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Sodium in PDB 2ahr: Crystal Structures of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes

Enzymatic activity of Crystal Structures of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes

All present enzymatic activity of Crystal Structures of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes:
1.5.1.2;

Protein crystallography data

The structure of Crystal Structures of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes, PDB code: 2ahr was solved by B.Nocek, L.Lezondra, D.Holzle, A.Joachimiak, Midwest Center Forstructural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 171.631, 109.646, 84.033, 90.00, 96.08, 90.00
R / Rfree (%) 17.3 / 21

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structures of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes (pdb code 2ahr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structures of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes, PDB code: 2ahr:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 2ahr

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Sodium binding site 1 out of 5 in the Crystal Structures of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structures of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1257

b:41.4
occ:1.00
 O A:HOH1579 2.3 43.0 1.0
O A:GLY89 2.3 38.1 1.0
O A:LEU256 2.4 42.5 1.0
O A:HOH1509 2.5 36.5 1.0
O A:ALA253 2.6 35.8 1.0
O A:LYS254 2.8 38.7 1.0
C A:GLY89 3.2 38.6 1.0
C A:LYS254 3.4 38.4 1.0
C A:LEU256 3.5 42.7 1.0
CA A:GLY89 3.5 37.7 1.0
NH1 A:ARG94 3.6 59.4 1.0
CA A:LYS254 3.7 37.5 1.0
C A:ALA253 3.7 35.6 1.0
N A:LEU256 4.0 41.1 1.0
N A:LYS254 4.1 36.3 1.0
CA A:LEU256 4.2 41.7 1.0
N A:SER255 4.3 38.6 1.0
O A:HOH1517 4.4 59.4 1.0
OXT A:LEU256 4.4 43.8 1.0
C A:SER255 4.5 40.5 1.0
CB A:LEU256 4.5 42.0 1.0
N A:ILE90 4.5 39.1 1.0
O A:HOH1572 4.7 44.1 1.0
CA A:SER255 4.9 40.0 1.0
OD2 A:ASP156 4.9 36.1 1.0
CZ A:ARG94 4.9 59.0 1.0
N A:GLY89 4.9 37.2 1.0
CA A:ALA253 5.0 35.5 1.0

Sodium binding site 2 out of 5 in 2ahr

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Sodium binding site 2 out of 5 in the Crystal Structures of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structures of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1258

b:46.3
occ:1.00
 O B:GLY89 2.3 43.1 1.0
O B:HOH1566 2.4 41.6 1.0
O B:LEU256 2.4 49.9 1.0
O B:HOH1511 2.4 38.8 1.0
O B:ALA253 2.5 40.2 1.0
O B:LYS254 2.9 43.9 1.0
C B:GLY89 3.3 43.7 1.0
C B:LYS254 3.4 43.5 1.0
CA B:GLY89 3.5 43.1 1.0
C B:LEU256 3.5 49.7 1.0
C B:ALA253 3.6 39.8 1.0
NH1 B:ARG94 3.6 54.9 1.0
CA B:LYS254 3.7 42.4 1.0
O B:HOH1537 3.8 65.8 1.0
O B:HOH1593 4.0 59.6 1.0
N B:LYS254 4.1 40.6 1.0
N B:LEU256 4.1 48.4 1.0
CA B:LEU256 4.2 49.3 1.0
CB B:LEU256 4.4 49.3 1.0
OXT B:LEU256 4.4 50.1 1.0
N B:SER255 4.4 44.9 1.0
N B:ILE90 4.5 43.8 1.0
C B:SER255 4.6 47.5 1.0
OD2 B:ASP156 4.7 40.1 1.0
O B:HOH1558 4.7 47.8 1.0
CZ B:ARG94 4.8 57.4 1.0
CA B:ALA253 4.9 38.9 1.0
N B:GLY89 4.9 43.1 1.0

Sodium binding site 3 out of 5 in 2ahr

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Sodium binding site 3 out of 5 in the Crystal Structures of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structures of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1259

b:48.4
occ:1.00
 O C:GLY89 2.4 51.4 1.0
O C:HOH1574 2.4 50.9 1.0
O C:ALA253 2.5 43.0 1.0
O C:LEU256 2.5 49.5 1.0
O C:HOH1511 2.6 46.0 1.0
O C:LYS254 2.7 45.8 1.0
C C:LYS254 3.3 45.4 1.0
C C:GLY89 3.3 51.6 1.0
CA C:GLY89 3.5 51.3 1.0
C C:LEU256 3.6 49.6 1.0
C C:ALA253 3.6 42.8 1.0
CA C:LYS254 3.6 44.6 1.0
O C:HOH1549 3.8 59.4 1.0
N C:LEU256 3.9 48.2 1.0
NH1 C:ARG94 3.9 67.5 1.0
N C:LYS254 4.1 43.4 1.0
CA C:LEU256 4.1 49.1 1.0
N C:SER255 4.3 45.9 1.0
CB C:LEU256 4.4 49.0 1.0
C C:SER255 4.5 47.5 1.0
OXT C:LEU256 4.5 50.0 1.0
N C:ILE90 4.5 52.0 1.0
OD2 C:ASP156 4.7 38.6 1.0
O C:HOH1587 4.7 57.9 1.0
CA C:SER255 4.8 47.1 1.0
CA C:ALA253 4.8 42.2 1.0
CZ C:ARG94 4.9 67.7 1.0
CB C:LYS254 5.0 44.3 1.0

Sodium binding site 4 out of 5 in 2ahr

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Sodium binding site 4 out of 5 in the Crystal Structures of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structures of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1260

b:37.0
occ:1.00
 O D:HOH1656 2.3 41.7 1.0
O D:LEU256 2.3 41.9 1.0
O D:GLY89 2.4 39.9 1.0
O D:HOH1657 2.4 41.8 1.0
O D:ALA253 2.5 35.0 1.0
O D:LYS254 2.7 37.5 1.0
C D:LYS254 3.3 37.5 1.0
NH2 D:ARG94 3.3 57.7 1.0
C D:GLY89 3.3 40.0 1.0
C D:LEU256 3.4 42.3 1.0
C D:ALA253 3.5 34.2 1.0
CA D:LYS254 3.5 36.7 1.0
O D:HOH1646 3.6 72.8 1.0
CA D:GLY89 3.6 39.6 1.0
O D:HOH1625 3.7 62.4 1.0
N D:LEU256 3.9 40.8 1.0
N D:LYS254 4.0 35.2 1.0
CA D:LEU256 4.1 41.5 1.0
O D:HOH1624 4.2 65.5 1.0
N D:SER255 4.2 37.6 1.0
OXT D:LEU256 4.3 43.0 1.0
C D:SER255 4.4 40.1 1.0
CB D:LEU256 4.4 41.1 1.0
N D:ILE90 4.6 40.3 1.0
CZ D:ARG94 4.6 56.8 1.0
OD2 D:ASP156 4.8 38.4 1.0
CA D:SER255 4.8 39.4 1.0
CA D:ALA253 4.8 33.8 1.0
O D:HOH1553 4.9 38.6 1.0
O D:SER255 4.9 40.8 1.0
CB D:LYS254 4.9 36.3 1.0

Sodium binding site 5 out of 5 in 2ahr

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Sodium binding site 5 out of 5 in the Crystal Structures of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structures of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1261

b:40.5
occ:1.00
 O E:HOH1583 2.4 38.2 1.0
O E:HOH1590 2.4 39.0 1.0
O E:GLY89 2.4 41.2 1.0
O E:LEU256 2.5 43.4 1.0
O E:ALA253 2.5 35.9 1.0
O E:LYS254 2.9 39.1 1.0
C E:GLY89 3.3 41.0 1.0
C E:LYS254 3.4 38.8 1.0
CA E:GLY89 3.5 40.4 1.0
C E:LEU256 3.6 43.4 1.0
CA E:LYS254 3.6 37.6 1.0
C E:ALA253 3.6 35.2 1.0
NH1 E:ARG94 3.6 53.9 1.0
O E:HOH1593 3.9 50.4 1.0
N E:LEU256 4.0 42.0 1.0
N E:LYS254 4.0 36.1 1.0
CA E:LEU256 4.2 42.7 1.0
N E:SER255 4.3 39.3 1.0
O E:HOH1531 4.4 52.5 1.0
O E:HOH1588 4.4 61.4 1.0
C E:SER255 4.5 41.1 1.0
CB E:LEU256 4.5 42.6 1.0
OXT E:LEU256 4.5 43.7 1.0
N E:ILE90 4.6 41.6 1.0
OD2 E:ASP156 4.8 38.5 1.0
O E:HOH1556 4.8 51.1 1.0
CA E:ALA253 4.9 34.4 1.0
CZ E:ARG94 4.9 53.9 1.0
CA E:SER255 4.9 40.6 1.0
CB E:LYS254 4.9 37.6 1.0
N E:GLY89 4.9 39.8 1.0
O E:SER255 5.0 41.4 1.0

Reference:

B.Nocek, C.Chang, H.Li, L.Lezondra, D.Holzle, F.Collart, A.Joachimiak. Crystal Structures of Delta(1)-Pyrroline-5-Carboxylate Reductase From Human Pathogens Neisseria Meningitides and Streptococcus Pyogenes J.Mol.Biol. V. 354 91 2005.
ISSN: ISSN 0022-2836
PubMed: 16233902
DOI: 10.1016/J.JMB.2005.08.036
Page generated: Tue Dec 15 05:45:17 2020

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