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Manganese in PDB 4cck: 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66) in Complex with Mn(II) and N-Oxalylglycine (Nog)

Enzymatic activity of 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66) in Complex with Mn(II) and N-Oxalylglycine (Nog)

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

Protein crystallography data

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

Resolution Low / High (Å) 81.10 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 101.410, 80.710, 151.540, 90.00, 94.54, 90.00
R / Rfree (%) 18.6 / 19.7

Manganese Binding Sites:

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

Manganese binding site 1 out of 4 in 4cck

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Manganese binding site 1 out of 4 in the 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66) in Complex with Mn(II) and N-Oxalylglycine (Nog)


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) in Complex with Mn(II) and N-Oxalylglycine (Nog) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn901

b:18.4
occ:1.00
 O A:HOH2105 2.2 48.3 1.0
O2' A:OGA902 2.3 41.3 1.0
OD2 A:ASP342 2.3 43.0 1.0
NE2 A:HIS405 2.4 30.8 1.0
NE2 A:HIS340 2.4 36.6 1.0
O2 A:OGA902 2.4 39.1 1.0
CE1 A:HIS340 3.0 34.8 1.0
C2 A:OGA902 3.0 41.6 1.0
CG A:ASP342 3.1 39.6 1.0
C1 A:OGA902 3.1 41.4 1.0
OD1 A:ASP342 3.2 42.8 1.0
CE1 A:HIS405 3.2 31.2 1.0
CD2 A:HIS405 3.4 30.2 1.0
CD2 A:HIS340 3.6 35.7 1.0
ND1 A:HIS340 4.2 35.2 1.0
N1 A:OGA902 4.3 40.5 1.0
O1 A:OGA902 4.4 36.9 1.0
O A:HOH2079 4.4 58.9 1.0
ND1 A:HIS405 4.4 29.2 1.0
O A:HOH2104 4.5 47.1 1.0
CG A:HIS340 4.5 36.4 1.0
CG A:HIS405 4.5 29.4 1.0
CB A:ASP342 4.5 35.3 1.0
OH A:TYR328 4.6 31.8 1.0

Manganese binding site 2 out of 4 in 4cck

Go back to Manganese Binding Sites List in 4cck
Manganese binding site 2 out of 4 in the 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66) in Complex with Mn(II) and N-Oxalylglycine (Nog)


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) in Complex with Mn(II) and N-Oxalylglycine (Nog) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn901

b:18.3
occ:1.00
 O2' B:OGA902 2.2 42.4 1.0
O2 B:OGA902 2.4 45.1 1.0
O B:HOH2066 2.4 50.7 1.0
NE2 B:HIS340 2.4 35.3 1.0
NE2 B:HIS405 2.4 38.6 1.0
OD2 B:ASP342 2.4 38.8 1.0
C2 B:OGA902 3.0 42.6 1.0
OD1 B:ASP342 3.0 40.2 1.0
C1 B:OGA902 3.1 42.5 1.0
CG B:ASP342 3.1 39.3 1.0
CE1 B:HIS405 3.2 39.5 1.0
CE1 B:HIS340 3.2 32.9 1.0
CD2 B:HIS340 3.4 35.5 1.0
CD2 B:HIS405 3.5 38.3 1.0
N1 B:OGA902 4.3 43.5 1.0
O1 B:OGA902 4.3 37.9 1.0
ND1 B:HIS340 4.4 31.0 1.0
ND1 B:HIS405 4.4 39.6 1.0
CG B:HIS340 4.5 33.1 1.0
CG B:HIS405 4.5 39.3 1.0
CB B:ASP342 4.6 36.8 1.0
OH B:TYR328 4.6 39.0 1.0
C4 B:OGA902 5.0 45.8 1.0

Manganese binding site 3 out of 4 in 4cck

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Manganese binding site 3 out of 4 in the 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66) in Complex with Mn(II) and N-Oxalylglycine (Nog)


Mono view


Stereo pair view

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

b:20.3
occ:1.00
 O2' C:OGA902 2.2 41.1 1.0
O C:HOH2090 2.3 49.1 1.0
O2 C:OGA902 2.4 39.3 1.0
OD2 C:ASP342 2.4 38.7 1.0
NE2 C:HIS405 2.4 32.2 1.0
NE2 C:HIS340 2.5 39.2 1.0
C2 C:OGA902 3.0 40.3 1.0
C1 C:OGA902 3.1 40.7 1.0
CG C:ASP342 3.1 35.9 1.0
OD1 C:ASP342 3.2 38.0 1.0
CE1 C:HIS405 3.2 31.5 1.0
CE1 C:HIS340 3.3 36.3 1.0
CD2 C:HIS340 3.5 38.6 1.0
CD2 C:HIS405 3.6 32.9 1.0
N1 C:OGA902 4.3 41.0 1.0
O1 C:OGA902 4.3 38.2 1.0
ND1 C:HIS405 4.4 30.3 1.0
ND1 C:HIS340 4.5 35.4 1.0
OH C:TYR328 4.5 37.4 1.0
CG C:HIS405 4.6 32.0 1.0
CB C:ASP342 4.6 33.3 1.0
CG C:HIS340 4.6 36.6 1.0

Manganese binding site 4 out of 4 in 4cck

Go back to Manganese Binding Sites List in 4cck
Manganese binding site 4 out of 4 in the 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66) in Complex with Mn(II) and N-Oxalylglycine (Nog)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66) in Complex with Mn(II) and N-Oxalylglycine (Nog) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn901

b:28.7
occ:1.00
 O2 D:OGA902 2.3 54.0 1.0
O D:HOH2054 2.3 50.4 1.0
OD2 D:ASP342 2.4 46.1 1.0
O2' D:OGA902 2.4 53.4 1.0
NE2 D:HIS405 2.4 46.2 1.0
NE2 D:HIS340 2.6 48.6 1.0
C1 D:OGA902 3.1 54.5 1.0
C2 D:OGA902 3.1 54.0 1.0
CG D:ASP342 3.1 45.0 1.0
OD1 D:ASP342 3.2 46.4 1.0
CE1 D:HIS340 3.3 48.3 1.0
CE1 D:HIS405 3.4 45.6 1.0
CD2 D:HIS405 3.4 45.5 1.0
CD2 D:HIS340 3.6 49.0 1.0
O1 D:OGA902 4.3 52.5 1.0
ND1 D:HIS340 4.4 48.2 1.0
N1 D:OGA902 4.4 53.1 1.0
ND1 D:HIS405 4.5 46.5 1.0
O D:HOH2053 4.5 55.8 1.0
CG D:HIS405 4.6 46.0 1.0
CG D:HIS340 4.6 48.6 1.0
CB D:ASP342 4.6 42.5 1.0
OH D:TYR328 4.6 38.6 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 18:54:03 2024

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