Atomistry » Sodium » PDB 5lq7-5m1e » 5m1e
Atomistry »
  Sodium »
    PDB 5lq7-5m1e »
      5m1e »

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: Mon Oct 7 22:28:09 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy