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

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

All present enzymatic activity of Crystal Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes:
1.2.1.5;

Protein crystallography data

The structure of Crystal Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes, PDB code: 2amf 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 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 171.822, 109.960, 84.158, 90.00, 95.38, 90.00
R / Rfree (%) 17.3 / 21.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes (pdb code 2amf). 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 Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes, PDB code: 2amf:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 2amf

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Sodium binding site 1 out of 5 in the Crystal Structure 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 Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na850

b:33.6
occ:1.00
 O A:GLY89 2.2 33.6 1.0
O A:HOH4412 2.4 36.7 1.0
O A:HOH4334 2.5 27.7 1.0
O A:LEU256 2.5 37.5 1.0
O A:ALA253 2.6 29.7 1.0
O A:LYS254 2.8 32.0 1.0
C A:GLY89 3.2 33.6 1.0
C A:LYS254 3.3 32.6 1.0
CA A:GLY89 3.4 33.0 1.0
C A:LEU256 3.5 37.5 1.0
CA A:LYS254 3.6 32.1 1.0
C A:ALA253 3.6 29.6 1.0
NH1 A:ARG94 3.9 47.3 1.0
O A:HOH4488 3.9 49.3 1.0
N A:LEU256 4.0 36.2 1.0
N A:LYS254 4.0 30.3 1.0
O A:HOH4343 4.1 51.5 1.0
CA A:LEU256 4.2 36.8 1.0
N A:SER255 4.3 33.6 1.0
N A:ILE90 4.4 34.1 1.0
OXT A:LEU256 4.4 38.2 1.0
CB A:LEU256 4.5 36.7 1.0
C A:SER255 4.6 35.6 1.0
O A:HOH4403 4.7 34.7 1.0
OD2 A:ASP156 4.7 30.8 1.0
N A:GLY89 4.8 32.8 1.0
CB A:LYS254 4.9 32.2 1.0
CA A:SER255 4.9 34.5 1.0
CA A:ALA253 5.0 28.3 1.0
CA A:ILE90 5.0 34.1 1.0

Sodium binding site 2 out of 5 in 2amf

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Sodium binding site 2 out of 5 in the Crystal Structure 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 Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na851

b:35.6
occ:1.00
 O B:GLY89 2.2 34.0 1.0
O B:LEU256 2.2 36.9 1.0
O B:HOH4335 2.5 28.6 1.0
O B:HOH4394 2.5 45.0 1.0
O B:ALA253 2.6 30.3 1.0
O B:LYS254 2.8 34.1 1.0
C B:GLY89 3.2 33.8 1.0
C B:LEU256 3.4 37.2 1.0
C B:LYS254 3.4 33.7 1.0
CA B:GLY89 3.4 33.2 1.0
CA B:LYS254 3.6 32.9 1.0
C B:ALA253 3.6 30.1 1.0
NH1 B:ARG94 3.7 46.7 1.0
N B:LYS254 4.0 30.9 1.0
O B:HOH4429 4.1 49.5 1.0
O B:HOH4362 4.1 51.2 1.0
N B:LEU256 4.1 36.7 1.0
CA B:LEU256 4.2 37.0 1.0
OXT B:LEU256 4.2 37.7 1.0
N B:ILE90 4.4 33.9 1.0
N B:SER255 4.5 34.4 1.0
CB B:LEU256 4.5 36.7 1.0
C B:SER255 4.6 36.2 1.0
OD2 B:ASP156 4.6 31.6 1.0
O B:HOH4387 4.7 36.6 1.0
N B:GLY89 4.9 32.9 1.0
CZ B:ARG94 4.9 48.4 1.0
CB B:LYS254 4.9 33.0 1.0
CA B:ALA253 5.0 29.3 1.0

Sodium binding site 3 out of 5 in 2amf

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Sodium binding site 3 out of 5 in the Crystal Structure 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 Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na852

b:39.0
occ:1.00
 O C:LEU256 2.2 37.7 1.0
O C:GLY89 2.4 33.9 1.0
O C:HOH4411 2.5 45.4 1.0
O C:ALA253 2.5 30.1 1.0
O C:LYS254 2.7 33.4 1.0
O C:HOH4332 2.8 40.3 1.0
C C:LYS254 3.3 33.5 1.0
C C:GLY89 3.3 34.2 1.0
C C:LEU256 3.4 37.4 1.0
CA C:LYS254 3.6 32.7 1.0
CA C:GLY89 3.6 33.8 1.0
C C:ALA253 3.6 30.1 1.0
N C:LEU256 4.0 36.4 1.0
NH1 C:ARG94 4.0 46.5 1.0
N C:LYS254 4.0 31.4 1.0
CA C:LEU256 4.2 36.8 1.0
N C:SER255 4.2 33.9 1.0
OXT C:LEU256 4.3 37.9 1.0
C C:SER255 4.4 35.8 1.0
O C:HOH4426 4.5 43.7 1.0
O C:HOH4377 4.5 53.5 1.0
CB C:LEU256 4.5 36.5 1.0
N C:ILE90 4.6 34.8 1.0
OD2 C:ASP156 4.6 29.5 1.0
CA C:SER255 4.8 35.0 1.0
CA C:ALA253 4.9 29.2 1.0
CB C:LYS254 5.0 33.0 1.0
CZ C:ARG94 5.0 47.8 1.0

Sodium binding site 4 out of 5 in 2amf

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Sodium binding site 4 out of 5 in the Crystal Structure 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 Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na853

b:33.9
occ:1.00
 O D:GLY89 2.2 33.3 1.0
O D:HOH4486 2.3 29.9 1.0
O D:LEU256 2.4 36.4 1.0
O D:HOH4485 2.5 36.8 1.0
O D:ALA253 2.6 30.2 1.0
O D:LYS254 2.9 33.3 1.0
C D:GLY89 3.2 33.5 1.0
C D:LYS254 3.4 33.3 1.0
NH2 D:ARG94 3.4 48.9 1.0
CA D:GLY89 3.5 32.8 1.0
C D:LEU256 3.6 36.9 1.0
CA D:LYS254 3.6 32.8 1.0
C D:ALA253 3.7 30.1 1.0
O D:HOH4452 3.8 46.1 1.0
O D:HOH4475 4.0 55.8 1.0
N D:LYS254 4.1 31.3 1.0
N D:LEU256 4.1 35.9 1.0
CA D:LEU256 4.3 36.6 1.0
N D:SER255 4.4 33.9 1.0
N D:ILE90 4.4 33.8 1.0
OXT D:LEU256 4.5 37.3 1.0
CZ D:ARG94 4.6 48.1 1.0
C D:SER255 4.6 35.9 1.0
O D:HOH4374 4.7 35.9 1.0
OD2 D:ASP156 4.7 29.5 1.0
CB D:LEU256 4.7 36.1 1.0
O D:HOH4453 4.9 47.5 1.0
CB D:LYS254 5.0 32.9 1.0
CA D:ILE90 5.0 34.3 1.0
N D:GLY89 5.0 32.8 1.0
CA D:ALA253 5.0 29.2 1.0

Sodium binding site 5 out of 5 in 2amf

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Sodium binding site 5 out of 5 in the Crystal Structure 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 Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na854

b:32.3
occ:1.00
 O E:LEU256 2.2 35.5 1.0
O E:HOH4412 2.4 29.1 1.0
O E:GLY89 2.4 33.3 1.0
O E:ALA253 2.6 29.6 1.0
O E:HOH4419 2.6 29.6 1.0
O E:LYS254 2.8 33.1 1.0
C E:LYS254 3.3 33.0 1.0
C E:GLY89 3.3 33.0 1.0
C E:LEU256 3.4 36.6 1.0
CA E:GLY89 3.5 32.7 1.0
CA E:LYS254 3.6 32.2 1.0
NH1 E:ARG94 3.6 45.9 1.0
C E:ALA253 3.7 29.7 1.0
N E:LEU256 3.9 35.9 1.0
O E:HOH4422 3.9 38.0 1.0
CA E:LEU256 4.1 36.3 1.0
N E:LYS254 4.1 30.5 1.0
N E:SER255 4.2 33.4 1.0
OXT E:LEU256 4.3 36.7 1.0
O E:HOH4356 4.3 41.0 1.0
C E:SER255 4.3 35.5 1.0
O E:HOH4417 4.4 49.1 1.0
CB E:LEU256 4.5 36.0 1.0
N E:ILE90 4.6 33.2 1.0
CA E:SER255 4.8 34.5 1.0
OD2 E:ASP156 4.8 30.7 1.0
CZ E:ARG94 4.9 47.4 1.0
O E:SER255 4.9 36.0 1.0
CB E:LYS254 5.0 32.9 1.0
N E:GLY89 5.0 32.8 1.0
CA E:ALA253 5.0 28.7 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 01:52:17 2024

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