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Manganese in PDB 6zuc: X-Ray Crystal Structure of the CSPYL1-LIG1-HAB1 Ternary Complex

Enzymatic activity of X-Ray Crystal Structure of the CSPYL1-LIG1-HAB1 Ternary Complex

All present enzymatic activity of X-Ray Crystal Structure of the CSPYL1-LIG1-HAB1 Ternary Complex:
3.1.3.16;

Protein crystallography data

The structure of X-Ray Crystal Structure of the CSPYL1-LIG1-HAB1 Ternary Complex, PDB code: 6zuc was solved by A.Albert, L.Infantes, J.L.Benavente, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.73 / 2.37
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.959, 62.733, 186.926, 90, 90, 90
R / Rfree (%) 18.1 / 24.3

Other elements in 6zuc:

The structure of X-Ray Crystal Structure of the CSPYL1-LIG1-HAB1 Ternary Complex also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Crystal Structure of the CSPYL1-LIG1-HAB1 Ternary Complex (pdb code 6zuc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the X-Ray Crystal Structure of the CSPYL1-LIG1-HAB1 Ternary Complex, PDB code: 6zuc:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6zuc

Go back to Manganese Binding Sites List in 6zuc
Manganese binding site 1 out of 4 in the X-Ray Crystal Structure of the CSPYL1-LIG1-HAB1 Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Crystal Structure of the CSPYL1-LIG1-HAB1 Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn601

b:68.6
occ:1.00
 OE2 B:GLU302 2.2 71.3 1.0
O B:HOH765 2.5 54.5 1.0
OD1 B:ASP298 2.6 47.0 1.0
O B:GLY401 2.6 38.5 1.0
OD2 B:ASP298 2.6 40.3 1.0
O B:HOH702 2.7 51.3 1.0
O B:HOH717 2.9 43.9 1.0
CG B:ASP298 2.9 47.7 1.0
CD B:GLU302 3.3 72.0 1.0
C B:GLY401 3.7 35.5 1.0
N B:GLY401 4.0 32.2 1.0
OE1 B:GLU302 4.1 77.0 1.0
CD B:PRO411 4.1 40.1 1.0
CA B:GLY401 4.2 33.7 1.0
CG B:GLU302 4.3 58.8 1.0
O B:VAL409 4.4 47.8 1.0
CB B:ASP298 4.5 45.0 1.0
O B:ASP402 4.5 44.0 1.0
CG B:PRO411 4.6 47.1 1.0
C B:ASP402 4.7 47.2 1.0
O B:SER399 4.7 45.6 1.0
N B:ASP402 4.8 33.6 1.0
N B:ARG403 4.9 49.4 1.0
CA B:ARG403 4.9 54.1 1.0
C B:ILE400 4.9 35.8 1.0

Manganese binding site 2 out of 4 in 6zuc

Go back to Manganese Binding Sites List in 6zuc
Manganese binding site 2 out of 4 in the X-Ray Crystal Structure of the CSPYL1-LIG1-HAB1 Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Crystal Structure of the CSPYL1-LIG1-HAB1 Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn602

b:60.1
occ:1.00
 O B:HOH713 1.9 50.6 1.0
O B:HOH736 2.1 57.3 1.0
O B:GLY244 2.1 51.6 1.0
OD1 B:ASP243 2.4 39.3 1.0
O B:HOH771 2.7 59.3 1.0
C B:GLY244 3.3 34.4 1.0
CG B:ASP243 3.5 43.5 1.0
MN B:MN603 3.7 58.1 1.0
OD2 B:ASP243 3.9 41.5 1.0
O B:HOH749 3.9 42.7 1.0
N B:HIS245 4.1 43.6 1.0
O B:HOH707 4.2 33.8 1.0
N B:GLY244 4.2 24.6 1.0
CA B:HIS245 4.2 50.9 1.0
O B:HOH719 4.2 47.9 1.0
OE1 B:GLU203 4.3 62.2 1.0
C B:ASP243 4.3 29.1 1.0
CA B:GLY244 4.3 25.8 1.0
OD1 B:ASP204 4.4 38.4 1.0
CB B:HIS245 4.5 40.9 1.0
O B:ASP243 4.5 27.6 1.0
OD1 B:ASP492 4.6 47.6 1.0
CB B:GLU203 4.6 42.6 1.0
CB B:ASP243 4.7 31.0 1.0
OD1 B:ASN493 4.8 32.5 1.0
O B:HOH747 4.9 41.0 1.0
CA B:ASP243 4.9 23.7 1.0
OG A:SER114 4.9 55.6 1.0
OD2 B:ASP492 4.9 54.8 1.0
O B:HOH737 5.0 55.3 1.0

Manganese binding site 3 out of 4 in 6zuc

Go back to Manganese Binding Sites List in 6zuc
Manganese binding site 3 out of 4 in the X-Ray Crystal Structure of the CSPYL1-LIG1-HAB1 Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Crystal Structure of the CSPYL1-LIG1-HAB1 Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn603

b:58.1
occ:1.00
 OD1 B:ASP432 2.3 45.6 1.0
OD2 B:ASP243 2.4 41.5 1.0
OD2 B:ASP492 2.4 54.8 1.0
O B:HOH707 2.5 33.8 1.0
O B:HOH747 2.7 41.0 1.0
CG B:ASP432 3.2 24.7 1.0
O B:HOH737 3.3 55.3 1.0
CG B:ASP243 3.3 43.5 1.0
O B:HOH771 3.3 59.3 1.0
OD2 B:ASP432 3.3 43.2 1.0
OD1 B:ASP243 3.4 39.3 1.0
CG B:ASP492 3.5 36.3 1.0
MN B:MN602 3.7 60.1 1.0
OD1 B:ASP492 3.9 47.6 1.0
O B:HOH712 4.3 36.9 1.0
O B:HOH713 4.4 50.6 1.0
O B:HOH721 4.5 50.0 1.0
CB B:ASP432 4.6 30.7 1.0
N B:GLY433 4.7 29.0 1.0
CB B:ASP243 4.7 31.0 1.0
CB B:ASP492 4.7 26.7 1.0
N B:ASP432 4.8 33.6 1.0
O A:HOH435 5.0 63.1 1.0

Manganese binding site 4 out of 4 in 6zuc

Go back to Manganese Binding Sites List in 6zuc
Manganese binding site 4 out of 4 in the X-Ray Crystal Structure of the CSPYL1-LIG1-HAB1 Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Crystal Structure of the CSPYL1-LIG1-HAB1 Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn604

b:104.9
occ:1.00
 O B:HOH716 2.0 100.8 1.0
O B:HOH758 2.3 76.7 1.0
O B:HOH777 2.6 82.8 1.0
O B:HOH775 2.7 58.5 1.0
OD2 B:ASP432 2.7 43.2 1.0
OD2 B:ASP436 2.8 51.2 1.0
OD1 B:ASP436 3.4 59.9 1.0
CG B:ASP436 3.5 45.9 1.0
CG B:ASP432 3.7 24.7 1.0
NZ B:LYS365 3.9 42.0 1.0
OD2 B:ASP346 4.0 51.6 1.0
CB B:ASP432 4.1 30.7 1.0
O B:HOH747 4.2 41.0 1.0
O B:HOH721 4.5 50.0 1.0
OD1 B:ASP432 4.7 45.6 1.0
CE B:LYS365 4.9 51.4 1.0
CG B:ASP346 4.9 50.9 1.0
CB B:ASP436 5.0 37.4 1.0

Reference:

A.Albert, L.Infantes, J.L.Benavente. X-Ray Crystal Structure of the CSPYL1-LIG1-HAB1 Ternary Complex To Be Published.
Page generated: Sat Aug 21 17:06:08 2021

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