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Sodium in PDB 3tf9: Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon

Protein crystallography data

The structure of Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon, PDB code: 3tf9 was solved by M.B.Winter, M.A.Herzik Jr., J.Kuriyan, M.A.Marletta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.98 / 2.59
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 124.404, 124.404, 124.404, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.5

Other elements in 3tf9:

The structure of Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon also contains other interesting chemical elements:

Xenon (Xe) 2 atoms
Iron (Fe) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon (pdb code 3tf9). 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 An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon, PDB code: 3tf9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3tf9

Go back to Sodium Binding Sites List in 3tf9
Sodium binding site 1 out of 2 in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon


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 An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na191

b:78.2
occ:1.00
H3 A:MET1 2.0 76.7 1.0
HD21 A:ASN6 2.5 69.5 1.0
O A:SER44 2.7 68.4 1.0
OG1 A:THR48 2.8 54.2 1.0
HB A:VAL47 2.9 80.2 1.0
HB2 A:TYR43 2.9 53.6 1.0
H A:THR48 3.0 73.9 1.0
N A:MET1 3.0 63.9 1.0
HB2 A:MET1 3.0 69.4 1.0
HA A:ASP45 3.1 82.1 1.0
HG1 A:THR48 3.2 65.1 1.0
ND2 A:ASN6 3.3 57.9 1.0
H2 A:MET1 3.4 76.7 1.0
HB3 A:TYR43 3.4 53.6 1.0
H1 A:MET1 3.4 76.7 1.0
C A:SER44 3.5 63.2 1.0
O A:MET1 3.6 57.7 1.0
CB A:TYR43 3.6 44.6 1.0
N A:THR48 3.6 61.6 1.0
HB A:THR48 3.7 65.6 1.0
CB A:THR48 3.8 54.7 1.0
CA A:ASP45 3.8 68.4 1.0
CB A:MET1 3.8 57.8 1.0
HD22 A:ASN6 3.8 69.5 1.0
CB A:VAL47 3.8 66.8 1.0
CA A:MET1 3.9 63.5 1.0
O A:TYR43 3.9 56.5 1.0
H A:VAL47 3.9 72.9 1.0
N A:ASP45 4.0 58.5 1.0
O A:ASP45 4.0 58.1 1.0
C A:TYR43 4.0 60.7 1.0
HG12 A:VAL47 4.1 70.8 1.0
OD1 A:ASN6 4.1 64.4 1.0
C A:ASP45 4.1 63.9 1.0
C A:MET1 4.1 56.5 1.0
CG A:ASN6 4.2 65.4 1.0
CA A:THR48 4.3 59.8 1.0
HG3 A:MET1 4.3 96.6 1.0
N A:VAL47 4.3 60.7 1.0
CG1 A:VAL47 4.4 59.0 1.0
CA A:VAL47 4.4 65.2 1.0
HG11 A:VAL47 4.4 70.8 1.0
C A:VAL47 4.4 67.1 1.0
N A:SER44 4.4 53.4 1.0
CA A:TYR43 4.4 57.1 1.0
HB3 A:MET1 4.5 69.4 1.0
CA A:SER44 4.6 66.1 1.0
CG A:MET1 4.6 80.4 1.0
H A:TYR43 4.6 66.9 1.0
HA A:THR48 4.6 71.8 1.0
H A:ASP45 4.7 70.2 1.0
CG A:TYR43 4.7 51.8 1.0
HA A:MET1 4.8 76.2 1.0
HG23 A:VAL47 4.8 63.2 1.0
CG2 A:VAL47 4.8 52.7 1.0
OD2 A:ASP45 4.8 61.9 1.0
HG21 A:VAL47 4.9 63.2 1.0
H A:SER44 4.9 64.1 1.0

Sodium binding site 2 out of 2 in 3tf9

Go back to Sodium Binding Sites List in 3tf9
Sodium binding site 2 out of 2 in the Crystal Structure of An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon


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 An H-Nox Protein From Nostoc Sp. Pcc 7120 Under 1 Atm of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na191

b:91.2
occ:1.00
H3 B:MET1 2.4 91.2 1.0
OG1 B:THR48 2.4 61.2 1.0
HG1 B:THR48 2.6 73.5 1.0
HB B:VAL47 2.7 90.4 1.0
OD1 B:ASN6 2.8 81.7 1.0
HB2 B:TYR43 2.9 68.9 1.0
O B:SER44 3.0 84.1 1.0
HB2 B:MET1 3.0 60.4 1.0
H B:THR48 3.0 84.1 1.0
HD21 B:ASN6 3.1 72.3 1.0
N B:MET1 3.3 76.0 1.0
HB3 B:TYR43 3.4 68.9 1.0
HA B:ASP45 3.4 73.7 1.0
N B:THR48 3.5 70.0 1.0
CB B:TYR43 3.6 57.4 1.0
CB B:THR48 3.6 75.1 1.0
O B:MET1 3.6 68.4 1.0
CB B:VAL47 3.7 75.3 1.0
CG B:ASN6 3.7 70.7 1.0
H2 B:MET1 3.7 91.2 1.0
ND2 B:ASN6 3.7 60.2 1.0
HB B:THR48 3.8 90.2 1.0
CB B:MET1 3.8 50.3 1.0
C B:SER44 3.9 77.5 1.0
H1 B:MET1 3.9 91.2 1.0
HG12 B:VAL47 4.0 94.5 1.0
CA B:MET1 4.0 55.7 1.0
H B:VAL47 4.1 99.0 1.0
CA B:THR48 4.1 70.9 1.0
CA B:ASP45 4.1 61.4 1.0
C B:MET1 4.2 64.3 1.0
HG11 B:VAL47 4.2 94.5 1.0
CG1 B:VAL47 4.2 78.7 1.0
C B:VAL47 4.3 74.7 1.0
CA B:VAL47 4.3 76.6 1.0
HA B:THR48 4.3 85.2 1.0
O B:ASP45 4.3 68.5 1.0
HB3 B:MET1 4.4 60.4 1.0
C B:TYR43 4.4 66.8 1.0
O B:TYR43 4.4 76.7 1.0
N B:ASP45 4.4 63.0 1.0
C B:ASP45 4.4 71.9 1.0
N B:VAL47 4.4 82.5 1.0
CG B:TYR43 4.5 61.2 1.0
HD22 B:ASN6 4.5 72.3 1.0
HG21 B:VAL47 4.6 76.5 1.0
CG2 B:VAL47 4.6 63.7 1.0
CA B:TYR43 4.6 58.5 1.0
HG23 B:VAL47 4.6 76.5 1.0
HG3 B:MET1 4.7 85.8 1.0
N B:SER44 4.8 75.7 1.0
CG B:MET1 4.8 71.5 1.0
H B:TYR43 4.9 82.1 1.0
HA B:MET1 4.9 66.8 1.0
CG2 B:THR48 4.9 49.8 1.0

Reference:

M.B.Winter, M.A.Herzik, J.Kuriyan, M.A.Marletta. Tunnels Modulate Ligand Flux in A Heme Nitric Oxide/Oxygen Binding (H-Nox) Domain. Proc.Natl.Acad.Sci.Usa V. 108 E881 2011.
ISSN: ISSN 0027-8424
PubMed: 21997213
DOI: 10.1073/PNAS.1114038108
Page generated: Tue Dec 15 06:26:06 2020

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