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Manganese in PDB 5rb0: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010020A

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010020A, PDB code: 5rb0 was solved by M.Snee, R.Nowak, C.Johansson, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.80 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.520, 93.920, 92.910, 90.00, 107.88, 90.00
R / Rfree (%) 19.8 / 24.5

Other elements in 5rb0:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010020A also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010020A (pdb code 5rb0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010020A, PDB code: 5rb0:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 5rb0

Go back to Manganese Binding Sites List in 5rb0
Manganese binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010020A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010020A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1805

b:62.4
occ:1.00
NE2 A:HIS1560 2.4 27.6 1.0
NE2 A:HIS1689 2.4 21.9 1.0
O A:HOH2174 2.7 68.0 1.0
OD2 A:ASP1562 2.7 50.7 1.0
O A:HOH1908 3.0 37.0 1.0
CE1 A:HIS1560 3.1 26.8 1.0
CE1 A:HIS1689 3.2 23.3 1.0
CD2 A:HIS1689 3.5 23.0 1.0
CD2 A:HIS1560 3.5 25.2 1.0
CG A:ASP1562 3.8 44.5 1.0
OD1 A:ASP1562 4.1 51.9 1.0
ND1 A:HIS1560 4.3 26.8 1.0
ND1 A:HIS1689 4.4 24.1 1.0
CG A:HIS1560 4.5 25.3 1.0
CG A:HIS1689 4.6 23.9 1.0
O A:HOH1970 5.0 53.6 1.0

Manganese binding site 2 out of 2 in 5rb0

Go back to Manganese Binding Sites List in 5rb0
Manganese binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010020A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with FM010020A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1803

b:50.4
occ:1.00
OD2 B:ASP1562 2.2 40.8 1.0
NE2 B:HIS1689 2.3 24.8 1.0
NE2 B:HIS1560 2.3 27.3 1.0
CE1 B:HIS1689 3.0 27.2 1.0
CE1 B:HIS1560 3.2 28.6 1.0
CG B:ASP1562 3.2 37.7 1.0
CD2 B:HIS1689 3.4 26.5 1.0
CD2 B:HIS1560 3.4 25.9 1.0
OD1 B:ASP1562 3.6 38.4 1.0
ND1 B:HIS1689 4.2 25.9 1.0
ND1 B:HIS1560 4.3 27.5 1.0
CG B:HIS1689 4.4 25.8 1.0
CG B:HIS1560 4.5 27.1 1.0
CB B:ASP1562 4.5 34.5 1.0

Reference:

M.Snee, R.Nowak, C.Johansson, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, U.Oppermann. Pandda Analysis Group Deposition of Human JMJD1B Screened Against the Dspl Fragment Library To Be Published.
Page generated: Sun Oct 6 02:51:20 2024

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