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Sodium in PDB 7mgu: Improved Ligand Discovery Using Micro-Beam Data Collection at the Edge of Protein Crystals

Enzymatic activity of Improved Ligand Discovery Using Micro-Beam Data Collection at the Edge of Protein Crystals

All present enzymatic activity of Improved Ligand Discovery Using Micro-Beam Data Collection at the Edge of Protein Crystals:
3.2.1.8;

Protein crystallography data

The structure of Improved Ligand Discovery Using Micro-Beam Data Collection at the Edge of Protein Crystals, PDB code: 7mgu was solved by A.S.Soares, J.Jakoncic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.42 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.41, 38.99, 57.11, 90, 107.64, 90
R / Rfree (%) 12.9 / 14.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Improved Ligand Discovery Using Micro-Beam Data Collection at the Edge of Protein Crystals (pdb code 7mgu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Improved Ligand Discovery Using Micro-Beam Data Collection at the Edge of Protein Crystals, PDB code: 7mgu:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 7mgu

Go back to Sodium Binding Sites List in 7mgu
Sodium binding site 1 out of 5 in the Improved Ligand Discovery Using Micro-Beam Data Collection at the Edge of Protein Crystals


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Improved Ligand Discovery Using Micro-Beam Data Collection at the Edge of Protein Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:16.7
occ:1.00
 OH A:TYR87 2.7 9.6 1.0
O A:TYR171 2.8 7.8 1.0
O A:TRP79 3.1 8.5 1.0
O A:ASP170 3.3 8.5 1.0
CE A:MET169 3.5 13.0 1.0
CE2 A:TYR87 3.5 8.5 1.0
CZ A:TYR87 3.5 8.6 1.0
C A:TYR171 3.5 7.4 1.0
SD A:MET169 3.6 15.2 1.0
CB A:GLN172 3.7 6.4 1.0
N A:TRP79 3.8 7.8 1.0
CB A:MET169 3.8 10.2 1.0
C A:ASP170 3.8 8.0 1.0
N A:ASP170 4.0 8.5 1.0
C A:TRP79 4.0 7.6 1.0
CA A:GLN172 4.1 7.0 1.0
CG A:MET169 4.1 12.8 1.0
N A:GLN172 4.1 7.3 1.0
NE2 A:GLN172 4.3 10.0 1.0
CA A:MET169 4.3 8.9 1.0
CG A:GLN172 4.3 7.8 1.0
CA A:GLY54 4.3 8.7 1.0
CA A:GLY78 4.3 7.8 1.0
N A:TYR171 4.4 7.8 1.0
C A:GLY78 4.4 6.8 1.0
N A:GLY54 4.4 9.3 1.0
CD A:GLN172 4.5 8.2 1.0
CA A:TYR171 4.5 7.5 1.0
C A:MET169 4.5 8.8 1.0
CA A:TRP79 4.6 7.5 1.0
CA A:ASP170 4.6 8.6 1.0
CD2 A:TYR87 4.8 7.8 1.0
CE1 A:TYR87 4.8 8.6 1.0
C A:GLY54 4.9 8.5 1.0

Sodium binding site 2 out of 5 in 7mgu

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Sodium binding site 2 out of 5 in the Improved Ligand Discovery Using Micro-Beam Data Collection at the Edge of Protein Crystals


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Improved Ligand Discovery Using Micro-Beam Data Collection at the Edge of Protein Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:18.0
occ:1.00
 OD2 A:ASP111 2.7 10.8 1.0
OH A:TYR115 2.8 8.9 1.0
NE2 A:HIS155 2.8 8.8 1.0
CZ A:TYR115 3.3 8.2 1.0
CG A:ASP111 3.6 11.1 1.0
CG1 A:VAL150 3.7 10.2 1.0
CE1 A:TYR115 3.7 8.2 1.0
CD2 A:HIS155 3.7 8.0 1.0
OG A:SER110 3.7 11.4 1.0
CE1 A:HIS155 3.7 9.0 1.0
CB A:ASP111 3.7 9.2 1.0
CB A:SER110 3.9 10.8 1.0
CA A:VAL150 3.9 9.0 1.0
CG2 A:VAL150 4.0 10.9 1.0
CB A:VAL150 4.0 9.5 1.0
O A:SER110 4.1 10.4 1.0
OE2 A:GLU91 4.2 12.3 1.0
CE2 A:TYR115 4.2 8.4 1.0
N A:ASN151 4.3 8.9 0.5
C A:SER110 4.3 9.8 1.0
N A:ASN151 4.4 8.5 0.5
NH2 A:ARG145 4.4 12.0 1.0
CG2 A:ILE89 4.5 7.7 1.0
NH1 A:ARG141 4.5 9.1 1.0
O A:SER149 4.5 9.2 0.5
O A:SER149 4.5 10.0 0.5
C A:VAL150 4.6 9.8 1.0
CD1 A:TYR115 4.7 8.4 1.0
CA A:SER110 4.7 10.2 1.0
N A:ASP111 4.7 9.2 1.0
OD1 A:ASP111 4.8 12.4 1.0
CA A:ASP111 4.9 9.2 1.0
OE1 A:GLU91 4.9 12.5 1.0
ND1 A:HIS155 4.9 9.2 1.0
CG A:HIS155 4.9 8.3 1.0
O A:ASN151 4.9 9.2 0.5
CD A:GLU91 4.9 11.4 1.0

Sodium binding site 3 out of 5 in 7mgu

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Sodium binding site 3 out of 5 in the Improved Ligand Discovery Using Micro-Beam Data Collection at the Edge of Protein Crystals


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Improved Ligand Discovery Using Micro-Beam Data Collection at the Edge of Protein Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:17.7
occ:1.00
 NA A:NA206 2.8 17.0 1.0
OE1 A:GLU177 2.8 12.7 1.0
CE2 A:TYR88 3.4 12.0 1.0
CD1 A:TYR77 3.4 8.6 1.0
CB A:GLU177 3.5 8.8 1.0
CG1 A:VAL46 3.5 11.1 1.0
CG A:TYR77 3.6 7.6 1.0
CE1 A:TYR77 3.8 8.8 1.0
CD A:GLU177 3.8 13.3 1.0
CB A:ALA175 3.8 9.6 1.0
CD2 A:TYR77 4.0 7.9 1.0
CG2 A:VAL46 4.0 9.8 1.0
OH A:TYR88 4.0 13.3 1.0
CB A:TYR77 4.1 7.9 1.0
CZ A:TYR88 4.1 10.0 1.0
CD2 A:TYR88 4.1 10.5 1.0
CG A:GLU177 4.2 10.0 1.0
CZ A:TYR77 4.2 9.2 1.0
CE2 A:TYR77 4.4 8.8 1.0
CB A:VAL46 4.4 8.8 1.0
CA A:GLU177 4.5 8.4 1.0
N A:GLU177 4.6 8.0 1.0
O A:ALA175 4.8 7.7 1.0
OG A:SER75 4.9 10.9 1.0
C A:VAL176 4.9 8.3 1.0
C A:ALA175 4.9 7.3 1.0
OE2 A:GLU177 5.0 14.8 1.0

Sodium binding site 4 out of 5 in 7mgu

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Sodium binding site 4 out of 5 in the Improved Ligand Discovery Using Micro-Beam Data Collection at the Edge of Protein Crystals


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Improved Ligand Discovery Using Micro-Beam Data Collection at the Edge of Protein Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:19.3
occ:1.00
 O A:TYR96 2.7 12.3 1.0
N A:TYR96 2.9 12.7 1.0
O A:SER72 3.0 9.5 1.0
N A:SER72 3.0 9.3 1.0
OD1 A:ASN71 3.2 14.9 1.0
N A:GLY94 3.4 10.7 1.0
CA A:ASN71 3.4 10.9 1.0
C A:TYR96 3.4 12.7 1.0
CA A:TYR96 3.4 12.9 1.0
CB A:TYR96 3.5 14.9 1.0
N A:THR95 3.6 12.2 1.0
C A:ASN71 3.7 9.9 1.0
C A:GLY94 3.7 14.2 1.0
C A:SER72 3.7 8.6 1.0
CG A:ASN71 3.8 12.7 1.0
CA A:GLY94 3.9 12.3 1.0
CE1 A:TYR73 3.9 12.5 1.0
CA A:SER72 4.0 9.2 1.0
CB A:PHE93 4.0 10.4 1.0
CD1 A:TYR73 4.1 10.9 1.0
C A:THR95 4.1 16.1 1.0
CB A:ASN71 4.1 10.7 1.0
O A:GLY70 4.1 12.7 1.0
CD1 A:PHE93 4.3 12.9 1.0
O A:GLY94 4.4 15.2 1.0
C A:PHE93 4.4 11.6 1.0
CA A:THR95 4.4 13.8 1.0
N A:ASN71 4.5 10.6 1.0
CG A:TYR96 4.6 15.2 1.0
CG A:PHE93 4.6 11.9 1.0
CA A:PHE93 4.6 9.8 1.0
N A:ASN97 4.7 12.2 1.0
C A:GLY70 4.7 10.6 1.0
OG1 A:THR95 4.7 14.9 1.0
CD2 A:TYR96 4.8 14.3 1.0
ND2 A:ASN71 4.8 14.6 1.0
N A:TYR73 4.9 8.5 1.0
O A:ASN71 4.9 9.4 1.0
O A:HOH414 5.0 14.7 1.0

Sodium binding site 5 out of 5 in 7mgu

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Sodium binding site 5 out of 5 in the Improved Ligand Discovery Using Micro-Beam Data Collection at the Edge of Protein Crystals


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Improved Ligand Discovery Using Micro-Beam Data Collection at the Edge of Protein Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:17.0
occ:1.00
 NA A:NA204 2.8 17.7 1.0
OG A:SER75 2.8 10.9 1.0
O A:ALA175 3.0 7.7 1.0
CB A:SER75 3.3 8.9 1.0
O A:TYR73 3.4 8.8 1.0
N A:SER75 3.5 7.0 1.0
CB A:TYR73 3.6 9.3 1.0
C A:TYR73 3.6 8.6 1.0
CB A:GLU177 3.8 8.8 1.0
N A:GLU177 3.8 8.0 1.0
C A:ALA175 3.8 7.3 1.0
CA A:SER75 4.0 7.0 1.0
N A:LEU74 4.0 7.1 1.0
C A:LEU74 4.0 7.8 1.0
CA A:LEU74 4.1 7.9 1.0
CB A:ALA175 4.1 9.6 1.0
CA A:TYR73 4.3 8.5 1.0
C A:VAL176 4.3 8.3 1.0
CE2 A:TYR88 4.3 12.0 1.0
CA A:GLU177 4.4 8.4 1.0
CA A:VAL176 4.4 7.9 1.0
CD2 A:TYR73 4.4 10.5 1.0
CD2 A:TYR88 4.5 10.5 1.0
CG A:TYR73 4.5 9.0 1.0
N A:VAL176 4.5 7.2 1.0
OE1 A:GLU177 4.5 12.7 1.0
CA A:ALA175 4.5 8.1 1.0
O A:SER75 4.6 8.2 1.0
C A:SER75 4.7 7.7 1.0
O A:LEU74 4.9 8.3 1.0
CB A:TYR77 5.0 7.9 1.0
N A:TYR73 5.0 8.5 1.0

Reference:

A.S.Soares, J.Jakoncic. Improved Ligand Discovery Using Micro-Beam Data Collection at the Edge of Protein Crystals To Be Published.
Page generated: Tue Oct 8 17:57:50 2024

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