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Sodium in PDB 3nps: Crystal Structure of Membrane-Type Serine Protease 1 (Mt-SP1) in Complex with the Fab Inhibitor S4

Enzymatic activity of Crystal Structure of Membrane-Type Serine Protease 1 (Mt-SP1) in Complex with the Fab Inhibitor S4

All present enzymatic activity of Crystal Structure of Membrane-Type Serine Protease 1 (Mt-SP1) in Complex with the Fab Inhibitor S4:
3.4.21.109;

Protein crystallography data

The structure of Crystal Structure of Membrane-Type Serine Protease 1 (Mt-SP1) in Complex with the Fab Inhibitor S4, PDB code: 3nps was solved by A.Baharuddin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.64 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.161, 83.988, 101.394, 90.00, 91.45, 90.00
R / Rfree (%) 18.8 / 22.8

Other elements in 3nps:

The structure of Crystal Structure of Membrane-Type Serine Protease 1 (Mt-SP1) in Complex with the Fab Inhibitor S4 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Membrane-Type Serine Protease 1 (Mt-SP1) in Complex with the Fab Inhibitor S4 (pdb code 3nps). 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 Membrane-Type Serine Protease 1 (Mt-SP1) in Complex with the Fab Inhibitor S4, PDB code: 3nps:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 3nps

Go back to Sodium Binding Sites List in 3nps
Sodium binding site 1 out of 5 in the Crystal Structure of Membrane-Type Serine Protease 1 (Mt-SP1) in Complex with the Fab Inhibitor S4


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 Membrane-Type Serine Protease 1 (Mt-SP1) in Complex with the Fab Inhibitor S4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na245

b:40.8
occ:1.00
 O A:HOH340 3.7 39.8 1.0
OE1 A:GLU159 4.0 36.5 1.0
O A:HOH324 4.3 32.4 1.0
O A:HOH339 4.7 36.5 1.0
O A:HOH305 4.7 31.0 1.0

Sodium binding site 2 out of 5 in 3nps

Go back to Sodium Binding Sites List in 3nps
Sodium binding site 2 out of 5 in the Crystal Structure of Membrane-Type Serine Protease 1 (Mt-SP1) in Complex with the Fab Inhibitor S4


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 Membrane-Type Serine Protease 1 (Mt-SP1) in Complex with the Fab Inhibitor S4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na246

b:39.7
occ:1.00
 O A:TRP141 3.6 19.8 1.0
CA A:GLY193 3.7 17.3 1.0
C1 A:EDO4 3.7 30.7 1.0
O A:GLN192 3.7 17.5 1.0
O1 A:EDO4 3.8 33.5 1.0
CA A:GLY142 3.8 18.5 1.0
CD2 A:HIS40 4.0 22.3 1.0
C2 A:EDO4 4.0 30.1 1.0
CD2 A:HIS143 4.2 20.1 1.0
CA A:GLY151 4.2 21.9 1.0
C A:TRP141 4.2 18.4 1.0
C A:GLY142 4.4 18.0 1.0
N A:GLY142 4.4 16.4 1.0
C A:GLN192 4.5 16.7 1.0
N A:GLY193 4.5 18.2 1.0
N A:HIS143 4.5 18.8 1.0
C A:GLY193 4.6 17.3 1.0
NE2 A:HIS40 4.6 19.7 1.0
NE2 A:HIS143 4.6 24.2 1.0
O A:GLY193 4.7 18.3 1.0
O A:HIS40 4.7 23.2 1.0
N A:GLY151 4.8 22.7 1.0
O A:HOH476 4.9 42.8 1.0

Sodium binding site 3 out of 5 in 3nps

Go back to Sodium Binding Sites List in 3nps
Sodium binding site 3 out of 5 in the Crystal Structure of Membrane-Type Serine Protease 1 (Mt-SP1) in Complex with the Fab Inhibitor S4


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 Membrane-Type Serine Protease 1 (Mt-SP1) in Complex with the Fab Inhibitor S4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na218

b:49.0
occ:1.00
 OG B:SER132 3.7 29.4 0.5
O B:SER128 4.2 28.3 1.0
O B:SER130 4.2 27.6 1.0

Sodium binding site 4 out of 5 in 3nps

Go back to Sodium Binding Sites List in 3nps
Sodium binding site 4 out of 5 in the Crystal Structure of Membrane-Type Serine Protease 1 (Mt-SP1) in Complex with the Fab Inhibitor S4


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 Membrane-Type Serine Protease 1 (Mt-SP1) in Complex with the Fab Inhibitor S4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na219

b:53.3
occ:1.00
 O B:HOH562 4.2 25.8 1.0
O B:ASP208 4.2 30.7 1.0
CD1 B:ILE195 4.2 28.2 1.0
CB B:ASP208 4.4 29.1 1.0
CG2 B:ILE195 4.5 24.0 1.0
CG1 B:ILE195 4.6 25.0 1.0
CB B:LYS210 4.6 26.0 1.0
N B:LYS210 4.6 24.5 1.0
O B:HOH672 4.6 39.4 1.0
C B:ASP208 4.6 28.0 1.0

Sodium binding site 5 out of 5 in 3nps

Go back to Sodium Binding Sites List in 3nps
Sodium binding site 5 out of 5 in the Crystal Structure of Membrane-Type Serine Protease 1 (Mt-SP1) in Complex with the Fab Inhibitor S4


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 Membrane-Type Serine Protease 1 (Mt-SP1) in Complex with the Fab Inhibitor S4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na213

b:32.5
occ:1.00
 OG C:SER177 2.6 20.2 1.0
OE2 C:GLU161 2.7 29.3 1.0
O C:HOH524 2.8 33.7 1.0
O C:VAL146 3.1 25.3 1.0
CB C:SER177 3.4 20.2 1.0
CD C:GLU161 3.5 27.0 1.0
CG C:GLU161 3.6 23.2 1.0
CB C:VAL146 3.6 23.9 1.0
C C:VAL146 3.9 23.6 1.0
OG C:SER159 3.9 26.1 1.0
O C:HOH260 4.0 28.6 1.0
CG1 C:VAL146 4.0 26.0 1.0
CD1 C:TRP148 4.1 21.4 1.0
NE1 C:TRP148 4.1 19.4 1.0
CA C:VAL146 4.3 23.4 1.0
CB C:SER159 4.5 24.2 1.0
CG2 C:VAL146 4.6 25.6 1.0
CA C:SER177 4.6 19.0 1.0
O C:HOH271 4.6 49.1 1.0
OE1 C:GLU161 4.7 29.4 1.0
N C:VAL146 4.8 21.9 1.0
O C:HOH270 5.0 28.5 1.0
N C:GLN147 5.0 23.6 1.0

Reference:

E.L.Schneider, M.S.Lee, A.Baharuddin, D.H.Goetz, C.J.Farady, M.Ward, C.I.Wang, C.S.Craik. A Reverse Binding Motif That Contributes to Specific Protease Inhibition By Antibodies. J.Mol.Biol. V. 415 699 2012.
ISSN: ISSN 0022-2836
PubMed: 22154938
DOI: 10.1016/J.JMB.2011.11.036
Page generated: Mon Oct 7 11:53:20 2024

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