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Manganese in PDB 6s81: Crystal Structure of Methionine Adenosyltransferase From Pyrococcus Furiosus

Enzymatic activity of Crystal Structure of Methionine Adenosyltransferase From Pyrococcus Furiosus

All present enzymatic activity of Crystal Structure of Methionine Adenosyltransferase From Pyrococcus Furiosus:
2.5.1.6;

Protein crystallography data

The structure of Crystal Structure of Methionine Adenosyltransferase From Pyrococcus Furiosus, PDB code: 6s81 was solved by M.Degano, C.Minici, M.Porcelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 106.55 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.108, 133.900, 213.100, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 23.1

Other elements in 6s81:

The structure of Crystal Structure of Methionine Adenosyltransferase From Pyrococcus Furiosus also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Methionine Adenosyltransferase From Pyrococcus Furiosus (pdb code 6s81). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Methionine Adenosyltransferase From Pyrococcus Furiosus, PDB code: 6s81:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6s81

Go back to Manganese Binding Sites List in 6s81
Manganese binding site 1 out of 4 in the Crystal Structure of Methionine Adenosyltransferase From Pyrococcus Furiosus


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 Methionine Adenosyltransferase From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:30.0
occ:1.00
 O A:HOH787 2.2 33.1 1.0
OD2 A:ASP32 2.2 23.2 1.0
O A:HOH784 2.4 28.0 1.0
O A:HOH640 2.4 24.8 1.0
O A:HOH630 2.4 23.9 1.0
O A:HOH783 2.5 27.6 1.0
CG A:ASP32 3.2 22.5 1.0
OD1 A:ASP32 3.4 21.7 1.0
O C:HOH711 3.8 26.0 1.0
NZ A:LYS26 3.8 23.5 1.0
NH2 A:ARG286 4.0 26.0 1.0
O C:HOH755 4.1 27.7 1.0
O C:HOH623 4.1 30.2 1.0
O A:HOH797 4.3 36.2 1.0
CE1 A:HIS30 4.3 22.4 1.0
O C:HOH758 4.4 49.8 1.0
NE A:ARG286 4.4 27.4 1.0
O A:ASP281 4.4 24.8 1.0
CZ A:ARG286 4.5 26.7 1.0
CB A:ASP32 4.5 21.7 1.0
NE2 C:GLN64 4.5 24.2 1.0
CB A:ARG286 4.7 24.3 1.0
CE A:LYS26 4.8 23.3 1.0

Manganese binding site 2 out of 4 in 6s81

Go back to Manganese Binding Sites List in 6s81
Manganese binding site 2 out of 4 in the Crystal Structure of Methionine Adenosyltransferase From Pyrococcus Furiosus


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 Methionine Adenosyltransferase From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:25.7
occ:1.00
 O B:HOH777 2.1 28.6 1.0
OD2 B:ASP32 2.1 27.6 1.0
O D:HOH796 2.2 34.5 1.0
O B:HOH615 2.3 21.2 1.0
O B:HOH628 2.3 29.3 1.0
O B:HOH779 2.3 29.6 1.0
CG B:ASP32 3.1 20.2 1.0
OD1 B:ASP32 3.4 19.1 1.0
NZ B:LYS26 3.7 23.2 1.0
O D:HOH710 3.7 26.3 1.0
NH2 B:ARG286 4.1 25.9 1.0
O D:HOH696 4.2 33.5 1.0
O B:HOH781 4.2 31.9 1.0
CE1 B:HIS30 4.3 23.0 1.0
O B:HOH802 4.4 40.9 1.0
NE B:ARG286 4.4 25.3 1.0
O B:ASP281 4.5 23.7 1.0
CB B:ASP32 4.5 18.0 1.0
NE2 D:GLN64 4.6 23.5 1.0
CZ B:ARG286 4.6 25.3 1.0
CB B:ARG286 4.6 23.4 1.0
CE B:LYS26 4.8 22.2 1.0

Manganese binding site 3 out of 4 in 6s81

Go back to Manganese Binding Sites List in 6s81
Manganese binding site 3 out of 4 in the Crystal Structure of Methionine Adenosyltransferase From Pyrococcus Furiosus


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 Methionine Adenosyltransferase From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn502

b:26.8
occ:1.00
 O A:HOH792 2.2 25.8 1.0
OD2 C:ASP32 2.2 21.3 1.0
O C:HOH781 2.3 31.7 1.0
O C:HOH625 2.3 25.7 1.0
O C:HOH637 2.3 23.9 1.0
O C:HOH776 2.4 30.4 1.0
CG C:ASP32 3.2 20.2 1.0
OD1 C:ASP32 3.4 20.3 1.0
NZ C:LYS26 3.8 23.1 1.0
O A:HOH770 3.9 30.0 1.0
NH2 C:ARG286 4.1 26.2 1.0
O A:HOH631 4.2 22.4 1.0
CE1 C:HIS30 4.3 24.0 1.0
O C:HOH790 4.4 37.0 1.0
O C:ASP281 4.4 26.6 1.0
NE2 A:GLN64 4.4 24.0 1.0
CB C:ASP32 4.5 20.5 1.0
NE C:ARG286 4.6 25.1 1.0
CZ C:ARG286 4.6 25.6 1.0
CB C:ARG286 4.7 24.0 1.0
CE C:LYS26 4.9 23.4 1.0

Manganese binding site 4 out of 4 in 6s81

Go back to Manganese Binding Sites List in 6s81
Manganese binding site 4 out of 4 in the Crystal Structure of Methionine Adenosyltransferase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Methionine Adenosyltransferase From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn502

b:24.3
occ:1.00
 O B:HOH796 2.0 24.2 1.0
OD2 D:ASP32 2.2 25.9 1.0
O D:HOH781 2.2 26.8 1.0
O D:HOH658 2.2 33.3 1.0
O B:HOH623 2.3 20.7 1.0
O D:HOH790 2.4 27.8 1.0
CG D:ASP32 3.1 20.2 1.0
OD1 D:ASP32 3.3 19.0 1.0
NZ D:LYS26 3.7 23.9 1.0
O B:HOH775 3.8 29.1 1.0
NH2 D:ARG286 4.1 24.6 1.0
O B:HOH651 4.2 26.4 1.0
CE1 D:HIS30 4.3 21.6 1.0
O D:HOH806 4.4 54.6 1.0
O D:ASP281 4.4 23.7 1.0
O B:HOH818 4.4 51.0 1.0
NE2 B:GLN64 4.5 22.0 1.0
CB D:ASP32 4.5 19.8 1.0
NE D:ARG286 4.5 22.9 1.0
CZ D:ARG286 4.5 23.9 1.0
CB D:ARG286 4.6 21.8 1.0
CE D:LYS26 4.8 24.6 1.0

Reference:

C.Minici, L.Mosca, C.Paola Ilisso, G.Cacciapuoti, M.Porcelli, M.Degano. Structures of Catalytic Cycle Intermediates of the Pyrococcus Furiosus Methionine Adenosyltransferase Demonstrate Negative Cooperativity in the Archaeal Orthologues. J.Struct.Biol. 07462 2020.
ISSN: ESSN 1095-8657
PubMed: 31962159
DOI: 10.1016/J.JSB.2020.107462
Page generated: Sun Oct 6 07:05:48 2024

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