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Manganese in PDB 4ccn: 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 L299C/C300S) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-2)

Enzymatic activity of 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 L299C/C300S) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-2)

All present enzymatic activity of 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 L299C/C300S) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-2):
1.14.11.27;

Protein crystallography data

The structure of 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 L299C/C300S) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-2), PDB code: 4ccn 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) 44.19 / 2.23
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 155.165, 83.721, 97.034, 90.00, 100.35, 90.00
R / Rfree (%) 23.8 / 24.8

Manganese Binding Sites:

The binding sites of Manganese atom in the 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 L299C/C300S) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-2) (pdb code 4ccn). 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 L299C/C300S) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-2), PDB code: 4ccn:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 4ccn

Go back to Manganese Binding Sites List in 4ccn
Manganese binding site 1 out of 2 in the 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 L299C/C300S) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-2)


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 L299C/C300S) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn901

b:26.5
occ:1.00
 O2' A:OGA902 2.1 33.8 1.0
OD2 A:ASP342 2.2 30.9 1.0
O A:HOH2076 2.2 30.3 1.0
NE2 A:HIS340 2.3 22.4 1.0
O2 A:OGA902 2.4 34.8 1.0
NE2 A:HIS405 2.4 22.7 1.0
C2 A:OGA902 2.9 35.4 1.0
C1 A:OGA902 3.0 35.8 1.0
CG A:ASP342 3.1 30.2 1.0
CE1 A:HIS405 3.2 21.5 1.0
CD2 A:HIS340 3.3 17.2 1.0
CE1 A:HIS340 3.3 17.4 1.0
OD1 A:ASP342 3.4 29.2 1.0
CD2 A:HIS405 3.4 21.4 1.0
N1 A:OGA902 4.2 37.4 1.0
O1 A:OGA902 4.3 35.1 1.0
CB C:HIS216 4.3 31.6 1.0
ND1 A:HIS405 4.4 20.9 1.0
ND1 A:HIS340 4.4 21.3 1.0
CG A:HIS340 4.4 19.7 1.0
OH A:TYR328 4.5 25.5 1.0
CG A:HIS405 4.5 21.2 1.0
CB A:ASP342 4.5 26.0 1.0
N C:HIS216 4.7 35.2 1.0
C4 A:OGA902 4.9 39.5 1.0

Manganese binding site 2 out of 2 in 4ccn

Go back to Manganese Binding Sites List in 4ccn
Manganese binding site 2 out of 2 in the 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 L299C/C300S) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-2)


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 L299C/C300S) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn901

b:19.7
occ:1.00
 O2' B:OGA902 2.1 27.2 1.0
O B:HOH2078 2.1 18.3 1.0
NE2 B:HIS405 2.2 20.3 1.0
NE2 B:HIS340 2.3 23.3 1.0
OD2 B:ASP342 2.3 24.0 1.0
O2 B:OGA902 2.4 22.3 1.0
C2 B:OGA902 2.9 27.9 1.0
CE1 B:HIS340 2.9 17.4 1.0
C1 B:OGA902 3.0 27.3 1.0
CE1 B:HIS405 3.1 18.1 1.0
CD2 B:HIS405 3.2 20.5 1.0
CG B:ASP342 3.2 24.5 1.0
OD1 B:ASP342 3.5 28.2 1.0
CD2 B:HIS340 3.5 18.3 1.0
ND1 B:HIS340 4.2 21.7 1.0
N1 B:OGA902 4.2 32.7 1.0
ND1 B:HIS405 4.3 20.1 1.0
O1 B:OGA902 4.3 25.1 1.0
CG B:HIS405 4.3 19.1 1.0
CG B:HIS340 4.5 20.4 1.0
CB D:HIS216 4.5 36.0 1.0
OH B:TYR328 4.6 26.2 1.0
CB B:ASP342 4.6 20.9 1.0
N D:HIS216 4.7 35.8 1.0
C4 B:OGA902 4.8 33.3 1.0
CB D:ASN215 4.9 34.7 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: Sat Oct 5 18:54:14 2024

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