Atomistry » Sodium » PDB 7m6k-7mq3 » 7mgu
Atomistry »
  Sodium »
    PDB 7m6k-7mq3 »
      7mgu »

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

Go back to Sodium Binding Sites List in 7mgu
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

Go back to Sodium Binding Sites List in 7mgu
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

Go back to Sodium Binding Sites List in 7mgu
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

Go back to Sodium Binding Sites List in 7mgu
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy