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Sodium in PDB 6nsi: Crystal Structure of Fe(III)-Bound Ytga From Chlamydia Trachomatis

Protein crystallography data

The structure of Crystal Structure of Fe(III)-Bound Ytga From Chlamydia Trachomatis, PDB code: 6nsi was solved by Z.Luo, R.Campbell, S.L.Begg, B.Kobe, C.A.Mcdevitt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.08 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 47.841, 61.072, 105.500, 90.00, 96.95, 90.00
R / Rfree (%) 18 / 22.5

Other elements in 6nsi:

The structure of Crystal Structure of Fe(III)-Bound Ytga From Chlamydia Trachomatis also contains other interesting chemical elements:

Iron (Fe) 1 atom
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Fe(III)-Bound Ytga From Chlamydia Trachomatis (pdb code 6nsi). 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 Fe(III)-Bound Ytga From Chlamydia Trachomatis, PDB code: 6nsi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6nsi

Go back to Sodium Binding Sites List in 6nsi
Sodium binding site 1 out of 2 in the Crystal Structure of Fe(III)-Bound Ytga From Chlamydia Trachomatis


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 Fe(III)-Bound Ytga From Chlamydia Trachomatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:32.1
occ:1.00
O A:SER258 2.3 30.8 1.0
OD1 A:ASP261 2.3 33.8 1.0
O A:HOH636 2.5 39.0 1.0
CG A:ASP261 3.4 33.0 1.0
C A:SER258 3.5 30.4 1.0
OD2 A:ASP261 3.9 31.8 1.0
CA A:SER258 4.1 31.0 1.0
N A:ASP261 4.5 24.9 1.0
N A:ALA259 4.5 26.7 1.0
CB A:ASP261 4.5 30.2 1.0
CB A:SER258 4.6 35.4 1.0
CA A:ASP261 4.6 30.7 1.0
O A:ALA259 4.7 29.3 1.0
CA A:ALA259 4.7 27.6 1.0
C A:ALA259 4.7 35.1 1.0
O A:HOH677 4.9 39.2 1.0

Sodium binding site 2 out of 2 in 6nsi

Go back to Sodium Binding Sites List in 6nsi
Sodium binding site 2 out of 2 in the Crystal Structure of Fe(III)-Bound Ytga From Chlamydia Trachomatis


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 Fe(III)-Bound Ytga From Chlamydia Trachomatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:51.2
occ:1.00
OG A:SER246 3.5 39.9 1.0
O A:HOH549 3.6 47.8 1.0
CB A:SER246 4.2 31.1 1.0
OD2 A:ASP249 4.2 39.3 1.0
CB A:ARG248 4.2 28.8 1.0
OD1 A:ASP249 4.3 42.3 1.0
CG A:ASP249 4.5 39.5 1.0
CG A:ARG248 4.8 37.3 1.0

Reference:

Z.Luo, S.L.Neville, R.Campbell, J.R.Morey, S.Menon, M.Thomas, B.A.Eijkelkamp, M.P.Ween, W.M.Huston, B.Kobe, C.A.Mcdevitt. The Structure and Metal Binding Properties Ofchlamydia Trachomatisytga. J.Bacteriol. 2019.
ISSN: ESSN 1098-5530
PubMed: 31611288
DOI: 10.1128/JB.00580-19
Page generated: Tue Dec 15 12:39:52 2020

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