 1.0
C E:MET224 3.5 20.2 1.0
C E:CME226 3.5 21.9 1.0
N E:CME226 3.9 23.6 1.0
C E:ALA225 3.9 20.3 1.0
N E:VAL229 4.1 18.3 1.0
CA E:VAL229 4.2 17.8 1.0
CA E:ALA225 4.2 20.7 1.0
O E:PRO227 4.2 21.3 1.0
O E:HOH662 4.3 30.4 1.0
C E:PRO227 4.3 20.8 1.0
N E:ALA225 4.3 20.2 1.0
CA E:PRO227 4.3 21.8 1.0
O E:HOH473 4.4 25.6 1.0
N E:PRO227 4.4 21.7 1.0
CB E:VAL229 4.4 17.9 1.0
O E:ALA225 4.4 21.4 1.0
CA E:CME226 4.4 23.3 1.0
CA E:MET224 4.5 19.8 1.0
N E:ASP230 4.5 17.6 1.0
O E:HOH645 4.6 33.4 1.0
OD1 E:ASP230 4.6 18.7 1.0
CA E:ASP230 4.7 18.0 1.0
O E:HOH685 4.8 34.8 1.0
N E:ASP228 4.8 19.8 1.0

Sodium binding site 10 out of 13 in 5ibx

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Sodium binding site 10 out of 13 in the 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na301

b:26.4
occ:1.00
 O F:MET224 2.3 28.7 1.0
O F:HOH624 2.4 31.6 1.0
O F:VAL229 2.4 24.9 1.0
O F:HOH618 2.4 27.2 1.0
O F:CYS226 2.6 28.4 1.0
O F:HOH410 2.7 28.5 1.0
C F:VAL229 3.5 24.2 1.0
C F:MET224 3.5 28.6 1.0
C F:CYS226 3.7 29.8 1.0
O F:HOH419 4.1 31.5 1.0
C F:ALA225 4.1 30.9 1.0
N F:VAL229 4.1 25.0 1.0
N F:CYS226 4.2 29.9 1.0
O F:PRO227 4.3 28.8 1.0
CA F:VAL229 4.3 23.8 1.0
O F:ALA225 4.3 32.2 1.0
C F:PRO227 4.4 28.4 1.0
CA F:MET224 4.4 27.7 1.0
CA F:PRO227 4.5 30.4 1.0
N F:ALA225 4.5 30.1 1.0
N F:PRO227 4.5 30.0 1.0
N F:ASP230 4.5 23.2 1.0
CA F:ALA225 4.5 31.4 1.0
CA F:CYS226 4.6 30.5 1.0
OD1 F:ASP230 4.6 24.5 1.0
CB F:VAL229 4.6 24.5 1.0
O F:HOH670 4.7 29.9 1.0
CA F:ASP230 4.7 23.7 1.0
CE F:MET224 4.8 30.6 1.0
O F:HOH632 4.9 37.0 1.0
N F:ASP228 4.9 27.1 1.0

Reference:

G.Minasov, L.Shuvalova, I.Dubrovska, K.Flores, S.Shatsman, K.Kwon, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases. 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (Tim) From Streptococcus Pneumoniae To Be Published.
Page generated: Mon Oct 7 21:34:08 2024

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