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Sodium in PDB 5tr9: Crystal Structure of A Ferredoxin Nadp+ Reductase From Neisseria Gonorrhoeae with Bound Fad

Protein crystallography data

The structure of Crystal Structure of A Ferredoxin Nadp+ Reductase From Neisseria Gonorrhoeae with Bound Fad, PDB code: 5tr9 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.06 / 1.65
Space group I 21 3
Cell size a, b, c (Å), α, β, γ (°) 163.010, 163.010, 163.010, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 16.3

Other elements in 5tr9:

The structure of Crystal Structure of A Ferredoxin Nadp+ Reductase From Neisseria Gonorrhoeae with Bound Fad also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 28 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Ferredoxin Nadp+ Reductase From Neisseria Gonorrhoeae with Bound Fad (pdb code 5tr9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of A Ferredoxin Nadp+ Reductase From Neisseria Gonorrhoeae with Bound Fad, PDB code: 5tr9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5tr9

Go back to Sodium Binding Sites List in 5tr9
Sodium binding site 1 out of 2 in the Crystal Structure of A Ferredoxin Nadp+ Reductase From Neisseria Gonorrhoeae with Bound Fad


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 A Ferredoxin Nadp+ Reductase From Neisseria Gonorrhoeae with Bound Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na318

b:29.3
occ:1.00
O B:ALA108 2.4 18.1 1.0
O B:HOH588 2.4 31.2 1.0
O B:HOH629 2.4 31.8 1.0
O B:HOH639 2.4 40.0 1.0
O B:HOH600 2.4 32.8 1.0
ND2 B:ASN107 2.4 25.0 1.0
CG B:ASN107 3.3 29.2 1.0
OD1 B:ASN107 3.5 38.2 1.0
C B:ALA108 3.6 15.4 1.0
O B:HOH422 4.2 41.2 1.0
O B:HOH529 4.3 26.8 1.0
O B:HOH696 4.3 35.6 1.0
N B:ALA108 4.3 17.4 1.0
O B:HOH610 4.3 23.4 1.0
N B:THR109 4.5 15.2 1.0
CA B:THR109 4.5 18.8 1.0
CA B:ALA108 4.5 15.6 1.0
CB B:ASN107 4.7 24.1 1.0
NE2 B:GLN49 4.8 17.8 1.0
O B:HOH539 4.8 32.0 1.0
C B:ASN107 4.9 20.1 1.0

Sodium binding site 2 out of 2 in 5tr9

Go back to Sodium Binding Sites List in 5tr9
Sodium binding site 2 out of 2 in the Crystal Structure of A Ferredoxin Nadp+ Reductase From Neisseria Gonorrhoeae with Bound Fad


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 A Ferredoxin Nadp+ Reductase From Neisseria Gonorrhoeae with Bound Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na319

b:35.3
occ:1.00
O B:HOH594 2.3 30.0 1.0
O B:GLY199 2.3 25.6 0.6
O B:HOH587 2.4 39.9 1.0
O B:ASN196 2.4 31.4 0.6
OG B:SER201 2.5 24.6 0.2
OG B:SER201 2.5 24.2 0.8
O B:HOH630 2.5 50.3 1.0
C B:ASN196 3.5 27.3 0.6
C B:GLY199 3.6 26.7 0.6
CB B:SER201 3.6 22.4 0.8
N B:SER201 3.7 21.2 1.0
CB B:SER201 3.8 23.2 0.2
N B:ASN196 4.1 33.6 0.6
O B:GLY199 4.1 25.8 0.4
C B:LEU200 4.2 16.6 0.6
CA B:SER201 4.2 20.4 0.8
CA B:ASN196 4.2 30.7 0.6
CA B:SER201 4.3 20.8 0.2
O B:ASN196 4.3 31.9 0.4
CA B:LEU200 4.3 19.8 0.6
N B:GLY199 4.4 27.8 0.6
N B:LEU200 4.4 20.9 0.6
O B:HOH534 4.4 22.6 1.0
CB B:ASN196 4.4 31.1 0.6
O B:SER201 4.5 22.2 1.0
C B:LEU200 4.5 16.8 0.4
N B:PRO197 4.5 28.3 0.6
CA B:GLY199 4.6 24.4 0.6
CA B:LEU200 4.6 18.9 0.4
CA B:PRO197 4.7 34.0 0.6
C B:SER201 4.8 19.1 1.0
C B:PRO197 4.9 35.7 0.6
O B:LEU200 5.0 19.2 0.6

Reference:

S.J.Mayclin, D.Fox Iii, D.D.Lorimer, T.E.Edwards. Crystal Structure of A Ferredoxin Nadp+ Reductase From Neisseria Gonorrhoeae with Bound Fad To Be Published.
Page generated: Tue Dec 15 11:38:03 2020

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