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Sodium in PDB 5nj9: E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound

Protein crystallography data

The structure of E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound, PDB code: 5nj9 was solved by D.Ghilarov, M.Serebryakova, C.E.M.Stevenson, S.J.Hearnshaw, D.Volkov, A.Maxwell, D.M.Lawson, K.Severinov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.77 / 1.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.630, 173.530, 82.860, 90.00, 90.03, 90.00
R / Rfree (%) 14.9 / 18.2

Other elements in 5nj9:

The structure of E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound (pdb code 5nj9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound, PDB code: 5nj9:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5nj9

Go back to Sodium Binding Sites List in 5nj9
Sodium binding site 1 out of 4 in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:16.5
occ:1.00
 O A:HOH1105 2.3 20.8 1.0
OG A:SER117 2.4 12.7 1.0
O A:HOH978 2.4 14.3 1.0
O A:HOH1020 2.5 17.7 1.0
O A:HOH1021 2.6 12.7 1.0
O A:HOH1101 3.2 18.7 1.0
CB A:SER117 3.4 14.2 1.0
O A:HOH878 4.3 14.4 1.0
N A:SER117 4.5 11.9 1.0
CA A:SER117 4.5 11.8 1.0
O A:HOH886 4.6 13.1 1.0
O A:HOH1071 4.6 22.7 1.0
O A:HOH805 4.6 27.5 1.0
O A:HOH865 4.9 17.1 1.0

Sodium binding site 2 out of 4 in 5nj9

Go back to Sodium Binding Sites List in 5nj9
Sodium binding site 2 out of 4 in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na706

b:19.9
occ:1.00
 O B:HOH1197 2.3 25.7 1.0
O B:SER30 2.4 17.9 1.0
O B:SER33 2.4 12.8 1.0
O B:HOH966 2.5 34.1 1.0
O B:HOH1175 2.5 37.1 1.0
C B:SER30 3.5 14.2 1.0
C B:SER33 3.7 10.5 1.0
CA B:SER30 4.1 11.5 1.0
O B:HOH996 4.2 12.6 1.0
CA B:ASP34 4.3 11.4 1.0
N B:ASP34 4.5 10.5 1.0
C B:ASP34 4.5 12.8 1.0
CB B:SER30 4.5 14.5 1.0
N B:SER33 4.6 11.2 1.0
O B:ASP34 4.6 13.4 1.0
N B:GLY31 4.6 16.2 1.0
CA B:SER33 4.7 10.0 1.0
CA B:GLY31 4.9 14.7 1.0
OG B:SER33 5.0 12.5 1.0

Sodium binding site 3 out of 4 in 5nj9

Go back to Sodium Binding Sites List in 5nj9
Sodium binding site 3 out of 4 in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na504

b:17.8
occ:1.00
 O C:HOH990 2.2 18.8 1.0
O C:HOH974 2.4 33.1 1.0
O C:HOH970 2.4 22.6 1.0
O C:ILE84 2.4 11.4 1.0
O C:HOH814 2.7 13.6 1.0
OD1 C:ASN14 2.7 19.3 1.0
CG C:ASN14 3.5 14.1 1.0
C C:ILE84 3.5 9.6 1.0
CB C:ASN14 3.9 12.9 1.0
N C:ILE84 4.1 8.1 1.0
CA C:ILE84 4.3 8.9 1.0
CA C:ASN14 4.4 13.6 1.0
O D:HOH1184 4.4 35.7 1.0
ND2 C:ASN14 4.5 14.1 1.0
CB C:ILE84 4.5 9.7 1.0
N C:SER85 4.5 9.3 1.0
CB C:SER85 4.6 11.7 1.0
CA C:SER85 4.7 9.5 1.0
O C:ASN14 4.9 17.0 1.0

Sodium binding site 4 out of 4 in 5nj9

Go back to Sodium Binding Sites List in 5nj9
Sodium binding site 4 out of 4 in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na706

b:23.2
occ:1.00
 O D:HOH1202 2.3 21.0 1.0
O D:HOH1212 2.3 34.7 1.0
O D:SER30 2.4 17.2 0.5
O D:SER30 2.4 17.1 0.5
O D:SER33 2.4 11.9 1.0
O D:HOH1181 3.0 31.2 1.0
C D:SER30 3.5 14.1 0.5
C D:SER30 3.5 14.8 0.5
C D:SER33 3.7 10.8 1.0
CA D:SER30 4.1 11.5 0.5
OG D:SER30 4.1 19.8 0.5
CA D:SER30 4.2 13.7 0.5
O D:HOH1042 4.2 11.9 1.0
CA D:ASP34 4.3 9.4 1.0
O D:HOH1123 4.4 24.4 1.0
N D:ASP34 4.4 8.2 1.0
C D:ASP34 4.5 8.6 1.0
CB D:SER30 4.5 10.7 0.5
N D:SER33 4.6 13.0 1.0
N D:GLY31 4.6 17.8 1.0
O D:ASP34 4.6 11.2 1.0
O D:HOH957 4.7 30.2 1.0
CB D:SER30 4.7 15.9 0.5
CA D:SER33 4.7 12.3 1.0
CA D:GLY31 4.9 18.3 1.0

Reference:

D.Ghilarov, M.Serebryakova, C.E.M.Stevenson, S.J.Hearnshaw, D.S.Volkov, A.Maxwell, D.M.Lawson, K.Severinov. The Origins of Specificity in the Microcin-Processing Protease Tldd/E. Structure V. 25 1549 2017.
ISSN: ISSN 1878-4186
PubMed: 28943336
DOI: 10.1016/J.STR.2017.08.006
Page generated: Mon Oct 7 22:59:19 2024

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