Sodium in PDB 9f7l: Bartonella Henselae Nrnc Bound to Deoxy-Pgg

The structure of Bartonella Henselae Nrnc Bound to Deoxy-Pgg, PDB code: 9f7l was solved by S.Mortensen, H.Sondermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.57 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.334, 128.047, 128.71, 90, 94.82, 90
R / Rfree (%)	17.6 / 21

The structure of Bartonella Henselae Nrnc Bound to Deoxy-Pgg also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Sodium atom in the Bartonella Henselae Nrnc Bound to Deoxy-Pgg (pdb code 9f7l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 17 binding sites of Sodium where determined in the Bartonella Henselae Nrnc Bound to Deoxy-Pgg, PDB code: 9f7l:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 17 in the Bartonella Henselae Nrnc Bound to Deoxy-Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bartonella Henselae Nrnc Bound to Deoxy-Pgg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:43.4 occ:0.69 O A:HOH432 2.4 43.6 1.0 O A:HOH451 2.6 43.6 1.0 CA A:ARG67 3.6 43.2 1.0 CG A:ARG67 3.8 45.0 1.0 N A:ARG67 3.9 41.2 1.0 OG A:SER70 3.9 43.5 1.0 CB A:ARG67 3.9 42.1 1.0 C A:VAL66 4.3 40.6 1.0 O A:HOH511 4.3 47.9 1.0 O A:VAL66 4.4 40.0 1.0 CG1 A:VAL66 4.5 37.1 1.0 O A:PRO63 4.6 41.8 1.0 CD A:ARG67 4.8 48.1 1.0 C A:ARG67 4.9 42.0 1.0

Sodium binding site 2 out of 17 in the Bartonella Henselae Nrnc Bound to Deoxy-Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bartonella Henselae Nrnc Bound to Deoxy-Pgg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:49.0 occ:0.91 OD2 A:ASP25 2.3 43.7 1.0 OE2 A:GLU27 2.3 45.7 1.0 OP1 B:DG604 2.3 48.2 1.0 OD2 A:ASP155 2.8 54.1 1.0 CD A:GLU27 3.1 42.5 1.0 O A:THR26 3.1 38.8 1.0 CG A:ASP25 3.2 42.8 1.0 OE1 A:GLU27 3.3 41.5 1.0 OD1 A:ASP25 3.5 46.1 1.0 P B:DG604 3.7 43.8 1.0 CG A:ASP155 3.9 55.0 1.0 O A:HOH443 3.9 38.5 1.0 CE1 A:TYR151 3.9 57.8 1.0 OE1 A:GLN42 3.9 42.7 1.0 OH A:TYR151 4.1 65.2 1.0 C A:THR26 4.1 38.0 1.0 CB A:ASP155 4.1 52.0 1.0 O A:HOH525 4.4 46.0 1.0 CG A:GLU27 4.4 39.0 1.0 C5' B:DG604 4.4 38.2 1.0 O5' B:DG604 4.4 40.9 1.0 CZ A:TYR151 4.4 65.5 1.0 CB A:ASP25 4.5 40.9 1.0 OP2 B:DG604 4.5 44.0 1.0 N A:THR26 4.6 38.7 1.0 O3' B:DG603 4.7 43.4 1.0 CD1 A:TYR151 4.9 59.0 1.0 N A:GLU27 4.9 39.2 1.0 CD A:GLN42 4.9 41.0 1.0

Sodium binding site 3 out of 17 in the Bartonella Henselae Nrnc Bound to Deoxy-Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Bartonella Henselae Nrnc Bound to Deoxy-Pgg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:44.5 occ:0.68 O A:HOH444 2.4 35.4 1.0 OD2 A:ASP84 2.4 40.5 1.0 O A:HIS79 2.5 34.4 1.0 OD1 A:ASP25 2.7 46.1 1.0 O A:HOH525 2.8 46.0 1.0 CG A:ASP84 3.4 37.9 1.0 O A:HOH443 3.4 38.5 1.0 O A:HOH475 3.5 43.8 1.0 C A:HIS79 3.6 35.7 1.0 OD1 A:ASP84 3.7 39.3 1.0 CG A:ASP25 3.7 42.8 1.0 N A:HIS79 4.1 35.1 1.0 CA A:HIS79 4.3 36.1 1.0 O A:PHE80 4.3 31.8 1.0 CB A:HIS79 4.4 34.2 1.0 O3' B:DG603 4.4 43.4 1.0 OD2 A:ASP25 4.4 43.7 1.0 CB A:ASP25 4.6 40.9 1.0 C A:PHE80 4.6 34.0 1.0 N A:PHE80 4.7 33.7 1.0 CA A:ASP25 4.7 37.8 1.0 C4' B:DG603 4.7 39.3 1.0 OP1 B:DG604 4.7 48.2 1.0 CB A:ASP84 4.7 35.0 1.0 O A:VAL24 4.9 36.6 1.0 CB A:PHE80 4.9 35.8 1.0 CB A:PHE78 5.0 33.5 1.0 CA A:PHE80 5.0 35.1 1.0 C5' B:DG603 5.0 37.5 1.0

Sodium binding site 4 out of 17 in the Bartonella Henselae Nrnc Bound to Deoxy-Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Bartonella Henselae Nrnc Bound to Deoxy-Pgg within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:50.7 occ:0.60 OE2 C:GLU27 2.3 40.6 1.0 OD2 C:ASP155 2.3 51.4 1.0 OD2 C:ASP25 2.3 44.1 1.0 OP1 D:DG604 2.3 52.2 1.0 CD C:GLU27 3.1 38.2 1.0 CG C:ASP25 3.3 42.2 1.0 OE1 C:GLU27 3.4 38.8 1.0 CG C:ASP155 3.4 51.3 1.0 O C:THR26 3.5 40.3 1.0 P D:DG604 3.6 47.9 1.0 OD1 C:ASP25 3.7 42.1 1.0 OH C:TYR151 3.8 58.3 1.0 CB C:ASP155 3.8 44.6 1.0 O C:HOH491 4.0 45.8 1.0 OE1 C:GLN42 4.0 42.8 1.0 CE2 C:TYR151 4.1 51.2 1.0 OP2 D:DG604 4.2 49.4 1.0 O5' D:DG604 4.2 45.3 1.0 CZ C:TYR151 4.3 55.4 1.0 CG C:GLU27 4.4 37.6 1.0 OD1 C:ASP155 4.5 49.4 1.0 C C:THR26 4.6 38.5 1.0 C5' D:DG604 4.6 39.9 1.0 CB C:ASP25 4.7 39.0 1.0 O3' D:DG603 4.8 49.1 1.0

Sodium binding site 5 out of 17 in the Bartonella Henselae Nrnc Bound to Deoxy-Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Bartonella Henselae Nrnc Bound to Deoxy-Pgg within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:45.4 occ:0.76 OD2 C:ASP84 2.4 40.1 1.0 O C:HIS79 2.5 35.2 1.0 O C:HOH491 2.6 45.8 1.0 O C:HOH433 2.6 32.8 1.0 OD1 C:ASP25 2.7 42.1 1.0 CG C:ASP84 3.4 38.0 1.0 C C:HIS79 3.6 37.0 1.0 OD1 C:ASP84 3.6 39.6 1.0 O C:HOH472 3.8 41.0 1.0 CG C:ASP25 3.8 42.2 1.0 O C:PHE80 4.2 33.5 1.0 N C:HIS79 4.2 37.2 1.0 O3' D:DG603 4.3 49.1 1.0 CA C:HIS79 4.3 37.6 1.0 OP1 D:DG604 4.5 52.2 1.0 CB C:HIS79 4.5 36.8 1.0 C C:PHE80 4.5 35.0 1.0 CB C:ASP25 4.6 39.0 1.0 OD2 C:ASP25 4.6 44.1 1.0 N C:PHE80 4.7 36.5 1.0 CB C:ASP84 4.7 35.4 1.0 C4' D:DG603 4.7 44.3 1.0 CA C:ASP25 4.7 38.2 1.0 CB C:PHE80 4.8 36.1 1.0 CB C:PHE78 4.9 35.2 1.0 C5' D:DG603 4.9 40.6 1.0 CA C:PHE80 4.9 37.5 1.0 O C:VAL24 4.9 37.3 1.0

Sodium binding site 6 out of 17 in the Bartonella Henselae Nrnc Bound to Deoxy-Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Bartonella Henselae Nrnc Bound to Deoxy-Pgg within 5.0Å range: probe atom residue distance (Å) B Occ E:Na301 b:50.1 occ:0.67 OE2 E:GLU27 2.3 44.8 1.0 OP1 F:DG604 2.3 49.0 1.0 OD2 E:ASP25 2.3 44.8 1.0 O E:HOH401 2.9 47.6 1.0 O E:THR26 2.9 43.3 1.0 CD E:GLU27 3.0 44.8 1.0 OD2 E:ASP155 3.1 55.2 1.0 CG E:ASP25 3.2 43.5 1.0 OE1 E:GLU27 3.2 45.4 1.0 OD1 E:ASP25 3.4 43.1 1.0 NE2 E:GLN42 3.7 41.9 1.0 P F:DG604 3.7 46.8 1.0 O E:HOH434 3.8 45.1 1.0 C E:THR26 4.0 40.5 1.0 CG E:ASP155 4.0 53.9 1.0 CG E:GLU27 4.1 42.5 1.0 CB E:ASP155 4.2 48.7 1.0 O F:HOH705 4.2 44.6 1.0 O5' F:DG604 4.3 45.4 1.0 C5' F:DG604 4.3 43.1 1.0 CE1 E:TYR151 4.4 59.5 1.0 CB E:ASP25 4.5 40.8 1.0 OP2 F:DG604 4.5 46.6 1.0 N E:THR26 4.5 40.0 1.0 OH E:TYR151 4.6 68.1 1.0 O3' F:DG603 4.7 47.9 1.0 N E:GLU27 4.7 39.2 1.0 CD E:GLN42 4.8 42.8 1.0 CA E:GLU27 4.9 40.8 1.0 CZ E:TYR151 4.9 65.4 1.0 CA E:THR26 4.9 40.0 1.0 OE1 E:GLN42 5.0 42.0 1.0

Sodium binding site 7 out of 17 in the Bartonella Henselae Nrnc Bound to Deoxy-Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Bartonella Henselae Nrnc Bound to Deoxy-Pgg within 5.0Å range: probe atom residue distance (Å) B Occ E:Na302 b:43.4 occ:0.58 O E:HOH405 2.2 45.1 1.0 O E:HOH456 2.3 38.1 1.0 OD2 E:ASP84 2.4 40.5 1.0 OD1 E:ASP25 2.4 43.1 1.0 O E:HOH401 2.6 47.6 1.0 O E:HIS79 2.7 37.9 1.0 O F:HOH705 2.9 44.6 1.0 O E:HOH505 3.2 42.4 1.0 CG E:ASP84 3.3 38.8 1.0 O E:HOH434 3.4 45.1 1.0 OD1 E:ASP84 3.4 39.5 1.0 CG E:ASP25 3.5 43.5 1.0 C E:HIS79 3.9 37.1 1.0 N E:HIS79 4.2 37.1 1.0 OD2 E:ASP25 4.3 44.8 1.0 CB E:ASP25 4.3 40.8 1.0 CA E:ASP25 4.4 40.1 1.0 CA E:HIS79 4.4 38.5 1.0 O3' F:DG603 4.5 47.9 1.0 O E:PHE80 4.5 34.8 1.0 CB E:HIS79 4.6 37.1 1.0 O E:VAL24 4.7 38.0 1.0 CB E:ASP84 4.7 35.7 1.0 OP1 F:DG604 4.7 49.0 1.0 C E:PHE80 4.8 37.2 1.0 N E:THR26 4.8 40.0 1.0 N E:PHE80 5.0 35.5 1.0 CB E:PHE78 5.0 35.7 1.0

Sodium binding site 8 out of 17 in the Bartonella Henselae Nrnc Bound to Deoxy-Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Bartonella Henselae Nrnc Bound to Deoxy-Pgg within 5.0Å range: probe atom residue distance (Å) B Occ G:Na301 b:54.8 occ:0.77 OP1 H:DG604 2.3 48.2 1.0 OE2 G:GLU27 2.3 54.0 1.0 OD2 G:ASP155 2.3 54.0 1.0 OD2 G:ASP25 2.4 51.3 1.0 CD G:GLU27 3.2 50.4 1.0 CG G:ASP155 3.4 55.3 1.0 OE1 G:GLU27 3.4 48.8 1.0 CG G:ASP25 3.4 46.7 1.0 P H:DG604 3.5 45.9 1.0 O H:HOH701 3.6 47.5 1.0 O G:THR26 3.7 46.5 1.0 CE2 G:TYR151 3.8 63.2 1.0 OD1 G:ASP25 3.8 46.8 1.0 CB G:ASP155 3.8 53.1 1.0 OP2 H:DG604 4.0 49.1 1.0 OE1 G:GLN42 4.1 47.5 1.0 O5' H:DG604 4.2 45.1 1.0 OH G:TYR151 4.3 64.6 1.0 O H:HOH706 4.3 49.5 1.0 CZ G:TYR151 4.4 64.1 1.0 O G:HOH443 4.4 47.7 1.0 C5' H:DG604 4.5 45.7 1.0 OD1 G:ASP155 4.5 56.0 1.0 CG G:GLU27 4.5 50.0 1.0 CD2 G:TYR151 4.7 60.6 1.0 CB G:ASP25 4.7 46.2 1.0 O3' H:DG603 4.7 48.1 1.0 C G:THR26 4.8 44.7 1.0

Sodium binding site 9 out of 17 in the Bartonella Henselae Nrnc Bound to Deoxy-Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Bartonella Henselae Nrnc Bound to Deoxy-Pgg within 5.0Å range: probe atom residue distance (Å) B Occ G:Na302 b:45.4 occ:0.63 O G:HOH429 2.3 39.8 1.0 OD2 G:ASP84 2.4 44.4 1.0 O H:HOH701 2.5 47.5 1.0 O G:HOH486 2.5 45.7 1.0 O G:HIS79 2.6 41.5 1.0 OD1 G:ASP25 2.6 46.8 1.0 O H:HOH706 3.1 49.5 1.0 CG G:ASP84 3.4 43.8 1.0 O G:HOH444 3.4 44.9 1.0 CG G:ASP25 3.5 46.7 1.0 O G:HOH443 3.7 47.7 1.0 C G:HIS79 3.7 40.8 1.0 OD1 G:ASP84 3.8 46.6 1.0 N G:HIS79 4.0 39.8 1.0 CA G:HIS79 4.2 40.7 1.0 CB G:ASP25 4.3 46.2 1.0 OD2 G:ASP25 4.3 51.3 1.0 CB G:HIS79 4.3 38.7 1.0 CA G:ASP25 4.4 44.3 1.0 O G:PHE80 4.4 37.8 1.0 O G:VAL24 4.6 43.9 1.0 OP1 H:DG604 4.6 48.2 1.0 O3' H:DG603 4.7 48.1 1.0 CB G:ASP84 4.7 40.6 1.0 C G:PHE80 4.7 38.3 1.0 N G:PHE80 4.8 39.1 1.0 CB G:PHE78 4.9 39.4 1.0 N G:THR26 4.9 44.5 1.0

Sodium binding site 10 out of 17 in the Bartonella Henselae Nrnc Bound to Deoxy-Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Bartonella Henselae Nrnc Bound to Deoxy-Pgg within 5.0Å range: probe atom residue distance (Å) B Occ I:Na301 b:51.6 occ:0.75 OP1 J:DG604 2.2 51.4 1.0 OD2 I:ASP25 2.3 49.7 1.0 OE2 I:GLU27 2.5 50.7 1.0 O I:THR26 2.5 44.8 1.0 CG I:ASP25 2.8 46.3 1.0 OD1 I:ASP25 2.9 45.1 1.0 O I:HOH403 3.0 48.1 1.0 O I:HOH431 3.1 44.1 1.0 CD I:GLU27 3.1 48.9 1.0 OE1 I:GLU27 3.4 46.7 1.0 C I:THR26 3.6 44.7 1.0 OD2 I:ASP155 3.6 62.4 1.0 P J:DG604 3.7 48.9 1.0 OE1 I:GLN42 3.9 44.5 1.0 N I:THR26 4.0 40.4 1.0 C5' J:DG604 4.0 47.9 1.0 CB I:ASP25 4.1 44.1 1.0 O5' J:DG604 4.2 49.2 1.0 CG I:GLU27 4.3 46.9 1.0 O I:HOH508 4.3 51.5 1.0 O3' J:DG603 4.4 47.2 1.0 CA I:THR26 4.4 42.3 1.0 N I:GLU27 4.4 42.6 1.0 CA I:GLU27 4.7 43.5 1.0 CG I:ASP155 4.7 63.4 1.0 OP2 J:DG604 4.7 58.7 1.0 C I:ASP25 4.7 42.6 1.0 CD I:GLN42 4.8 43.0 1.0 NA I:NA302 4.9 45.0 0.6 CA I:ASP25 4.9 41.5 1.0

S.Mortensen, H.Sondermann. Unique Dinucleases with Dna Specificity Are Associated with Genomic Islands in Actinomycetes and Clostridia To Be Published.