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Manganese 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:

Sodium (Na) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of N-Terminally Tagged Ubid From E. Coli Reconstituted with Prfmn Cofactor, PDB code: 5m1e:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 5m1e

Go back to Manganese Binding Sites List in 5m1e
Manganese 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 Manganese with other atoms in the Mn 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:Mn501

b:70.0
occ:1.00
 OE2 A:GLU241 2.0 96.5 1.0
ND2 A:ASN175 2.0 84.8 1.0
OD1 A:ASN175 2.1 80.4 1.0
OE1 A:GLU241 2.1 76.3 1.0
OAK A:7D9502 2.1 61.6 1.0
O A:HOH607 2.4 58.2 1.0
O A:HOH601 2.4 65.1 1.0
CG A:ASN175 2.4 73.7 1.0
CD A:GLU241 2.5 70.4 1.0
NA A:NA503 3.3 60.7 1.0
PBJ A:7D9502 3.5 69.0 1.0
CB A:ASN175 4.0 67.7 1.0
OAJ A:7D9502 4.0 62.3 1.0
CG A:GLU241 4.1 68.8 1.0
O A:HOH602 4.2 51.9 1.0
OAT A:7D9502 4.4 60.1 1.0
O A:LEU176 4.4 61.3 1.0
OAF A:7D9502 4.4 57.9 1.0
O A:VAL235 4.5 82.5 1.0
CG2 A:VAL235 4.5 87.8 1.0
CA A:ASN175 4.6 66.4 1.0
O A:LEU239 4.7 73.2 1.0
N A:LEU176 4.8 64.4 1.0
CA A:ASP237 4.8 81.0 1.0
OD1 A:ASP237 4.8 81.2 1.0
O A:PRO236 4.9 84.5 1.0
CA A:GLY198 5.0 64.1 1.0

Manganese binding site 2 out of 3 in 5m1e

Go back to Manganese Binding Sites List in 5m1e
Manganese 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 Manganese with other atoms in the Mn 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:Mn501

b:64.5
occ:1.00
 OE1 B:GLU241 1.9 92.4 1.0
O B:HOH615 2.0 64.1 1.0
OD1 B:ASN175 2.0 60.0 1.0
O B:HOH604 2.1 68.8 1.0
OE2 B:GLU241 2.1 73.3 1.0
OAK B:7D9502 2.2 48.6 1.0
CD B:GLU241 2.4 71.1 1.0
CG B:ASN175 3.1 55.6 1.0
NA B:NA503 3.5 64.5 1.0
PBJ B:7D9502 3.5 54.3 1.0
O B:HOH623 3.5 72.5 1.0
ND2 B:ASN175 3.6 56.5 1.0
OAJ B:7D9502 3.8 63.2 1.0
CG B:GLU241 4.0 67.7 1.0
CB B:ASN175 4.3 60.0 1.0
O B:VAL235 4.3 85.8 1.0
OAT B:7D9502 4.3 48.6 1.0
O B:LEU176 4.4 59.0 1.0
CG2 B:VAL235 4.4 94.3 1.0
OAF B:7D9502 4.5 45.3 1.0
O B:LEU239 4.7 78.8 1.0
CA B:ASP237 4.8 78.3 1.0
OD1 B:ASP237 4.8 73.5 1.0
CA B:ASN175 4.9 62.7 1.0
O B:PRO236 4.9 86.4 1.0
N B:LEU176 4.9 58.2 1.0

Manganese binding site 3 out of 3 in 5m1e

Go back to Manganese Binding Sites List in 5m1e
Manganese 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 Manganese with other atoms in the Mn 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:Mn501

b:0.6
occ:1.00
 OE2 C:GLU241 1.9 0.9 1.0
OD1 C:ASN175 1.9 0.6 1.0
OE1 C:GLU241 2.0 0.5 1.0
CD C:GLU241 2.3 0.8 1.0
OAK C:7D9502 2.6 85.8 1.0
CG C:ASN175 3.0 0.6 1.0
NA C:NA503 3.6 75.8 1.0
ND2 C:ASN175 3.7 99.8 1.0
PBJ C:7D9502 3.8 76.5 1.0
CG C:GLU241 3.9 0.3 1.0
OAJ C:7D9502 4.0 72.6 1.0
CB C:ASN175 4.2 0.8 1.0
O C:VAL235 4.3 0.2 1.0
CG2 C:VAL235 4.3 0.4 1.0
O C:LEU176 4.4 91.0 1.0
O C:LEU239 4.5 0.5 1.0
CA C:ASN175 4.7 0.7 1.0
CA C:ASP237 4.7 0.5 1.0
OAF C:7D9502 4.7 63.5 1.0
O C:PRO236 4.7 0.3 1.0
N C:LEU176 4.8 0.8 1.0
OD1 C:ASP237 4.8 0.9 1.0
CB C:GLU241 5.0 0.6 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: Sat Aug 16 18:31:39 2025

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