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Manganese in PDB 5raj: Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with BD009815A

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with BD009815A, PDB code: 5raj 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) 64.58 / 1.61
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.560, 93.330, 93.897, 90.00, 108.12, 90.00
R / Rfree (%) 19.1 / 22.3

Other elements in 5raj:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with BD009815A also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with BD009815A (pdb code 5raj). 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 BD009815A, PDB code: 5raj:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 5raj

Go back to Manganese Binding Sites List in 5raj
Manganese binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with BD009815A


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 BD009815A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1806

b:16.6
occ:1.00
NE2 A:HIS1560 2.1 17.3 1.0
OD2 A:ASP1562 2.1 21.6 1.0
NE2 A:HIS1689 2.2 16.0 1.0
CE1 A:HIS1560 3.0 17.6 1.0
CE1 A:HIS1689 3.0 17.6 1.0
CD2 A:HIS1560 3.1 17.7 1.0
CD2 A:HIS1689 3.2 16.0 1.0
CG A:ASP1562 3.4 29.6 1.0
O A:HOH1976 3.8 22.0 1.0
OD1 A:ASP1562 3.9 39.6 1.0
ND1 A:HIS1560 4.1 18.9 1.0
ND1 A:HIS1689 4.2 17.0 1.0
CG A:HIS1560 4.2 16.7 1.0
CG A:HIS1689 4.3 16.9 1.0
O A:HOH2142 4.3 32.0 1.0
OH A:TYR1541 4.4 21.1 1.0
O A:HOH2193 4.4 24.5 1.0
CB A:ASP1562 4.8 26.3 1.0

Manganese binding site 2 out of 2 in 5raj

Go back to Manganese Binding Sites List in 5raj
Manganese binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD1B in Complex with BD009815A


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 BD009815A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1802

b:17.0
occ:1.00
NE2 B:HIS1560 2.0 18.1 1.0
OD2 B:ASP1562 2.1 19.9 1.0
NE2 B:HIS1689 2.1 17.9 1.0
CE1 B:HIS1560 2.9 22.4 1.0
CE1 B:HIS1689 3.0 18.4 1.0
CG B:ASP1562 3.1 19.2 1.0
CD2 B:HIS1560 3.1 20.2 1.0
CD2 B:HIS1689 3.2 20.4 1.0
OD1 B:ASP1562 3.5 21.1 1.0
ND1 B:HIS1560 4.1 19.9 1.0
ND1 B:HIS1689 4.1 19.8 1.0
CG B:HIS1560 4.2 21.7 1.0
CG B:HIS1689 4.2 18.8 1.0
OH B:TYR1541 4.4 21.4 1.0
CB B:ASP1562 4.5 19.0 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: Tue Dec 15 04:46:04 2020

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