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Sodium in PDB 6pbr: Catalytic Domain of E.Coli Dihydrolipoamide Succinyltransferase in I4 Space Group

Enzymatic activity of Catalytic Domain of E.Coli Dihydrolipoamide Succinyltransferase in I4 Space Group

All present enzymatic activity of Catalytic Domain of E.Coli Dihydrolipoamide Succinyltransferase in I4 Space Group:
2.3.1.61;

Protein crystallography data

The structure of Catalytic Domain of E.Coli Dihydrolipoamide Succinyltransferase in I4 Space Group, PDB code: 6pbr was solved by B.Andi, A.S.Soares, W.Shi, M.R.Fuchs, S.Mcsweeney, Q.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.36 / 3.00
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 128.598, 128.598, 249.733, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 27.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Catalytic Domain of E.Coli Dihydrolipoamide Succinyltransferase in I4 Space Group (pdb code 6pbr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Catalytic Domain of E.Coli Dihydrolipoamide Succinyltransferase in I4 Space Group, PDB code: 6pbr:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6pbr

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Sodium binding site 1 out of 6 in the Catalytic Domain of E.Coli Dihydrolipoamide Succinyltransferase in I4 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Catalytic Domain of E.Coli Dihydrolipoamide Succinyltransferase in I4 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:52.5
occ:1.00
 OE2 A:GLU395 2.7 51.7 1.0
NZ A:LYS391 3.4 69.7 1.0
NZ B:LYS351 3.5 70.7 1.0
CD A:GLU395 3.7 53.4 1.0
CE A:MET366 3.8 60.5 1.0
CE A:MET355 4.0 61.9 1.0
OE1 A:GLU395 4.0 55.8 1.0
CB A:ASN208 4.2 44.7 1.0
N A:ASN208 4.3 52.4 1.0
SD A:MET366 4.3 61.1 1.0
OE2 A:GLU206 4.5 73.6 1.0
CG A:GLU206 4.6 61.6 1.0
CE A:LYS391 4.6 63.3 1.0
O A:GLU206 4.8 52.8 1.0
CA A:ASN208 4.9 48.4 1.0
CE B:LYS351 4.9 71.8 1.0
C A:VAL207 4.9 55.8 1.0
CD A:GLU206 5.0 62.2 1.0
CA A:VAL207 5.0 59.1 1.0

Sodium binding site 2 out of 6 in 6pbr

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Sodium binding site 2 out of 6 in the Catalytic Domain of E.Coli Dihydrolipoamide Succinyltransferase in I4 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Catalytic Domain of E.Coli Dihydrolipoamide Succinyltransferase in I4 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:41.0
occ:1.00
 OE2 B:GLU395 3.1 44.2 1.0
NZ C:LYS351 3.7 69.8 1.0
CE B:MET355 3.8 45.1 1.0
NZ B:LYS391 3.9 63.7 1.0
CD B:GLU395 4.0 45.1 1.0
CE B:LYS391 4.1 60.7 1.0
OE1 B:GLU395 4.2 47.1 1.0
CE B:MET366 4.3 57.9 1.0
CB B:ASN208 4.5 61.6 1.0
SD B:MET366 4.7 56.6 1.0
OE2 B:GLU206 4.7 71.9 1.0
N B:ASN208 4.8 63.0 1.0
CE C:LYS351 4.9 71.2 1.0

Sodium binding site 3 out of 6 in 6pbr

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Sodium binding site 3 out of 6 in the Catalytic Domain of E.Coli Dihydrolipoamide Succinyltransferase in I4 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Catalytic Domain of E.Coli Dihydrolipoamide Succinyltransferase in I4 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:29.1
occ:1.00
 OE2 C:GLU395 3.9 75.5 1.0
NZ A:LYS351 4.0 70.4 1.0
NZ C:LYS391 4.2 72.3 1.0
OE1 C:GLU395 4.3 67.9 1.0
CD C:GLU395 4.5 63.8 1.0
CE C:LYS391 4.5 64.9 1.0
CE A:LYS351 4.8 67.9 1.0
CE C:MET355 4.8 65.2 1.0

Sodium binding site 4 out of 6 in 6pbr

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Sodium binding site 4 out of 6 in the Catalytic Domain of E.Coli Dihydrolipoamide Succinyltransferase in I4 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Catalytic Domain of E.Coli Dihydrolipoamide Succinyltransferase in I4 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:43.9
occ:1.00
 OE2 D:GLU395 2.9 63.2 1.0
CD D:GLU395 3.6 61.0 1.0
OE1 D:GLU395 3.8 66.0 1.0
NZ E:LYS351 4.1 95.5 1.0
CB D:ASN208 4.2 63.4 1.0
NZ D:LYS391 4.3 72.0 1.0
CE D:MET355 4.4 70.9 1.0
CE D:LYS391 4.5 67.1 1.0
CE D:MET366 4.6 70.9 1.0
N D:ASN208 4.7 68.0 1.0
SD D:MET366 4.8 75.3 1.0
CG D:GLU395 5.0 59.0 1.0

Sodium binding site 5 out of 6 in 6pbr

Go back to Sodium Binding Sites List in 6pbr
Sodium binding site 5 out of 6 in the Catalytic Domain of E.Coli Dihydrolipoamide Succinyltransferase in I4 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Catalytic Domain of E.Coli Dihydrolipoamide Succinyltransferase in I4 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na501

b:41.2
occ:1.00
 OE1 E:GLU395 3.3 65.0 1.0
NZ F:LYS351 3.6 91.5 1.0
OE2 E:GLU395 4.0 65.5 1.0
CD E:GLU395 4.0 64.2 1.0
CE E:MET355 4.1 58.5 1.0
CE F:LYS351 4.3 85.7 1.0
CB E:ASN208 4.9 62.9 1.0
CE E:MET366 4.9 72.0 1.0

Sodium binding site 6 out of 6 in 6pbr

Go back to Sodium Binding Sites List in 6pbr
Sodium binding site 6 out of 6 in the Catalytic Domain of E.Coli Dihydrolipoamide Succinyltransferase in I4 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Catalytic Domain of E.Coli Dihydrolipoamide Succinyltransferase in I4 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na501

b:55.4
occ:1.00
 OE2 F:GLU395 3.0 57.3 1.0
NZ F:LYS391 3.5 76.6 1.0
NZ D:LYS351 3.8 83.7 1.0
CD F:GLU395 3.8 54.5 1.0
OE1 F:GLU395 3.9 54.7 1.0
CE F:MET355 4.5 67.3 1.0
CE F:MET366 4.5 79.8 1.0
CB F:ASN208 4.6 65.7 1.0
OE2 F:GLU206 4.7 62.2 1.0
CE D:LYS351 4.8 83.3 1.0
CE F:LYS391 4.9 71.1 1.0
SD F:MET366 4.9 79.6 1.0
N F:ASN208 4.9 74.0 1.0

Reference:

B.Andi, A.S.Soares, W.Shi, M.R.Fuchs, S.Mcsweeney, Q.Liu. Structure of the Dihydrolipoamide Succinyltransferase Catalytic Domain From Escherichia Coli in A Novel Crystal Form: A Tale of A Common Protein Crystallization Contaminant. Acta Crystallogr.,Sect.F V. 75 616 2019.
ISSN: ESSN 2053-230X
PubMed: 31475929
DOI: 10.1107/S2053230X19011488
Page generated: Tue Dec 15 12:45:10 2020

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