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Manganese in PDB 5lwb: Crystal Structure of Human JARID1B in Complex with S40650A

Protein crystallography data

The structure of Crystal Structure of Human JARID1B in Complex with S40650A, PDB code: 5lwb was solved by V.Srikannathasan, Y.V.Le Bihan, A.Szykowska, C.Johansson, C.Gileadi, C.H.Arrowsmith, A.M.Edwards, C.Bountra, F.Von Delft, U.Oppermann, K.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.18 / 2.39
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 142.360, 142.360, 151.540, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 21.8

Other elements in 5lwb:

The structure of Crystal Structure of Human JARID1B in Complex with S40650A also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human JARID1B in Complex with S40650A (pdb code 5lwb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Human JARID1B in Complex with S40650A, PDB code: 5lwb:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 5lwb

Go back to Manganese Binding Sites List in 5lwb
Manganese binding site 1 out of 3 in the Crystal Structure of Human JARID1B in Complex with S40650A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human JARID1B in Complex with S40650A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn802

b:62.3
occ:0.45
O A:HOH969 2.2 60.3 1.0
ND2 A:ASN91 2.6 45.2 1.0
O A:LEU413 2.6 56.8 1.0
O A:THR416 2.7 78.0 1.0
O A:GLU419 2.9 86.2 1.0
O A:LEU90 3.1 51.3 1.0
C A:LEU413 3.8 50.9 1.0
C A:GLU419 3.9 69.0 1.0
C A:THR416 3.9 73.6 1.0
O A:VAL414 3.9 55.0 1.0
CG A:ASN91 3.9 50.4 1.0
C A:VAL414 4.0 53.0 1.0
CA A:VAL414 4.0 43.7 1.0
C A:LEU90 4.1 48.7 1.0
CB A:GLU419 4.2 62.3 1.0
CA A:ASN91 4.3 49.8 1.0
N A:VAL414 4.4 44.5 1.0
N A:THR416 4.5 72.6 1.0
CB A:ASN91 4.6 50.6 1.0
CA A:GLU419 4.6 66.1 1.0
N A:ASN91 4.7 48.6 1.0
N A:SER415 4.7 48.5 1.0
CA A:THR416 4.7 74.3 1.0
OD1 A:ASN91 4.8 65.9 1.0
N A:ASP420 4.8 60.0 1.0
N A:GLU419 4.9 68.8 1.0
N A:ILE417 4.9 72.9 1.0
C A:SER415 4.9 66.5 1.0
CA A:ASP420 4.9 73.7 1.0
CA A:LEU413 5.0 51.2 1.0
CA A:ILE417 5.0 81.6 1.0

Manganese binding site 2 out of 3 in 5lwb

Go back to Manganese Binding Sites List in 5lwb
Manganese binding site 2 out of 3 in the Crystal Structure of Human JARID1B in Complex with S40650A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human JARID1B in Complex with S40650A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn812

b:41.7
occ:1.00
OE2 A:GLU501 2.0 47.3 1.0
O A:HOH910 2.1 42.0 1.0
NE2 A:HIS587 2.2 39.4 1.0
NE2 A:HIS499 2.2 48.1 1.0
N3 A:79H814 2.3 62.1 1.0
O A:HOH928 2.4 42.2 1.0
CE1 A:HIS499 3.0 48.7 1.0
CE1 A:HIS587 3.1 40.4 1.0
CD A:GLU501 3.1 47.8 1.0
CD2 A:HIS587 3.2 39.1 1.0
CD2 A:HIS499 3.3 40.4 1.0
C9 A:79H814 3.4 71.3 1.0
OE1 A:GLU501 3.6 54.0 1.0
O A:DMS808 4.1 0.1 1.0
ND1 A:HIS499 4.2 48.5 1.0
ND1 A:HIS587 4.2 38.2 1.0
CG A:HIS587 4.3 38.6 1.0
CG A:HIS499 4.3 45.6 1.0
OG A:SER507 4.3 47.7 1.0
O A:HOH971 4.3 49.9 1.0
CG A:GLU501 4.4 37.4 1.0
O A:HOH1022 4.4 82.0 1.0
C1 A:DMS808 4.7 49.7 1.0
C6 A:79H814 4.8 84.6 1.0

Manganese binding site 3 out of 3 in 5lwb

Go back to Manganese Binding Sites List in 5lwb
Manganese binding site 3 out of 3 in the Crystal Structure of Human JARID1B in Complex with S40650A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human JARID1B in Complex with S40650A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn813

b:0.5
occ:1.00
O A:HOH1021 2.9 65.5 1.0
O A:HOH1015 3.4 48.8 1.0
CE1 A:HIS622 3.6 62.9 1.0
NE2 A:HIS718 3.6 56.1 1.0
NE2 A:HIS622 4.1 58.3 1.0
CD2 A:HIS718 4.4 53.7 1.0
CE1 A:HIS718 4.6 49.4 1.0
CE A:LYS694 4.7 63.1 1.0
ND1 A:HIS622 4.8 64.6 1.0
CG A:LYS694 4.8 56.1 1.0

Reference:

V.Srikannathasan, V.Srikannathasan, Y.V.Le Bihan, A.Szykowska, C.Johansson, C.Gileadi, C.H.Arrowsmith, A.M.Edwards, C.Bountra, F.Von Delft, U.Oppermann, K.Huber. N/A N/A.
Page generated: Tue Dec 15 04:43:44 2020

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