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Sodium in PDB 5m1d: 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: 5m1d 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) 137.32 / 2.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 194.199, 194.199, 107.598, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 22.6

Other elements in 5m1d:

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 5m1d). 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: 5m1d:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5m1d

Go back to Sodium Binding Sites List in 5m1d
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:60.5
occ:0.50
 OE2 A:GLU241 2.2 0.2 1.0
O A:HOH604 2.3 67.5 1.0
O A:ALA231 2.4 93.8 1.0
O5' A:4LU502 2.6 0.2 1.0
O3P A:4LU502 2.9 99.2 1.0
O4' A:4LU502 2.9 83.1 1.0
CD A:GLU241 3.2 0.9 1.0
P A:4LU502 3.3 0.8 1.0
O A:LEU176 3.3 92.3 1.0
O A:THR233 3.6 0.3 1.0
C A:ALA231 3.6 88.7 1.0
C4' A:4LU502 3.6 0.6 1.0
C5' A:4LU502 3.6 0.0 1.0
CG A:GLU241 3.7 0.7 1.0
MN A:MN501 3.7 1.0 0.5
O2P A:4LU502 3.8 87.2 1.0
OE1 A:GLU241 4.3 0.6 1.0
OD1 A:ASN175 4.3 0.4 1.0
N A:VAL232 4.5 95.7 1.0
CA A:ALA231 4.5 86.0 1.0
C A:THR233 4.5 0.3 1.0
C A:LEU176 4.6 89.5 1.0
CA A:VAL232 4.6 97.5 1.0
O1P A:4LU502 4.6 83.3 1.0
C A:VAL232 4.6 1.0 1.0
O A:GLY230 4.7 87.6 1.0
N A:THR233 4.9 0.1 1.0
O A:VAL232 4.9 0.8 1.0
CA A:GLY177 4.9 81.2 1.0
CB A:GLU241 5.0 0.2 1.0

Sodium binding site 2 out of 3 in 5m1d

Go back to Sodium Binding Sites List in 5m1d
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:66.7
occ:1.00
 OE1 B:GLU241 2.2 0.5 1.0
O5' B:4LU502 2.2 52.2 1.0
O B:LEU176 2.4 52.8 1.0
O B:ALA231 2.5 53.8 1.0
O B:HOH657 2.6 64.7 1.0
O3P B:4LU502 2.6 52.4 1.0
P B:4LU502 3.0 53.7 1.0
CD B:GLU241 3.3 79.5 1.0
C5' B:4LU502 3.4 51.4 1.0
O4' B:4LU502 3.4 44.3 1.0
MN B:MN501 3.5 95.5 1.0
C4' B:4LU502 3.5 50.1 1.0
C B:LEU176 3.6 51.7 1.0
C B:ALA231 3.7 54.2 1.0
CA B:GLY177 3.9 47.3 1.0
O2P B:4LU502 4.0 59.8 1.0
CG B:GLU241 4.0 74.8 1.0
O1P B:4LU502 4.1 46.9 1.0
OE2 B:GLU241 4.1 96.0 1.0
N B:GLY177 4.2 50.0 1.0
ND2 B:ASN175 4.3 56.7 1.0
OD1 B:ASN175 4.3 69.4 1.0
CA B:ALA231 4.4 53.7 1.0
CG B:ASN175 4.6 57.4 1.0
N B:VAL232 4.7 56.8 1.0
O B:THR233 4.7 67.2 1.0
CA B:LEU176 4.7 54.5 1.0
N B:LEU176 4.9 54.9 1.0
CA B:VAL232 5.0 57.3 1.0

Sodium binding site 3 out of 3 in 5m1d

Go back to Sodium Binding Sites List in 5m1d
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:56.8
occ:0.50
 OE2 C:GLU241 2.1 0.7 1.0
O C:ALA231 2.5 95.2 1.0
O3P C:4LU502 2.5 95.7 1.0
O2P C:4LU502 2.9 0.7 1.0
O5' C:4LU502 2.9 0.6 1.0
P C:4LU502 3.0 0.6 1.0
O4' C:4LU502 3.1 0.9 1.0
CD C:GLU241 3.2 0.7 1.0
O C:LEU176 3.3 0.1 1.0
MN C:MN501 3.6 0.4 0.5
C C:ALA231 3.6 90.2 1.0
CG C:GLU241 3.7 0.1 1.0
C4' C:4LU502 3.7 99.3 1.0
O C:THR233 3.8 0.2 1.0
C5' C:4LU502 3.8 0.9 1.0
OE1 C:GLU241 4.2 0.0 1.0
CA C:ALA231 4.5 92.2 1.0
C C:LEU176 4.5 0.6 1.0
O1P C:4LU502 4.5 95.3 1.0
N C:VAL232 4.6 84.0 1.0
OD1 C:ASN175 4.6 0.3 1.0
CA C:VAL232 4.7 81.0 1.0
C C:THR233 4.7 0.4 1.0
O C:GLY230 4.8 85.8 1.0
C C:VAL232 4.9 84.9 1.0
CA C:GLY177 4.9 92.5 1.0
CA C:PRO234 5.0 0.8 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: Mon Oct 7 22:28:07 2024

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