Sodium in PDB 6nfp: 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168

Enzymatic activity of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168

All present enzymatic activity of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168:
3.5.3.1;

Protein crystallography data

The structure of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168, PDB code: 6nfp was solved by G.Minasov, Z.Wawrzak, E.Evdokimova, S.Grimshaw, K.Kwon, A.Savchenko, K.J.F.Satchell, A.Joachimiak, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.99 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.414, 143.989, 85.515, 90.00, 109.35, 90.00
R / Rfree (%) 13.9 / 16.6

Other elements in 6nfp:

The structure of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168 also contains other interesting chemical elements:

Magnesium (Mg) 12 atoms
Chlorine (Cl) 10 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168 (pdb code 6nfp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168, PDB code: 6nfp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6nfp

Go back to Sodium Binding Sites List in 6nfp
Sodium binding site 1 out of 3 in the 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:24.4
occ:1.00
 O A:ASP274 2.3 23.2 1.0
O A:HOH411 2.3 32.4 1.0
O D:ASP274 2.4 24.6 1.0
O D:HOH558 2.4 26.5 1.0
O D:HOH518 2.5 25.0 1.0
O A:HOH467 2.5 23.4 1.0
C D:ASP274 3.6 23.1 1.0
C A:ASP274 3.6 23.8 1.0
CA D:HIS275 4.2 26.9 1.0
CA A:HIS275 4.3 25.1 1.0
N D:HIS275 4.3 23.0 1.0
O D:PRO271 4.3 27.7 1.0
N A:HIS275 4.4 23.8 1.0
O A:HOH616 4.4 45.9 1.0
O A:ILE272 4.4 25.7 1.0
O D:HOH604 4.4 42.1 1.0
O A:PRO271 4.4 26.4 1.0
ND1 D:HIS275 4.4 43.2 1.0
O D:ILE272 4.5 26.1 1.0
O D:HOH522 4.5 31.9 1.0
O A:HOH545 4.5 34.0 1.0
N A:ASP274 4.6 23.2 1.0
N D:ASP274 4.6 23.7 1.0
N A:LYS276 4.6 25.1 0.4
N D:LYS276 4.6 25.1 1.0
N A:LYS276 4.6 25.2 0.6
CA A:ASP274 4.6 22.6 1.0
CA D:ASP274 4.6 23.1 1.0
CD2 A:HIS275 4.7 39.9 1.0
O A:HOH673 4.7 27.7 0.5
O D:HOH660 4.8 34.3 0.5
C D:HIS275 5.0 24.8 1.0
C A:LEU273 5.0 23.2 1.0
C A:HIS275 5.0 24.4 1.0

Sodium binding site 2 out of 3 in 6nfp

Go back to Sodium Binding Sites List in 6nfp
Sodium binding site 2 out of 3 in the 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:24.1
occ:1.00
 O C:ASP274 2.4 24.2 1.0
O B:ASP274 2.4 24.6 1.0
O C:HOH417 2.4 30.7 1.0
O C:HOH614 2.4 24.3 1.0
O B:HOH530 2.5 24.8 1.0
O C:HOH471 2.5 26.4 1.0
C B:ASP274 3.6 25.1 1.0
C C:ASP274 3.6 24.8 1.0
CA B:HIS275 4.2 25.7 0.3
CA B:HIS275 4.2 27.6 0.7
O C:HOH606 4.3 38.8 1.0
CA C:HIS275 4.3 26.8 1.0
O B:PRO271 4.3 28.0 1.0
N B:HIS275 4.3 25.0 0.7
N B:HIS275 4.3 24.5 0.3
O C:ILE272 4.4 26.9 1.0
N C:HIS275 4.4 24.3 1.0
O C:PRO271 4.4 26.2 1.0
O B:HOH594 4.4 42.1 1.0
O B:ILE272 4.5 25.8 1.0
N C:ASP274 4.5 22.7 1.0
O C:HOH564 4.6 36.4 1.0
ND1 C:HIS275 4.6 41.8 1.0
CD2 B:HIS275 4.6 36.8 0.7
O B:HOH551 4.6 29.6 1.0
N B:ASP274 4.6 24.6 1.0
N B:LYS276 4.6 25.7 1.0
N C:LYS276 4.6 26.3 1.0
CA C:ASP274 4.6 23.4 1.0
CA B:ASP274 4.6 23.7 1.0
O C:HOH652 4.7 48.6 1.0
O B:HOH659 4.9 44.6 0.7
C B:HIS275 5.0 25.3 0.3
C B:HIS275 5.0 26.0 0.7
C C:LEU273 5.0 24.0 1.0

Sodium binding site 3 out of 3 in 6nfp

Go back to Sodium Binding Sites List in 6nfp
Sodium binding site 3 out of 3 in the 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na302

b:26.3
occ:1.00
 O F:ASP274 2.4 26.9 1.0
O E:HOH520 2.4 25.8 1.0
O F:HOH411 2.4 34.8 1.0
O F:HOH514 2.4 26.2 1.0
O E:ASP274 2.4 26.1 1.0
O E:HOH591 2.4 29.6 1.0
C F:ASP274 3.6 26.9 1.0
C E:ASP274 3.6 27.2 1.0
CA F:HIS275 4.2 29.0 1.0
CA E:HIS275 4.2 29.5 1.0
O E:HOH588 4.3 49.2 1.0
N F:HIS275 4.3 26.2 1.0
N E:HIS275 4.3 26.8 1.0
O F:PRO271 4.4 29.9 1.0
O E:ILE272 4.4 28.1 1.0
O E:PRO271 4.5 28.4 1.0
O F:ILE272 4.5 30.1 1.0
O E:HOH569 4.5 45.5 1.0
O E:HOH498 4.5 33.0 1.0
CD2 E:HIS275 4.5 41.6 1.0
N F:ASP274 4.5 27.2 1.0
N E:ASP274 4.6 24.9 1.0
O F:HOH475 4.6 32.9 1.0
N F:LYS276 4.6 26.9 1.0
CA F:ASP274 4.6 24.8 1.0
N E:LYS276 4.6 27.6 1.0
CA E:ASP274 4.7 25.4 1.0
CD2 F:HIS275 4.7 40.9 1.0
O E:HOH625 4.8 49.3 1.0
O F:HOH629 4.8 47.7 1.0
C E:LEU273 5.0 25.0 1.0
C F:LEU273 5.0 26.9 1.0
C F:HIS275 5.0 27.4 1.0

Reference:

G.Minasov, Z.Wawrzak, E.Evdokimova, S.Grimshaw, K.Kwon, A.Savchenko, K.J.F.Satchell, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168 To Be Published.
Page generated: Tue Dec 15 12:38:51 2020

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