Atomistry » Sodium » PDB 1zum-2aoc » 2ahr
Atomistry »
  Sodium »
    PDB 1zum-2aoc »
      2ahr »

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

Go back to Sodium Binding Sites List in 2ahr
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

Go back to Sodium Binding Sites List in 2ahr
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

Go back to Sodium Binding Sites List in 2ahr
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

Go back to Sodium Binding Sites List in 2ahr
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

Go back to Sodium Binding Sites List in 2ahr
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: Mon Oct 7 01:52:02 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy