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

Protein crystallography data

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

Other elements in 7xjv:

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

Manganese (Mn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Alpha-1,3-Mannosyltransferase MNT2 From Saccharomyces Cerevisiae, Mn/Gdp-Mannose Form, PDB code: 7xjv:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 7xjv

Go back to Sodium Binding Sites List in 7xjv
Sodium binding site 1 out of 5 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 Sodium with other atoms in the Na 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:Na608

b:74.6
occ:1.00
 OE1 A:GLU123 2.3 100.5 1.0
NE2 A:HIS127 2.3 79.2 1.0
CD2 A:HIS127 3.2 79.5 1.0
CE1 A:HIS127 3.4 78.8 1.0
CD A:GLU123 3.4 98.9 1.0
CG A:GLU123 4.0 90.7 1.0
CG A:HIS127 4.4 79.7 1.0
CB A:GLU123 4.4 83.9 1.0
OE2 A:GLU123 4.4 104.0 1.0
ND1 A:HIS127 4.4 78.5 1.0
CA A:GLU123 4.6 77.0 1.0
O A:GLU123 4.9 71.2 1.0

Sodium binding site 2 out of 5 in 7xjv

Go back to Sodium Binding Sites List in 7xjv
Sodium binding site 2 out of 5 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 Sodium with other atoms in the Na 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:Na607

b:90.7
occ:1.00
 OE1 B:GLU313 2.3 88.2 1.0
OE2 B:GLU313 2.3 87.9 1.0
NE2 B:HIS300 2.3 108.0 1.0
CD B:GLU313 2.6 82.2 1.0
O B:HOH703 2.7 57.1 1.0
CD2 B:HIS300 2.9 108.8 1.0
CE1 B:HIS300 3.5 110.5 1.0
NE2 B:GLN310 4.0 78.4 1.0
CG B:GLU313 4.2 76.6 1.0
CG B:HIS300 4.2 108.6 1.0
ND1 B:HIS300 4.4 110.9 1.0
OE2 B:GLU296 4.8 142.6 1.0
CD B:GLN310 4.9 73.3 1.0
CB B:GLU313 4.9 73.5 1.0

Sodium binding site 3 out of 5 in 7xjv

Go back to Sodium Binding Sites List in 7xjv
Sodium binding site 3 out of 5 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 Sodium with other atoms in the Na 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:Na607

b:70.4
occ:1.00
 OE1 C:GLU123 2.3 88.9 1.0
NE2 C:HIS127 2.3 89.1 1.0
CD C:GLU123 3.1 93.1 1.0
OE2 C:GLU123 3.1 97.8 1.0
CE1 C:HIS127 3.2 92.1 1.0
CD2 C:HIS127 3.4 92.4 1.0
ND1 C:HIS127 4.4 93.3 1.0
CG C:HIS127 4.5 93.0 1.0
CG C:GLU123 4.5 89.2 1.0

Sodium binding site 4 out of 5 in 7xjv

Go back to Sodium Binding Sites List in 7xjv
Sodium binding site 4 out of 5 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 Sodium with other atoms in the Na 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
C:Na608

b:96.0
occ:1.00
 OE2 C:GLU313 2.3 95.0 1.0
OE1 C:GLU313 2.3 97.2 1.0
ND1 C:HIS300 2.3 114.5 1.0
CD C:GLU313 2.6 88.6 1.0
CE1 C:HIS300 2.8 123.1 1.0
CG C:HIS300 3.5 115.3 1.0
NE2 C:HIS300 4.1 121.0 1.0
CG C:GLU313 4.1 79.4 1.0
CB C:HIS300 4.2 109.3 1.0
CD2 C:HIS300 4.4 119.4 1.0
NE2 C:GLN310 4.5 74.8 1.0

Sodium binding site 5 out of 5 in 7xjv

Go back to Sodium Binding Sites List in 7xjv
Sodium binding site 5 out of 5 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 Sodium with other atoms in the Na binding site number 5 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:Na607

b:80.6
occ:1.00
 OE1 D:GLU123 2.3 90.0 1.0
OE2 D:GLU123 2.3 92.4 1.0
NE2 D:HIS127 2.3 87.4 1.0
CD D:GLU123 2.6 90.5 1.0
CE1 D:HIS127 3.2 88.5 1.0
CD2 D:HIS127 3.3 87.8 1.0
CG D:GLU123 4.1 85.7 1.0
ND1 D:HIS127 4.4 85.8 1.0
CG D:HIS127 4.4 84.0 1.0
CB D:GLU123 4.9 80.6 1.0
CD1 D:LEU126 4.9 77.7 1.0

Reference:

D.Hira, C.Kadooka, T.Oka. Crystal Structure of Alpha-1,3-Mannosyltransferase MNT2 From Saccharomyces Cerevisiae, Mn/Gdp-Mannose Form To Be Published.
Page generated: Mon Aug 18 12:35:50 2025

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