Atomistry » Manganese » PDB 4b5i-4dec » 4ccl
Atomistry »
  Manganese »
    PDB 4b5i-4dec »
      4ccl »

Manganese in PDB 4ccl: X-Ray Structure of E. Coli Ycfd

Protein crystallography data

The structure of X-Ray Structure of E. Coli Ycfd, PDB code: 4ccl was solved by M.A.Mcdonough, C.H.Ho, N.J.Kershaw, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.765 / 2.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 120.693, 120.693, 133.498, 90.00, 90.00, 90.00
R / Rfree (%) 19.83 / 24.9

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Structure of E. Coli Ycfd (pdb code 4ccl). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the X-Ray Structure of E. Coli Ycfd, PDB code: 4ccl:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4ccl

Go back to Manganese Binding Sites List in 4ccl
Manganese binding site 1 out of 4 in the X-Ray Structure of E. Coli Ycfd


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Structure of E. Coli Ycfd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1373

b:0.9
occ:0.50
OD2 A:ASP127 2.1 96.4 1.0
NE2 A:HIS125 2.2 0.8 1.0
NE2 A:HIS187 2.2 81.2 1.0
CE1 A:HIS187 3.0 83.4 1.0
CD2 A:HIS125 3.1 0.3 1.0
CE1 A:HIS125 3.1 0.8 1.0
CG A:ASP127 3.2 94.1 1.0
CD2 A:HIS187 3.4 79.9 1.0
OD1 A:ASP127 3.6 96.4 1.0
ND1 A:HIS125 4.1 0.2 1.0
CG A:HIS125 4.1 0.5 1.0
ND1 A:HIS187 4.2 82.2 1.0
CG A:HIS187 4.4 79.3 1.0
CB A:ASP127 4.5 84.2 1.0
CG1 A:VAL131 4.7 57.8 1.0

Manganese binding site 2 out of 4 in 4ccl

Go back to Manganese Binding Sites List in 4ccl
Manganese binding site 2 out of 4 in the X-Ray Structure of E. Coli Ycfd


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Structure of E. Coli Ycfd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1374

b:0.9
occ:1.00
OD2 A:ASP11 3.0 73.7 1.0
ND1 A:HIS16 3.8 65.8 1.0
CA A:PHE12 4.1 60.9 1.0
N A:PHE12 4.1 61.3 1.0
CG A:ASP11 4.1 71.5 1.0
CB A:PHE12 4.3 55.5 1.0
O A:ASN8 4.3 68.3 1.0
CE1 A:HIS16 4.3 72.0 1.0
NH1 A:ARG15 4.3 73.9 1.0
O3 A:SO41377 4.4 0.3 1.0
CD1 A:LEU7 4.4 80.0 1.0
C A:ASP11 4.4 63.6 1.0
CB A:ASP11 4.4 65.0 1.0
CD2 A:LEU24 4.5 75.9 1.0
O A:ASP11 4.7 67.3 1.0
CD1 A:PHE12 4.7 55.0 1.0
CB A:ASN8 5.0 70.8 1.0

Manganese binding site 3 out of 4 in 4ccl

Go back to Manganese Binding Sites List in 4ccl
Manganese binding site 3 out of 4 in the X-Ray Structure of E. Coli Ycfd


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Structure of E. Coli Ycfd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1373

b:0.1
occ:1.00
O B:ASP58 2.5 0.3 1.0
ND1 B:HIS56 3.5 84.2 1.0
C B:ASP58 3.5 0.8 1.0
CE1 B:HIS56 3.7 78.9 1.0
CA B:ASP58 4.1 0.1 1.0
N B:ASP58 4.5 0.2 1.0
N B:GLY59 4.6 0.5 1.0
CG B:HIS56 4.6 83.0 1.0
NE2 B:HIS56 4.9 77.2 1.0
CA B:GLY59 4.9 98.4 1.0

Manganese binding site 4 out of 4 in 4ccl

Go back to Manganese Binding Sites List in 4ccl
Manganese binding site 4 out of 4 in the X-Ray Structure of E. Coli Ycfd


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Structure of E. Coli Ycfd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1374

b:0.8
occ:1.00
O B:HOH2099 3.3 67.1 1.0
ND1 B:HIS329 3.6 85.7 1.0
CB B:ASP349 4.0 0.8 1.0
CB B:HIS329 4.1 80.5 1.0
N B:ALA350 4.1 94.6 1.0
N B:ASP349 4.2 0.3 1.0
CG B:HIS329 4.3 85.5 1.0
C B:ASP349 4.4 99.7 1.0
CA B:ASP349 4.4 0.8 1.0
CE1 B:HIS329 4.6 85.3 1.0
CA B:ALA350 4.7 85.9 1.0
CA B:HIS329 4.7 81.3 1.0
CD B:PRO331 4.8 78.2 1.0
CB B:ALA350 4.8 81.8 1.0
OD2 B:ASP349 4.9 0.6 1.0
CG B:PRO331 4.9 74.7 1.0
CG B:ASP349 4.9 0.7 1.0
O B:PHE347 4.9 76.2 1.0

Reference:

R.Chowdhury, R.Sekirnik, N.C.Brissett, T.Krojer, C.-H.Ho, S.S.Ng, I.J.Clifton, W.Ge, N.J.Kershaw, G.C.Fox, J.R.C.Muniz, M.Vollmar, C.Phillips, E.S.Pilka, K.L.Kavanagh, F.Von Deflt, U.Oppermann, M.A.Mcdonough, A.J.Doherty, C.J.Schofield. Ribosomal Oxygenases Are Structurally Conserved From Prokaryotes to Humans. Nature V. 510 422 2014.
ISSN: ISSN 0028-0836
PubMed: 24814345
DOI: 10.1038/NATURE13263
Page generated: Tue Dec 15 04:18:45 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy