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Sodium in PDB 5nja: E. Coli Microcin-Processing Metalloprotease Tldd/E with Angiotensin Analogue Bound

Protein crystallography data

The structure of E. Coli Microcin-Processing Metalloprotease Tldd/E with Angiotensin Analogue Bound, PDB code: 5nja 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) 86.76 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.630, 173.530, 83.060, 90.00, 90.00, 90.00
R / Rfree (%) 13 / 17.1

Other elements in 5nja:

The structure of E. Coli Microcin-Processing Metalloprotease Tldd/E with Angiotensin Analogue 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 Angiotensin Analogue Bound (pdb code 5nja). 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 Angiotensin Analogue Bound, PDB code: 5nja:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5nja

Go back to Sodium Binding Sites List in 5nja
Sodium binding site 1 out of 4 in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Angiotensin Analogue 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 Angiotensin Analogue Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:24.4
occ:1.00
 O A:HOH1107 2.3 23.8 1.0
OG A:SER117 2.5 19.8 1.0
O A:HOH1033 2.5 24.2 1.0
O A:HOH1029 2.5 22.0 1.0
O A:HOH956 2.7 20.7 1.0
O A:HOH1103 3.2 19.8 1.0
CB A:SER117 3.4 18.8 1.0
O A:HOH949 4.3 24.6 1.0
O A:HOH695 4.5 31.6 1.0
O A:HOH780 4.5 22.6 1.0
O A:HOH1093 4.6 28.4 1.0
CA A:SER117 4.6 16.6 1.0
N A:SER117 4.6 18.4 1.0
O A:HOH841 4.9 22.2 1.0
O A:HOH1127 5.0 38.4 1.0

Sodium binding site 2 out of 4 in 5nja

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Sodium binding site 2 out of 4 in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Angiotensin Analogue 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 Angiotensin Analogue Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na705

b:23.3
occ:1.00
 O B:HOH1164 2.3 29.8 1.0
O B:SER30 2.3 23.6 1.0
O B:HOH1204 2.4 29.8 1.0
O B:HOH891 2.4 29.6 1.0
O B:SER33 2.6 18.3 1.0
C B:SER30 3.5 16.7 1.0
C B:SER33 3.8 15.0 1.0
CA B:SER30 4.0 14.4 1.0
O B:HOH1043 4.2 16.8 1.0
CA B:ASP34 4.3 15.7 1.0
CB B:SER30 4.5 15.8 1.0
N B:ASP34 4.5 13.5 1.0
C B:ASP34 4.5 15.1 1.0
O B:ASP34 4.6 19.4 1.0
N B:GLY31 4.6 18.6 1.0
N B:SER33 4.7 16.8 1.0
CA B:SER33 4.9 16.2 1.0
CA B:GLY31 4.9 21.6 1.0
O B:HOH852 5.0 26.4 1.0

Sodium binding site 3 out of 4 in 5nja

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Sodium binding site 3 out of 4 in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Angiotensin Analogue 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 Angiotensin Analogue Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na504

b:21.6
occ:1.00
 O C:HOH988 2.2 25.2 1.0
O C:ILE84 2.4 16.6 1.0
O C:HOH984 2.4 28.6 1.0
O C:HOH970 2.4 30.4 1.0
O C:HOH868 2.7 20.3 1.0
OD1 C:ASN14 2.7 24.9 1.0
CG C:ASN14 3.5 16.7 1.0
C C:ILE84 3.5 13.8 1.0
CB C:ASN14 3.8 17.4 1.0
N C:ILE84 4.0 13.6 1.0
O C:HOH935 4.1 23.7 0.5
CA C:ILE84 4.2 13.2 1.0
CA C:ASN14 4.4 19.1 1.0
CB C:ILE84 4.5 13.8 1.0
ND2 C:ASN14 4.5 15.6 1.0
N C:SER85 4.5 14.1 1.0
O D:HOH1142 4.5 35.7 1.0
CB C:SER85 4.6 16.1 1.0
CA C:SER85 4.7 12.9 1.0
O C:ASN14 4.9 22.4 1.0

Sodium binding site 4 out of 4 in 5nja

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Sodium binding site 4 out of 4 in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Angiotensin Analogue 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 Angiotensin Analogue Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na706

b:24.8
occ:1.00
 O D:HOH1209 2.3 25.1 1.0
O D:SER30 2.3 21.3 0.5
O D:SER33 2.3 16.6 1.0
O D:SER30 2.4 21.1 0.5
O D:HOH1217 2.5 23.8 1.0
O D:HOH1179 2.7 31.1 1.0
C D:SER30 3.5 19.6 0.5
C D:SER30 3.5 18.3 0.5
C D:SER33 3.5 15.0 1.0
CA D:ASP34 4.2 15.2 1.0
CA D:SER30 4.2 14.6 0.5
O D:HOH1067 4.3 16.1 1.0
CA D:SER30 4.3 15.6 0.5
N D:ASP34 4.3 13.7 1.0
OG D:SER30 4.4 21.4 0.5
N D:SER33 4.4 16.5 1.0
C D:ASP34 4.5 14.3 1.0
N D:GLY31 4.6 21.5 1.0
O D:ASP34 4.6 16.6 1.0
CA D:SER33 4.6 16.0 1.0
CB D:SER30 4.7 14.8 0.5
O D:HOH1127 4.7 26.6 1.0
CA D:GLY31 4.8 20.5 1.0
C D:GLY31 4.9 19.2 1.0
O D:HOH963 4.9 31.4 1.0
O D:HOH1211 4.9 33.3 1.0
O D:HOH923 4.9 26.7 1.0
OG D:SER33 5.0 16.2 1.0
CB D:SER30 5.0 18.6 0.5

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 22:59:21 2024

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