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Sodium in PDB 5m1e: Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor

Enzymatic activity of Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor

All present enzymatic activity of Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor:
4.1.1.98;

Protein crystallography data

The structure of Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor, PDB code: 5m1e was solved by S.A.Marshall, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 94.03 / 2.62
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 194.520, 194.520, 107.410, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.2

Other elements in 5m1e:

The structure of Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor also contains other interesting chemical elements:

Manganese (Mn) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor (pdb code 5m1e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor, PDB code: 5m1e:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5m1e

Go back to Sodium Binding Sites List in 5m1e
Sodium binding site 1 out of 3 in the Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:60.7
occ:1.00
 OE2 A:GLU241 2.2 96.5 1.0
O A:HOH602 2.3 51.9 1.0
O A:LEU176 2.5 61.3 1.0
OAT A:7D9502 2.5 60.1 1.0
OAK A:7D9502 2.5 61.6 1.0
O A:ALA231 2.6 67.9 1.0
CD A:GLU241 2.7 70.4 1.0
PBJ A:7D9502 3.1 69.0 1.0
MN A:MN501 3.3 70.0 1.0
CG A:GLU241 3.4 68.8 1.0
OE1 A:GLU241 3.4 76.3 1.0
OD1 A:ASN175 3.6 80.4 1.0
C A:LEU176 3.7 60.2 1.0
C A:ALA231 3.7 66.7 1.0
OAG A:7D9502 3.7 57.4 1.0
CAP A:7D9502 3.7 54.6 1.0
CBD A:7D9502 3.9 61.1 1.0
OAJ A:7D9502 4.0 62.3 1.0
CA A:GLY177 4.2 54.6 1.0
O A:THR233 4.2 76.5 1.0
OAF A:7D9502 4.3 57.9 1.0
CA A:ALA231 4.4 63.8 1.0
N A:GLY177 4.4 58.8 1.0
CB A:GLU241 4.5 65.8 1.0
CG A:ASN175 4.6 73.7 1.0
N A:VAL232 4.7 68.5 1.0
N A:LEU176 4.8 64.4 1.0
CA A:LEU176 4.8 63.6 1.0
O A:GLY230 4.9 65.7 1.0
CA A:VAL232 5.0 66.7 1.0

Sodium binding site 2 out of 3 in 5m1e

Go back to Sodium Binding Sites List in 5m1e
Sodium binding site 2 out of 3 in the Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:64.5
occ:1.00
 OE1 B:GLU241 2.2 92.4 1.0
O B:LEU176 2.4 59.0 1.0
O B:ALA231 2.4 56.6 1.0
OAT B:7D9502 2.5 48.6 1.0
O B:HOH623 2.5 72.5 1.0
OAK B:7D9502 2.6 48.6 1.0
CD B:GLU241 3.0 71.1 1.0
PBJ B:7D9502 3.1 54.3 1.0
OAG B:7D9502 3.4 46.3 1.0
MN B:MN501 3.5 64.5 1.0
C B:ALA231 3.5 57.0 1.0
C B:LEU176 3.6 57.4 1.0
CG B:GLU241 3.6 67.7 1.0
CAP B:7D9502 3.7 54.1 1.0
CBD B:7D9502 3.7 54.8 1.0
OE2 B:GLU241 3.7 73.3 1.0
OAJ B:7D9502 3.9 63.2 1.0
CA B:GLY177 4.0 51.1 1.0
N B:GLY177 4.2 53.4 1.0
CA B:ALA231 4.2 54.6 1.0
OAF B:7D9502 4.3 45.3 1.0
O B:THR233 4.3 79.1 1.0
ND2 B:ASN175 4.4 56.5 1.0
OD1 B:ASN175 4.5 60.0 1.0
N B:VAL232 4.6 62.4 1.0
CA B:LEU176 4.7 58.0 1.0
CB B:GLU241 4.8 64.1 1.0
N B:LEU176 4.8 58.2 1.0
CG B:ASN175 4.8 55.6 1.0
O B:GLY230 4.8 57.8 1.0
CA B:VAL232 4.9 62.7 1.0
CB B:ALA231 4.9 54.2 1.0

Sodium binding site 3 out of 3 in 5m1e

Go back to Sodium Binding Sites List in 5m1e
Sodium binding site 3 out of 3 in the Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:75.8
occ:1.00
 OE2 C:GLU241 2.3 0.9 1.0
OAK C:7D9502 2.4 85.8 1.0
O C:ALA231 2.4 90.5 1.0
O C:LEU176 2.8 91.0 1.0
OAT C:7D9502 2.9 84.1 1.0
CD C:GLU241 3.0 0.8 1.0
PBJ C:7D9502 3.0 76.5 1.0
OAJ C:7D9502 3.0 72.6 1.0
OAG C:7D9502 3.4 78.5 1.0
CG C:GLU241 3.5 0.3 1.0
MN C:MN501 3.6 0.6 1.0
C C:ALA231 3.6 83.2 1.0
CAP C:7D9502 3.7 84.1 1.0
CBD C:7D9502 3.7 85.5 1.0
OE1 C:GLU241 3.7 0.5 1.0
O C:THR233 3.8 87.3 1.0
C C:LEU176 4.0 93.7 1.0
CA C:ALA231 4.3 86.7 1.0
CA C:GLY177 4.4 83.2 1.0
OAF C:7D9502 4.5 63.5 1.0
N C:VAL232 4.6 82.0 1.0
OD1 C:ASN175 4.6 0.6 1.0
O C:GLY230 4.7 93.7 1.0
CA C:VAL232 4.7 82.6 1.0
N C:GLY177 4.7 87.7 1.0
C C:THR233 4.8 98.7 1.0
C C:VAL232 4.8 83.3 1.0
CB C:GLU241 4.8 0.6 1.0
ND2 C:ASN175 4.8 99.8 1.0

Reference:

S.A.Marshall, K.Fisher, A.Ni Cheallaigh, M.D.White, K.A.Payne, D.A.Parker, S.E.Rigby, D.Leys. Oxidative Maturation and Structural Characterization of Prenylated Fmn Binding By Ubid, A Decarboxylase Involved in Bacterial Ubiquinone Biosynthesis. J. Biol. Chem. V. 292 4623 2017.
ISSN: ESSN 1083-351X
PubMed: 28057757
DOI: 10.1074/JBC.M116.762732
Page generated: Tue Dec 15 11:15:14 2020

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