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Sodium in PDB 5iqx: 1.05A Resolution Structure of Holo Hasap (R33A) From Pseudomonas Aeruginosa

Protein crystallography data

The structure of 1.05A Resolution Structure of Holo Hasap (R33A) From Pseudomonas Aeruginosa, PDB code: 5iqx was solved by R.Kumar, S.Lovell, K.P.Battaile, H.Yao, M.Rivera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.53 / 1.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 34.167, 47.161, 101.374, 90.00, 90.00, 90.00
R / Rfree (%) 11.3 / 12.9

Other elements in 5iqx:

The structure of 1.05A Resolution Structure of Holo Hasap (R33A) From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.05A Resolution Structure of Holo Hasap (R33A) From Pseudomonas Aeruginosa (pdb code 5iqx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 1.05A Resolution Structure of Holo Hasap (R33A) From Pseudomonas Aeruginosa, PDB code: 5iqx:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5iqx

Go back to Sodium Binding Sites List in 5iqx
Sodium binding site 1 out of 4 in the 1.05A Resolution Structure of Holo Hasap (R33A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.05A Resolution Structure of Holo Hasap (R33A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:19.9
occ:1.00
O A:HOH511 2.7 15.7 1.0
O A:HOH500 2.7 30.6 1.0
O A:GLN171 2.8 8.5 1.0
O A:HOH521 2.8 23.9 1.0
C A:GLN171 3.6 8.0 1.0
CA A:GLN171 3.7 8.5 1.0
CB A:ALA174 3.7 10.7 1.0
CB A:GLN171 3.9 9.3 1.0
N A:ALA175 3.9 9.5 1.0
CB A:ALA175 4.0 11.3 1.0
O A:HOH389 4.3 24.4 1.0
C A:ALA174 4.3 9.4 1.0
O A:HOH459 4.3 28.6 1.0
CG A:GLN171 4.4 11.0 1.0
CA A:ALA175 4.4 10.1 1.0
CA A:ALA174 4.5 9.3 1.0
O A:HOH495 4.7 31.9 1.0
N A:LEU172 4.8 7.3 1.0
CD2 A:LEU163 4.8 10.6 1.0
N A:ALA174 5.0 8.4 1.0
O A:ALA174 5.0 11.0 1.0

Sodium binding site 2 out of 4 in 5iqx

Go back to Sodium Binding Sites List in 5iqx
Sodium binding site 2 out of 4 in the 1.05A Resolution Structure of Holo Hasap (R33A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.05A Resolution Structure of Holo Hasap (R33A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:11.0
occ:1.00
OG A:SER79 2.4 14.3 1.0
O A:THR76 2.4 8.0 1.0
O A:HOH461 2.4 10.4 1.0
O A:HOH494 2.4 16.9 1.0
O A:HOH490 2.5 14.9 1.0
O A:HOH464 2.5 17.0 1.0
CB A:SER79 3.3 13.0 1.0
C A:THR76 3.3 6.9 1.0
O A:HOH529 3.6 13.3 1.0
O A:HOH526 3.8 26.1 1.0
N A:SER79 3.9 10.9 1.0
CA A:THR76 4.0 6.6 1.0
O A:HOH445 4.2 14.1 1.0
CA A:SER79 4.2 11.9 1.0
CB A:LEU77 4.2 8.2 1.0
N A:LEU77 4.3 6.4 1.0
N A:PHE78 4.3 9.1 1.0
O A:TYR75 4.4 7.0 1.0
O A:HOH507 4.4 22.4 1.0
CA A:LEU77 4.6 7.0 1.0
O A:HOH384 4.6 37.8 1.0
O A:HOH391 4.7 10.6 1.0
C A:LEU77 4.8 7.7 1.0
CB A:THR76 4.8 6.7 1.0
C A:PHE78 4.9 11.8 1.0

Sodium binding site 3 out of 4 in 5iqx

Go back to Sodium Binding Sites List in 5iqx
Sodium binding site 3 out of 4 in the 1.05A Resolution Structure of Holo Hasap (R33A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1.05A Resolution Structure of Holo Hasap (R33A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:18.3
occ:1.00
O A:HOH527 2.7 12.7 1.0
O A:HOH523 2.7 20.5 1.0
N A:ALA126 3.0 7.8 1.0
CB A:ALA126 3.2 9.7 1.0
CG2 A:ILE125 3.4 10.0 1.0
CB A:PRO124 3.6 9.4 0.6
N A:ILE125 3.6 7.5 1.0
CB A:PRO124 3.6 8.7 0.5
CA A:ALA126 3.7 8.5 1.0
C A:ILE125 4.0 7.6 1.0
C A:PRO124 4.1 7.3 1.0
CA A:ILE125 4.1 7.8 1.0
CA A:PRO124 4.3 7.8 0.6
CA A:PRO124 4.3 7.6 0.5
CB A:ILE125 4.3 8.4 1.0
CG A:PRO124 4.7 8.9 0.5
CG A:PRO124 4.8 9.7 0.6
O A:PRO124 4.9 7.3 1.0
C A:ALA126 5.0 8.1 1.0

Sodium binding site 4 out of 4 in 5iqx

Go back to Sodium Binding Sites List in 5iqx
Sodium binding site 4 out of 4 in the 1.05A Resolution Structure of Holo Hasap (R33A) From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1.05A Resolution Structure of Holo Hasap (R33A) From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:37.9
occ:1.00
O A:HOH393 2.7 12.8 1.0
O A:HOH525 2.7 31.4 1.0
NZ A:LYS157 3.0 13.1 0.5
O A:HOH478 3.4 33.3 1.0
CG A:LYS157 3.6 9.1 0.5
CE A:LYS157 3.6 10.6 0.5
CG A:LYS157 3.8 10.2 0.5
CD A:LYS157 3.8 9.9 0.5
CD A:LYS157 3.9 11.9 0.5
CE A:LYS157 4.0 12.1 0.5
O A:HOH524 4.3 11.9 1.0
CA A:ALA158 4.3 10.1 1.0
N A:ALA158 4.3 8.7 1.0
CB A:LYS157 4.4 8.3 0.5
C A:LYS157 4.5 8.6 1.0
CB A:LYS157 4.5 8.2 0.5
O A:LYS157 4.6 9.7 1.0
NZ A:LYS157 4.6 11.2 0.5
O A:HOH387 4.6 23.3 1.0
CB A:ALA158 4.7 11.3 1.0
O A:ALA154 4.9 7.9 1.0

Reference:

R.Kumar, Y.Qi, H.Matsumura, S.Lovell, H.Yao, K.P.Battaile, W.Im, P.Moenne-Loccoz, M.Rivera. Replacing Arginine 33 For Alanine in the Hemophore Hasa From Pseudomonas Aeruginosa Causes Closure of the H32 Loop in the Apo-Protein. Biochemistry V. 55 2622 2016.
ISSN: ISSN 0006-2960
PubMed: 27074415
DOI: 10.1021/ACS.BIOCHEM.6B00239
Page generated: Tue Dec 15 11:06:32 2020

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