Sodium in PDB 7bfz: X-Ray Structure of Human Prostate-Specific Membrane Antigen(Psma) in Complex with A Inhibitor Glu-490

Enzymatic activity of X-Ray Structure of Human Prostate-Specific Membrane Antigen(Psma) in Complex with A Inhibitor Glu-490

All present enzymatic activity of X-Ray Structure of Human Prostate-Specific Membrane Antigen(Psma) in Complex with A Inhibitor Glu-490:
3.4.17.21;

Protein crystallography data

The structure of X-Ray Structure of Human Prostate-Specific Membrane Antigen(Psma) in Complex with A Inhibitor Glu-490, PDB code: 7bfz was solved by A.Rakhimbekova, L.Motlova, C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.96 / 1.73
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.54, 130.103, 158.91, 90, 90, 90
R / Rfree (%) 16.3 / 18.3

Other elements in 7bfz:

The structure of X-Ray Structure of Human Prostate-Specific Membrane Antigen(Psma) in Complex with A Inhibitor Glu-490 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of Human Prostate-Specific Membrane Antigen(Psma) in Complex with A Inhibitor Glu-490 (pdb code 7bfz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of Human Prostate-Specific Membrane Antigen(Psma) in Complex with A Inhibitor Glu-490, PDB code: 7bfz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7bfz

Go back to Sodium Binding Sites List in 7bfz
Sodium binding site 1 out of 2 in the X-Ray Structure of Human Prostate-Specific Membrane Antigen(Psma) in Complex with A Inhibitor Glu-490


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Human Prostate-Specific Membrane Antigen(Psma) in Complex with A Inhibitor Glu-490 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na811

b:55.2
occ:1.00
OH A:TYR242 2.2 39.6 1.0
O A:HOH1241 2.3 40.1 1.0
OG1 A:THR558 2.9 32.9 1.0
OE1 A:GLU560 3.0 34.0 1.0
CZ A:TYR242 3.2 34.9 1.0
CE2 A:TYR242 3.4 34.5 1.0
CB A:GLU560 3.5 31.7 1.0
CE1 A:TYR151 3.5 34.6 1.0
CB A:THR558 3.5 31.4 1.0
CG2 A:THR558 3.6 31.1 1.0
CD A:GLU560 3.8 35.2 1.0
CG A:GLU560 3.8 33.5 1.0
CB A:PRO148 4.2 35.4 1.0
CD1 A:TYR151 4.3 33.6 1.0
OH A:TYR151 4.3 33.3 1.0
CZ A:TYR151 4.3 34.1 1.0
CE1 A:TYR242 4.4 32.8 1.0
CG A:PRO148 4.6 35.0 1.0
CA A:GLU560 4.6 31.6 1.0
N A:GLU560 4.6 30.6 1.0
CD2 A:TYR242 4.8 33.9 1.0
N A:LEU561 4.8 29.7 1.0
O A:PRO149 4.8 35.4 1.0
OE2 A:GLU560 4.9 34.0 1.0

Sodium binding site 2 out of 2 in 7bfz

Go back to Sodium Binding Sites List in 7bfz
Sodium binding site 2 out of 2 in the X-Ray Structure of Human Prostate-Specific Membrane Antigen(Psma) in Complex with A Inhibitor Glu-490


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of Human Prostate-Specific Membrane Antigen(Psma) in Complex with A Inhibitor Glu-490 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na812

b:57.0
occ:1.00
OE1 A:GLU486 2.4 59.1 1.0
O A:HOH1270 2.4 47.0 1.0
O A:HOH1249 2.6 42.2 1.0
O A:HOH1257 2.6 38.5 1.0
O A:HOH1109 2.6 40.5 1.0
CD A:GLU486 3.5 54.8 1.0
OH A:TYR572 3.8 43.0 1.0
N A:GLU486 3.9 43.0 1.0
NZ A:LYS500 4.0 39.6 1.0
O A:HOH909 4.0 52.1 1.0
CB A:GLU486 4.1 45.8 1.0
O A:ASN459 4.2 37.3 1.0
OE2 A:GLU486 4.4 51.2 1.0
CG A:GLU486 4.4 51.2 1.0
CA A:GLU486 4.6 45.1 1.0
CA A:ASP485 4.7 38.0 1.0
O A:GLU486 4.7 44.0 1.0
CB A:ASP485 4.7 37.2 1.0
O A:HOH1344 4.7 56.2 1.0
C A:ASP485 4.8 41.2 1.0
O6 A:NAG806 4.9 53.2 1.0
C6 A:NAG806 4.9 52.8 1.0

Reference:

A.Rakhimbekova, L.Motlova, C.Barinka. X-Ray Structure of Human Prostate-Specific Membrane Antigen(Psma) in Complex with A Inhibitor Glu-490 To Be Published.
Page generated: Sat Aug 21 17:20:18 2021

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