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Sodium in PDB 5tpi: 1.47 Angstrom Crystal Structure of the C-Terminal Substrate Binding Domain of Lysr Family Transcriptional Regulator From Klebsiella Pneumoniae.

Protein crystallography data

The structure of 1.47 Angstrom Crystal Structure of the C-Terminal Substrate Binding Domain of Lysr Family Transcriptional Regulator From Klebsiella Pneumoniae., PDB code: 5tpi was solved by G.Minasov, Z.Wawrzak, J.Sandoval, E.Evdokimova, S.Grimshaw, K.Kwon, A.Savchenko, W.F.Anderson, 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) 26.35 / 1.47
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 93.756, 40.228, 68.211, 90.00, 129.41, 90.00
R / Rfree (%) 13.7 / 18.1

Other elements in 5tpi:

The structure of 1.47 Angstrom Crystal Structure of the C-Terminal Substrate Binding Domain of Lysr Family Transcriptional Regulator From Klebsiella Pneumoniae. also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.47 Angstrom Crystal Structure of the C-Terminal Substrate Binding Domain of Lysr Family Transcriptional Regulator From Klebsiella Pneumoniae. (pdb code 5tpi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 1.47 Angstrom Crystal Structure of the C-Terminal Substrate Binding Domain of Lysr Family Transcriptional Regulator From Klebsiella Pneumoniae., PDB code: 5tpi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5tpi

Go back to Sodium Binding Sites List in 5tpi
Sodium binding site 1 out of 2 in the 1.47 Angstrom Crystal Structure of the C-Terminal Substrate Binding Domain of Lysr Family Transcriptional Regulator From Klebsiella Pneumoniae.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.47 Angstrom Crystal Structure of the C-Terminal Substrate Binding Domain of Lysr Family Transcriptional Regulator From Klebsiella Pneumoniae. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:22.8
occ:0.50
O A:HOH569 2.3 27.9 1.0
O A:SER241 2.4 17.4 1.0
O A:HOH506 2.7 31.5 1.0
C A:SER241 3.4 15.5 1.0
O A:HOH600 3.8 42.2 1.0
CA A:SER241 3.9 16.1 1.0
N A:MET242 4.4 16.0 0.5
N A:MET242 4.5 15.2 0.5
CB A:SER241 4.6 16.8 1.0
O A:HOH591 4.7 23.4 1.0
O A:HOH485 4.7 23.3 1.0
CD A:PRO243 4.8 16.6 1.0
CA A:MET242 4.8 15.2 0.5
CA A:MET242 4.9 13.5 0.5
O A:GLU240 4.9 18.7 1.0
N A:PRO243 5.0 15.5 1.0

Sodium binding site 2 out of 2 in 5tpi

Go back to Sodium Binding Sites List in 5tpi
Sodium binding site 2 out of 2 in the 1.47 Angstrom Crystal Structure of the C-Terminal Substrate Binding Domain of Lysr Family Transcriptional Regulator From Klebsiella Pneumoniae.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.47 Angstrom Crystal Structure of the C-Terminal Substrate Binding Domain of Lysr Family Transcriptional Regulator From Klebsiella Pneumoniae. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:44.9
occ:1.00
O A:HOH509 2.3 32.9 1.0
O A:HOH464 2.3 42.5 1.0
O A:HOH522 2.3 35.1 1.0
O A:HOH503 2.4 31.7 1.0
O A:ILE118 2.7 23.8 1.0
O A:HOH436 3.4 54.2 1.0
OD1 A:ASN112 3.5 21.0 1.0
C A:ILE118 3.7 22.5 1.0
CA A:HIS119 3.8 19.9 1.0
O A:PRO116 3.9 32.3 1.0
O A:HOH445 4.0 28.9 1.0
N A:HIS119 4.2 21.8 1.0
N A:LEU120 4.5 18.3 1.0
C A:PRO116 4.6 28.4 1.0
O A:TYR115 4.6 22.9 1.0
CG A:ASN112 4.7 19.2 1.0
CB A:HIS119 4.7 23.0 1.0
C A:HIS119 4.7 18.3 1.0
NE2 A:GLN88 4.7 60.5 1.0
N A:ILE118 4.8 23.3 1.0
O A:HOH510 4.8 38.0 1.0
ND1 A:HIS119 4.9 28.3 1.0
CA A:ILE118 4.9 22.5 1.0
CA A:PRO116 5.0 27.4 1.0
O A:ASN112 5.0 19.7 1.0

Reference:

G.Minasov, Z.Wawrzak, J.Sandoval, E.Evdokimova, S.Grimshaw, K.Kwon, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 1.47 Angstrom Crystal Structure of the C-Terminal Substrate Binding Domain of Lysr Family Transcriptional Regulator From Klebsiella Pneumoniae. To Be Published.
Page generated: Tue Dec 15 11:38:00 2020

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