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Sodium in PDB 5njc: E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd E263A Mutant) with Hexapeptide Bound

Protein crystallography data

The structure of E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd E263A Mutant) with Hexapeptide Bound, PDB code: 5njc 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) 65.29 / 1.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.290, 175.440, 84.330, 90.00, 90.01, 90.00
R / Rfree (%) 14.5 / 18.3

Other elements in 5njc:

The structure of E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd E263A Mutant) with Hexapeptide 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 (Tldd E263A Mutant) with Hexapeptide Bound (pdb code 5njc). 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 (Tldd E263A Mutant) with Hexapeptide Bound, PDB code: 5njc:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5njc

Go back to Sodium Binding Sites List in 5njc
Sodium binding site 1 out of 4 in the E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd E263A Mutant) with Hexapeptide 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 (Tldd E263A Mutant) with Hexapeptide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:54.8
occ:1.00
O A:HOH1027 2.3 23.0 1.0
O A:HOH936 2.8 27.2 1.0
O A:HOH1045 2.8 48.6 1.0
OG A:SER117 3.0 27.1 1.0
O A:HOH1086 3.1 35.3 1.0
CB A:SER117 3.7 23.6 1.0
O A:HOH869 4.1 21.5 1.0
O A:HOH727 4.2 19.9 1.0
N A:SER117 5.0 19.1 1.0
O A:HOH842 5.0 24.1 1.0
CA A:SER117 5.0 20.1 1.0

Sodium binding site 2 out of 4 in 5njc

Go back to Sodium Binding Sites List in 5njc
Sodium binding site 2 out of 4 in the E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd E263A Mutant) with Hexapeptide 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 (Tldd E263A Mutant) with Hexapeptide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na706

b:26.5
occ:1.00
O B:SER30 2.4 22.5 1.0
O B:HOH1184 2.4 32.9 1.0
O B:HOH1192 2.4 24.1 1.0
O B:HOH958 2.4 32.9 1.0
O B:SER33 2.5 18.6 1.0
C B:SER30 3.5 19.3 1.0
C B:SER33 3.8 17.8 1.0
CA B:SER30 4.1 16.2 1.0
O B:HOH1073 4.3 17.1 1.0
CA B:ASP34 4.4 14.6 1.0
N B:ASP34 4.5 14.6 1.0
C B:ASP34 4.5 14.7 1.0
O B:ASP34 4.6 19.2 1.0
N B:GLY31 4.6 21.8 1.0
CB B:SER30 4.6 18.1 1.0
N B:SER33 4.7 18.4 1.0
CA B:SER33 4.8 18.9 1.0
CA B:GLY31 4.9 23.3 1.0

Sodium binding site 3 out of 4 in 5njc

Go back to Sodium Binding Sites List in 5njc
Sodium binding site 3 out of 4 in the E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd E263A Mutant) with Hexapeptide 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 (Tldd E263A Mutant) with Hexapeptide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na504

b:23.6
occ:1.00
O C:HOH980 2.3 27.9 1.0
O C:ILE84 2.5 19.5 1.0
O C:HOH879 2.6 22.9 1.0
OD1 C:ASN14 2.7 25.3 1.0
O C:HOH978 2.7 28.1 1.0
O C:HOH979 2.7 36.2 1.0
CG C:ASN14 3.4 16.9 1.0
C C:ILE84 3.6 14.4 1.0
CB C:ASN14 3.9 14.3 1.0
N C:ILE84 4.1 15.5 1.0
CA C:ILE84 4.3 15.0 1.0
ND2 C:ASN14 4.4 17.5 1.0
CA C:ASN14 4.5 17.0 1.0
CB C:ILE84 4.6 14.8 1.0
N C:SER85 4.6 13.8 1.0
CB C:SER85 4.7 14.8 1.0
O D:HOH1194 4.7 66.8 1.0
CA C:SER85 4.9 14.3 1.0
O C:HOH926 5.0 34.3 1.0

Sodium binding site 4 out of 4 in 5njc

Go back to Sodium Binding Sites List in 5njc
Sodium binding site 4 out of 4 in the E. Coli Microcin-Processing Metalloprotease Tldd/E (Tldd E263A Mutant) with Hexapeptide 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 (Tldd E263A Mutant) with Hexapeptide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na706

b:26.1
occ:1.00
O D:HOH1203 2.4 35.5 1.0
O D:SER30 2.4 26.0 0.5
O D:SER30 2.4 26.2 0.5
O D:SER33 2.4 15.7 1.0
O D:HOH1226 2.4 24.6 1.0
O D:HOH1219 2.5 26.9 1.0
C D:SER30 3.6 18.9 0.5
C D:SER30 3.6 19.6 0.5
C D:SER33 3.6 16.2 1.0
CA D:SER30 4.3 14.7 0.5
CA D:ASP34 4.3 15.2 1.0
CA D:SER30 4.4 15.9 0.5
O D:HOH1042 4.4 15.3 1.0
N D:ASP34 4.4 16.5 1.0
OG D:SER30 4.4 23.6 0.5
N D:SER33 4.5 16.9 1.0
O D:HOH1145 4.6 29.2 1.0
C D:ASP34 4.6 12.8 1.0
N D:GLY31 4.6 24.8 1.0
O D:ASP34 4.7 16.0 1.0
CA D:SER33 4.7 15.6 1.0
CA D:GLY31 4.8 23.2 1.0
O D:HOH872 4.8 31.4 1.0
CB D:SER30 4.8 13.1 0.5
C D:GLY31 4.9 24.9 1.0
O D:HOH1017 5.0 25.7 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: Tue Dec 15 11:21:09 2020

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