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Manganese 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:

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

Manganese binding site 1 out of 3 in 5m1d

Go back to Manganese Binding Sites List in 5m1d
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:1.0
occ:0.50
 OE2 A:GLU241 1.9 0.2 1.0
OE1 A:GLU241 1.9 0.6 1.0
OD1 A:ASN175 2.0 0.4 1.0
ND2 A:ASN175 2.0 0.4 1.0
CG A:ASN175 2.2 0.0 1.0
CD A:GLU241 2.3 0.9 1.0
O3P A:4LU502 2.3 99.2 1.0
O A:HOH614 3.4 85.6 1.0
CB A:ASN175 3.6 0.9 1.0
NA A:NA503 3.7 60.5 0.5
CG A:GLU241 3.8 0.7 1.0
P A:4LU502 3.8 0.8 1.0
O A:LEU176 3.9 92.3 1.0
CA A:ASN175 4.0 0.8 1.0
N A:LEU176 4.1 96.5 1.0
O5' A:4LU502 4.5 0.2 1.0
C A:ASN175 4.5 97.9 1.0
C A:LEU176 4.6 89.5 1.0
O2P A:4LU502 4.6 87.2 1.0
O1P A:4LU502 4.7 83.3 1.0
O A:LEU239 4.7 0.2 1.0
CB A:GLU241 4.7 0.2 1.0
O A:HOH604 4.8 67.5 1.0
O A:PRO236 4.9 0.7 1.0
CG2 A:VAL235 4.9 0.0 1.0

Manganese binding site 2 out of 3 in 5m1d

Go back to Manganese Binding Sites List in 5m1d
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:95.5
occ:1.00
 O B:HOH615 1.9 96.8 1.0
OD1 B:ASN175 1.9 69.4 1.0
OE1 B:GLU241 2.0 0.5 1.0
OE2 B:GLU241 2.0 96.0 1.0
O B:HOH610 2.2 60.6 1.0
CD B:GLU241 2.3 79.5 1.0
O3P B:4LU502 2.3 52.4 1.0
CG B:ASN175 3.1 57.4 1.0
NA B:NA503 3.5 66.7 1.0
P B:4LU502 3.7 53.7 1.0
CG B:GLU241 3.8 74.8 1.0
ND2 B:ASN175 3.8 56.7 1.0
O B:HOH657 3.8 64.7 1.0
O2P B:4LU502 4.2 59.8 1.0
CB B:ASN175 4.2 56.5 1.0
O B:LEU176 4.3 52.8 1.0
O B:PRO236 4.4 85.7 1.0
O5' B:4LU502 4.5 52.2 1.0
CG2 B:VAL235 4.5 88.5 1.0
O B:VAL235 4.6 71.3 1.0
CA B:ASN175 4.7 58.9 1.0
O B:LEU239 4.7 88.5 1.0
N B:LEU176 4.7 54.9 1.0
O1P B:4LU502 4.8 46.9 1.0
OD1 B:ASP237 4.9 72.7 1.0
CA B:ASP237 4.9 76.8 1.0
CB B:GLU241 4.9 70.6 1.0

Manganese binding site 3 out of 3 in 5m1d

Go back to Manganese Binding Sites List in 5m1d
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:0.4
occ:0.50
 OE2 C:GLU241 1.9 0.7 1.0
OD1 C:ASN175 1.9 0.3 1.0
OE1 C:GLU241 1.9 0.0 1.0
CD C:GLU241 2.2 0.7 1.0
O3P C:4LU502 2.9 95.7 1.0
CG C:ASN175 3.0 0.9 1.0
NA C:NA503 3.6 56.8 0.5
CG C:GLU241 3.7 0.1 1.0
ND2 C:ASN175 3.8 0.3 1.0
CB C:ASN175 4.0 0.2 1.0
P C:4LU502 4.1 0.6 1.0
O C:LEU176 4.2 0.1 1.0
O2P C:4LU502 4.3 0.7 1.0
O C:PRO236 4.3 0.6 1.0
CA C:ASN175 4.4 0.3 1.0
O C:LEU239 4.4 0.6 1.0
CG2 C:VAL235 4.5 0.8 1.0
N C:LEU176 4.5 0.1 1.0
CB C:GLU241 4.7 0.8 1.0
O C:VAL235 4.8 0.8 1.0
CA C:ASP237 4.9 0.1 1.0
C C:ASN175 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: Sun Oct 6 01:53:53 2024

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