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Sodium in PDB 7g38: Crystal Structure of Rat Autotaxin in Complex with 3-[3-[[(4- Bromophenyl)Methylamino]Methyl]Indol-1-Yl]-N-Methylpropanamide

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[3-[[(4- Bromophenyl)Methylamino]Methyl]Indol-1-Yl]-N-Methylpropanamide

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[3-[[(4- Bromophenyl)Methylamino]Methyl]Indol-1-Yl]-N-Methylpropanamide:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-[3-[[(4- Bromophenyl)Methylamino]Methyl]Indol-1-Yl]-N-Methylpropanamide, PDB code: 7g38 was solved by M.Stihle, J.Benz, D.Hunziker, T.Lubbers, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.90 / 1.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.959, 91.792, 119.458, 90, 90, 90
R / Rfree (%) 18.7 / 21.5

Other elements in 7g38:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-[3-[[(4- Bromophenyl)Methylamino]Methyl]Indol-1-Yl]-N-Methylpropanamide also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Zinc (Zn) 1 atom
Bromine (Br) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 3-[3-[[(4- Bromophenyl)Methylamino]Methyl]Indol-1-Yl]-N-Methylpropanamide (pdb code 7g38). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Rat Autotaxin in Complex with 3-[3-[[(4- Bromophenyl)Methylamino]Methyl]Indol-1-Yl]-N-Methylpropanamide, PDB code: 7g38:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g38

Go back to Sodium Binding Sites List in 7g38
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-[3-[[(4- Bromophenyl)Methylamino]Methyl]Indol-1-Yl]-N-Methylpropanamide


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 Rat Autotaxin in Complex with 3-[3-[[(4- Bromophenyl)Methylamino]Methyl]Indol-1-Yl]-N-Methylpropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:19.8
occ:1.00
 OG A:SER807 2.3 17.6 1.0
O A:SER804 2.3 15.5 1.0
O A:HOH1583 2.3 24.9 1.0
O A:HOH1446 2.4 23.1 1.0
O A:ASN801 2.5 14.4 1.0
O A:HOH1301 2.5 22.2 1.0
C A:SER804 3.4 15.6 1.0
C A:ASN801 3.4 14.1 1.0
CB A:SER807 3.4 18.3 1.0
CA A:ASP802 3.8 16.1 1.0
N A:SER807 4.0 18.3 1.0
N A:ASP802 4.0 15.1 1.0
CA A:CYS805 4.2 18.0 1.0
O A:HOH1681 4.2 36.5 1.0
N A:CYS805 4.2 16.1 1.0
C A:ASP802 4.2 15.7 1.0
CA A:SER807 4.2 19.8 1.0
O A:ASP802 4.2 15.1 1.0
N A:SER804 4.3 14.5 1.0
C A:CYS805 4.3 20.5 1.0
CA A:SER804 4.3 14.0 1.0
CB A:ASN801 4.3 15.2 1.0
O A:CYS805 4.4 20.4 1.0
O A:HOH1332 4.4 28.8 1.0
CA A:ASN801 4.4 14.6 1.0
CB A:SER804 4.6 16.6 1.0
O A:HOH1161 4.7 25.7 1.0
OD1 A:ASP802 4.7 21.9 1.0
N A:ASN806 4.8 18.8 1.0
O A:HOH1622 4.9 40.0 1.0
O A:HOH1227 5.0 27.6 1.0
C A:SER807 5.0 21.6 1.0
N A:GLU803 5.0 13.9 1.0

Sodium binding site 2 out of 2 in 7g38

Go back to Sodium Binding Sites List in 7g38
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-[3-[[(4- Bromophenyl)Methylamino]Methyl]Indol-1-Yl]-N-Methylpropanamide


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 Rat Autotaxin in Complex with 3-[3-[[(4- Bromophenyl)Methylamino]Methyl]Indol-1-Yl]-N-Methylpropanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:23.4
occ:1.00
 O A:TYR669 2.3 23.1 1.0
O A:MET675 2.3 22.7 1.0
O A:ASP672 2.4 23.2 1.0
O A:HOH1464 2.4 30.7 1.0
O A:HOH1618 2.8 34.7 1.0
C A:MET675 3.4 19.9 1.0
C A:TYR669 3.5 23.3 1.0
C A:ASP672 3.5 25.5 1.0
N A:MET675 4.1 20.0 1.0
CA A:TYR669 4.2 20.7 1.0
N A:SER676 4.3 17.3 1.0
CA A:MET675 4.3 19.2 1.0
O A:LYS670 4.3 26.8 1.0
CA A:LYS673 4.3 27.3 1.0
CA A:SER676 4.4 16.4 1.0
N A:LYS673 4.4 24.5 1.0
C A:LYS673 4.4 24.9 1.0
CA A:ASP672 4.5 25.0 1.0
N A:LYS670 4.5 22.8 1.0
N A:ASP672 4.5 25.9 1.0
O A:HOH1661 4.5 33.3 1.0
C A:LYS670 4.6 25.8 1.0
CB A:TYR669 4.6 20.7 1.0
CB A:ASP672 4.6 24.3 1.0
O A:LYS673 4.6 28.2 1.0
CA A:LYS670 4.6 27.3 1.0
N A:GLN674 4.9 23.1 1.0
CB A:MET675 4.9 19.0 1.0

Reference:

D.Hunziker, S.C.Joachim, C.Ullmer, M.G.Rudolph. Crystal Structure of A Rat Autotaxin Complex To Be Published.
Page generated: Sat Feb 8 23:12:39 2025

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