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Manganese in PDB 4cco: 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3)

Enzymatic activity of 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3)

All present enzymatic activity of 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3):
1.14.11.27;

Protein crystallography data

The structure of 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3), PDB code: 4cco was solved by R.Chowdhury, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.70 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 155.390, 84.944, 97.300, 90.00, 100.30, 90.00
R / Rfree (%) 21 / 22.5

Manganese Binding Sites:

The binding sites of Manganese atom in the 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3) (pdb code 4cco). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3), PDB code: 4cco:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 4cco

Go back to Manganese Binding Sites List in 4cco
Manganese binding site 1 out of 2 in the 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn901

b:24.7
occ:1.00
 OD2 A:ASP342 2.0 34.0 1.0
O2 A:OGA902 2.2 28.7 1.0
O A:HOH2122 2.3 62.7 1.0
O2' A:OGA902 2.3 27.0 1.0
NE2 A:HIS340 2.3 24.1 1.0
NE2 A:HIS405 2.4 26.9 1.0
CG A:ASP342 3.0 32.7 1.0
C1 A:OGA902 3.0 29.7 1.0
C2 A:OGA902 3.0 30.1 1.0
CE1 A:HIS340 3.2 23.7 1.0
CE1 A:HIS405 3.3 26.0 1.0
OD1 A:ASP342 3.3 36.2 1.0
CD2 A:HIS405 3.4 26.4 1.0
CD2 A:HIS340 3.4 23.1 1.0
O1 A:OGA902 4.1 28.1 1.0
CB C:HIS216 4.2 56.7 1.0
CB A:ASP342 4.3 30.7 1.0
N1 A:OGA902 4.3 31.7 1.0
ND1 A:HIS340 4.3 25.2 1.0
ND1 A:HIS405 4.4 25.9 1.0
CG A:HIS340 4.5 24.7 1.0
CG A:HIS405 4.5 27.3 1.0
OH A:TYR328 4.6 23.6 1.0
CB C:ASN215 4.8 54.1 1.0
N C:HIS216 4.8 56.6 1.0
C4 A:OGA902 5.0 34.8 1.0

Manganese binding site 2 out of 2 in 4cco

Go back to Manganese Binding Sites List in 4cco
Manganese binding site 2 out of 2 in the 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn901

b:27.6
occ:1.00
 OD2 B:ASP342 2.2 24.8 1.0
NE2 B:HIS405 2.2 25.7 1.0
O2' B:OGA902 2.2 25.2 1.0
O B:HOH2123 2.3 48.8 1.0
O2 B:OGA902 2.3 28.2 1.0
NE2 B:HIS340 2.4 22.5 1.0
C2 B:OGA902 2.9 28.8 1.0
C1 B:OGA902 2.9 29.5 1.0
CE1 B:HIS340 3.1 22.0 1.0
CE1 B:HIS405 3.1 26.2 1.0
CG B:ASP342 3.1 24.2 1.0
CD2 B:HIS405 3.2 25.3 1.0
OD1 B:ASP342 3.5 29.1 1.0
CD2 B:HIS340 3.5 20.8 1.0
O1 B:OGA902 4.1 29.8 1.0
N1 B:OGA902 4.2 27.9 1.0
ND1 B:HIS405 4.2 26.3 1.0
ND1 B:HIS340 4.3 23.1 1.0
CG B:HIS405 4.3 26.4 1.0
CB D:HIS216 4.4 57.5 1.0
CB B:ASP342 4.5 23.5 1.0
CG B:HIS340 4.5 20.7 1.0
OD1 D:ASN215 4.5 60.7 1.0
OH B:TYR328 4.7 23.4 1.0
CB D:ASN215 4.7 59.3 1.0
C4 B:OGA902 4.9 29.8 1.0
N D:HIS216 4.9 60.1 1.0
CG D:ASN215 4.9 60.1 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 04:18:48 2020

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