Manganese in PDB 7xjv: Crystal Structure of Alpha-1,3-Mannosyltransferase MNT2 From Saccharomyces Cerevisiae, Mn/Gdp-Mannose Form

The structure of Crystal Structure of Alpha-1,3-Mannosyltransferase MNT2 From Saccharomyces Cerevisiae, Mn/Gdp-Mannose Form, PDB code: 7xjv was solved by D.Hira, C.Kadooka, T.Oka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	130.849, 131.189, 169.552, 90, 90, 90
R / Rfree (%)	21.4 / 25.1

The structure of Crystal Structure of Alpha-1,3-Mannosyltransferase MNT2 From Saccharomyces Cerevisiae, Mn/Gdp-Mannose Form also contains other interesting chemical elements:

Sodium

(Na)

5 atoms

The binding sites of Manganese atom in the Crystal Structure of Alpha-1,3-Mannosyltransferase MNT2 From Saccharomyces Cerevisiae, Mn/Gdp-Mannose Form (pdb code 7xjv). 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 Alpha-1,3-Mannosyltransferase MNT2 From Saccharomyces Cerevisiae, Mn/Gdp-Mannose Form, PDB code: 7xjv:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Alpha-1,3-Mannosyltransferase MNT2 From Saccharomyces Cerevisiae, Mn/Gdp-Mannose Form


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 Alpha-1,3-Mannosyltransferase MNT2 From Saccharomyces Cerevisiae, Mn/Gdp-Mannose Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:64.2 occ:1.00 OD2 A:ASP237 1.9 57.5 1.0 OD2 A:ASP239 2.0 71.2 1.0 OD1 A:ASP239 2.0 68.5 1.0 O3B A:GDD602 2.0 57.8 1.0 O2A A:GDD602 2.0 54.6 1.0 OD1 A:ASN419 2.0 70.7 1.0 ND2 A:ASN419 2.1 64.2 1.0 CG A:ASP239 2.2 68.0 1.0 CG A:ASN419 2.4 60.5 1.0 CG A:ASP237 3.0 54.4 1.0 PB A:GDD602 3.3 54.6 1.0 PA A:GDD602 3.3 57.0 1.0 CB A:ASP237 3.5 56.2 1.0 O3A A:GDD602 3.6 54.3 1.0 CB A:ASP239 3.7 61.0 1.0 CB A:ASN419 3.9 55.2 1.0 O2B A:GDD602 3.9 58.9 1.0 OD1 A:ASP237 4.1 49.4 1.0 C5' A:GDD602 4.2 58.0 1.0 O5' A:GDD602 4.3 58.9 1.0 C31 A:GDD602 4.4 59.5 1.0 O3' A:GDD602 4.4 59.7 1.0 O1 A:GOL603 4.4 72.5 1.0 O1A A:GDD602 4.4 57.8 1.0 C21 A:GDD602 4.5 59.7 1.0 N A:GLY420 4.5 55.5 1.0 O31 A:GDD602 4.5 62.0 1.0 O1B A:GDD602 4.6 57.3 1.0 CA A:ASP239 4.6 59.0 1.0 C A:ASP239 4.7 58.9 1.0 CA A:ASN419 4.7 55.5 1.0 C1 A:GOL603 4.8 72.3 1.0 N A:ASP239 4.8 58.9 1.0 N A:THR240 4.9 61.8 1.0 CA A:ASP237 5.0 56.5 1.0 C4' A:GDD602 5.0 58.7 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Alpha-1,3-Mannosyltransferase MNT2 From Saccharomyces Cerevisiae, Mn/Gdp-Mannose Form


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 Alpha-1,3-Mannosyltransferase MNT2 From Saccharomyces Cerevisiae, Mn/Gdp-Mannose Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn601 b:61.9 occ:1.00 OD2 B:ASP237 1.9 58.6 1.0 OD2 B:ASP239 2.0 62.1 1.0 OD1 B:ASP239 2.0 64.8 1.0 O2A B:GDD602 2.0 53.8 1.0 O3B B:GDD602 2.0 58.9 1.0 OD1 B:ASN419 2.0 67.5 1.0 ND2 B:ASN419 2.1 61.7 1.0 CG B:ASP239 2.2 59.0 1.0 CG B:ASN419 2.3 59.9 1.0 CG B:ASP237 3.1 56.3 1.0 PB B:GDD602 3.3 57.5 1.0 PA B:GDD602 3.3 52.4 1.0 CB B:ASP237 3.5 56.3 1.0 O3A B:GDD602 3.6 55.1 1.0 CB B:ASP239 3.7 55.8 1.0 CB B:ASN419 3.9 55.4 1.0 NZ B:LYS426 4.1 92.1 1.0 O2B B:GDD602 4.1 57.1 1.0 OD1 B:ASP237 4.2 54.4 1.0 C5' B:GDD602 4.2 52.0 1.0 O5' B:GDD602 4.3 50.7 1.0 O1A B:GDD602 4.4 53.5 1.0 C3 B:GOL603 4.4 85.2 1.0 N B:GLY420 4.5 51.6 1.0 C31 B:GDD602 4.5 57.1 1.0 O3' B:GDD602 4.5 53.8 1.0 C21 B:GDD602 4.5 58.1 1.0 O1B B:GDD602 4.6 56.2 1.0 CA B:ASP239 4.6 55.1 1.0 O31 B:GDD602 4.6 54.5 1.0 CA B:ASN419 4.7 54.5 1.0 C B:ASP239 4.7 54.6 1.0 N B:ASP239 4.8 54.1 1.0 N B:THR240 4.9 53.4 1.0 C B:ASN419 5.0 53.1 1.0 CA B:ASP237 5.0 55.7 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Alpha-1,3-Mannosyltransferase MNT2 From Saccharomyces Cerevisiae, Mn/Gdp-Mannose Form


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 Alpha-1,3-Mannosyltransferase MNT2 From Saccharomyces Cerevisiae, Mn/Gdp-Mannose Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn601 b:64.5 occ:1.00 OD2 C:ASP239 1.9 64.9 1.0 OD2 C:ASP237 2.0 64.0 1.0 OD1 C:ASN419 2.0 68.3 1.0 O2A C:GDD602 2.0 60.5 1.0 O3B C:GDD602 2.0 59.3 1.0 OD1 C:ASP239 2.0 64.3 1.0 ND2 C:ASN419 2.1 64.2 1.0 CG C:ASP239 2.2 63.1 1.0 CG C:ASN419 2.3 62.1 1.0 CG C:ASP237 3.1 59.7 1.0 PB C:GDD602 3.3 58.0 1.0 PA C:GDD602 3.3 59.2 1.0 CB C:ASP237 3.6 60.1 1.0 O3A C:GDD602 3.6 57.8 1.0 CB C:ASP239 3.7 59.6 1.0 CB C:ASN419 3.8 58.1 1.0 O2 C:GOL603 4.1 91.2 1.0 O2B C:GDD602 4.1 58.9 1.0 OD1 C:ASP237 4.2 58.8 1.0 C5' C:GDD602 4.2 58.3 1.0 O5' C:GDD602 4.3 60.7 1.0 O1A C:GDD602 4.4 63.4 1.0 C31 C:GDD602 4.5 61.0 1.0 N C:GLY420 4.5 60.2 1.0 O3' C:GDD602 4.5 58.0 1.0 C21 C:GDD602 4.5 61.6 1.0 O1B C:GDD602 4.5 61.0 1.0 CA C:ASP239 4.6 59.2 1.0 CA C:ASN419 4.7 57.9 1.0 O31 C:GDD602 4.7 61.5 1.0 C C:ASP239 4.7 60.0 1.0 N C:ASP239 4.8 59.2 1.0 O1 C:GOL603 4.9 81.1 1.0 N C:THR240 4.9 57.9 1.0 C C:ASN419 5.0 56.2 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Alpha-1,3-Mannosyltransferase MNT2 From Saccharomyces Cerevisiae, Mn/Gdp-Mannose Form


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 Alpha-1,3-Mannosyltransferase MNT2 From Saccharomyces Cerevisiae, Mn/Gdp-Mannose Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn601 b:63.1 occ:1.00 OD2 D:ASP237 1.9 58.3 1.0 OD2 D:ASP239 1.9 63.1 1.0 OD1 D:ASP239 2.0 64.4 1.0 OD1 D:ASN419 2.0 73.7 1.0 O2A D:GDD602 2.0 57.4 1.0 O3B D:GDD602 2.0 59.4 1.0 ND2 D:ASN419 2.1 68.3 1.0 CG D:ASP239 2.2 58.6 1.0 CG D:ASN419 2.3 65.7 1.0 CG D:ASP237 3.0 55.4 1.0 PB D:GDD602 3.3 56.0 1.0 PA D:GDD602 3.3 54.2 1.0 CB D:ASP237 3.5 56.5 1.0 O3A D:GDD602 3.6 54.9 1.0 CB D:ASP239 3.7 55.5 1.0 CB D:ASN419 3.9 60.7 1.0 NZ D:LYS426 3.9 85.5 1.0 O2B D:GDD602 4.1 55.1 1.0 OD1 D:ASP237 4.1 54.1 1.0 C5' D:GDD602 4.2 53.0 1.0 O5' D:GDD602 4.2 53.2 1.0 C31 D:GDD602 4.3 51.6 1.0 O2 D:GOL603 4.4 90.9 1.0 O3' D:GDD602 4.4 56.7 1.0 O31 D:GDD602 4.4 48.7 1.0 O1A D:GDD602 4.4 55.6 1.0 N D:GLY420 4.5 57.0 1.0 C21 D:GDD602 4.5 53.4 1.0 O1B D:GDD602 4.6 55.3 1.0 CA D:ASP239 4.6 54.9 1.0 CA D:ASN419 4.7 59.7 1.0 C D:ASP239 4.7 55.4 1.0 N D:ASP239 4.8 54.0 1.0 C4' D:GDD602 4.9 52.5 1.0 N D:THR240 4.9 57.3 1.0 CA D:ASP237 5.0 56.8 1.0 C D:ASN419 5.0 57.2 1.0 OG1 D:THR240 5.0 55.5 1.0

D.Hira, C.Kadooka, T.Oka. Crystal Structure of Alpha-1,3-Mannosyltransferase MNT2 From Saccharomyces Cerevisiae, Mn/Gdp-Mannose Form To Be Published.