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Sodium in PDB 6dwh: Crystal Structure of Complex of Bbki and Bovine Trypsin

Enzymatic activity of Crystal Structure of Complex of Bbki and Bovine Trypsin

All present enzymatic activity of Crystal Structure of Complex of Bbki and Bovine Trypsin:
3.4.21.4;

Protein crystallography data

The structure of Crystal Structure of Complex of Bbki and Bovine Trypsin, PDB code: 6dwh was solved by M.Li, A.Wlodawer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.91 / 2.00
Space group P 64
Cell size a, b, c (Å), α, β, γ (°) 207.809, 207.809, 107.167, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 22.3

Other elements in 6dwh:

The structure of Crystal Structure of Complex of Bbki and Bovine Trypsin also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Complex of Bbki and Bovine Trypsin (pdb code 6dwh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Complex of Bbki and Bovine Trypsin, PDB code: 6dwh:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 6dwh

Go back to Sodium Binding Sites List in 6dwh
Sodium binding site 1 out of 8 in the Crystal Structure of Complex of Bbki and Bovine Trypsin


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 Complex of Bbki and Bovine Trypsin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:28.8
occ:1.00
 O C:LEU137 2.6 24.5 1.0
OH C:TYR29 2.9 24.2 1.0
OG C:SER139 3.2 22.9 1.0
C C:LEU137 3.4 25.1 1.0
CG C:LEU137 3.7 26.6 1.0
CG C:PRO198 3.7 21.5 1.0
CE1 C:TYR29 3.8 24.6 1.0
CZ C:TYR29 3.8 24.5 1.0
O C:PRO198 3.8 21.6 1.0
CB C:SER139 3.9 23.0 1.0
CB C:LEU137 3.9 26.3 1.0
CB C:PRO198 4.0 21.3 1.0
CD2 C:LEU137 4.0 26.7 1.0
N C:SER139 4.0 23.2 1.0
CG2 C:VAL200 4.0 23.6 1.0
N C:ILE138 4.1 24.4 1.0
CB C:VAL200 4.2 23.5 1.0
CA C:ILE138 4.2 23.7 1.0
CG1 C:VAL27 4.2 27.1 1.0
C C:PRO198 4.3 21.6 1.0
C C:ILE138 4.3 23.6 1.0
N C:VAL200 4.3 23.3 1.0
CA C:LEU137 4.3 26.1 1.0
CA C:SER139 4.6 23.2 1.0
CA C:PRO198 4.8 21.3 1.0
CA C:VAL199 4.9 22.2 1.0
N C:VAL199 4.9 21.9 1.0
CA C:VAL200 4.9 23.7 1.0
C C:VAL199 5.0 22.6 1.0
CD C:PRO198 5.0 21.4 1.0
CD1 C:LEU137 5.0 26.9 1.0

Sodium binding site 2 out of 8 in 6dwh

Go back to Sodium Binding Sites List in 6dwh
Sodium binding site 2 out of 8 in the Crystal Structure of Complex of Bbki and Bovine Trypsin


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 Complex of Bbki and Bovine Trypsin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na301

b:21.2
occ:1.00
 OG1 E:THR125 3.8 35.4 1.0
CG E:LYS204 3.9 26.9 1.0
N E:THR125 3.9 34.5 1.0
N E:SER127 4.2 38.3 1.0
CE E:LYS204 4.4 27.6 1.0
O E:SER127 4.5 37.7 1.0
CA E:PRO124 4.6 32.3 1.0
CB E:THR125 4.7 35.8 1.0
CA E:THR125 4.7 35.5 1.0
CD E:LYS204 4.8 27.1 1.0
NE2 E:GLN210 4.8 21.6 1.0
CB E:LYS204 4.8 26.8 1.0
C E:PRO124 4.9 34.0 1.0
OG E:SER127 4.9 39.2 1.0
CB E:PRO124 4.9 31.8 1.0
C E:THR125 4.9 36.2 1.0

Sodium binding site 3 out of 8 in 6dwh

Go back to Sodium Binding Sites List in 6dwh
Sodium binding site 3 out of 8 in the Crystal Structure of Complex of Bbki and Bovine Trypsin


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 Complex of Bbki and Bovine Trypsin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na302

b:32.6
occ:1.00
 OG E:SER139 2.8 19.9 1.0
O E:LEU137 2.9 22.2 1.0
OH E:TYR29 2.9 20.2 1.0
C E:LEU137 3.5 22.4 1.0
CE1 E:TYR29 3.7 20.7 1.0
CZ E:TYR29 3.7 20.7 1.0
CG E:LEU137 3.8 24.1 1.0
CB E:SER139 3.8 19.9 1.0
CG E:PRO198 3.9 19.7 1.0
O E:PRO198 3.9 19.9 1.0
CD2 E:LEU137 3.9 24.4 1.0
CG1 E:VAL27 3.9 22.3 1.0
N E:SER139 4.0 20.1 1.0
CB E:LEU137 4.0 23.6 1.0
CG2 E:VAL200 4.0 22.9 1.0
CB E:PRO198 4.1 19.6 1.0
C E:ILE138 4.1 20.6 1.0
N E:ILE138 4.1 21.5 1.0
CA E:ILE138 4.2 20.8 1.0
CB E:VAL200 4.3 22.4 1.0
C E:PRO198 4.4 19.8 1.0
CA E:LEU137 4.4 23.4 1.0
N E:VAL200 4.5 21.8 1.0
CA E:SER139 4.6 19.9 1.0
O E:ILE138 4.7 20.6 1.0
CA E:PRO198 4.8 19.5 1.0
CD1 E:TYR29 5.0 21.2 1.0

Sodium binding site 4 out of 8 in 6dwh

Go back to Sodium Binding Sites List in 6dwh
Sodium binding site 4 out of 8 in the Crystal Structure of Complex of Bbki and Bovine Trypsin


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 Complex of Bbki and Bovine Trypsin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na201

b:49.8
occ:1.00
 NZ C:LYS60 4.0 35.7 1.0
N I:VAL3 4.3 30.5 1.0
CG2 I:VAL3 4.3 29.2 1.0
CE C:LYS60 4.4 34.7 1.0
CB I:VAL3 4.4 28.7 1.0
OG I:SER2 4.8 39.5 1.0
CB I:SER2 5.0 37.3 1.0
CA I:SER2 5.0 36.0 1.0

Sodium binding site 5 out of 8 in 6dwh

Go back to Sodium Binding Sites List in 6dwh
Sodium binding site 5 out of 8 in the Crystal Structure of Complex of Bbki and Bovine Trypsin


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 Complex of Bbki and Bovine Trypsin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na202

b:49.4
occ:1.00
 O I:HOH301 2.3 37.7 1.0
O I:GLY9 3.1 25.9 1.0
NE2 I:GLN10 3.1 30.9 1.0
C I:GLY9 3.8 25.7 1.0
CA I:GLY9 4.3 26.0 1.0
O I:ASN8 4.4 26.6 1.0
CD I:GLN10 4.4 29.4 1.0
N I:GLN10 4.7 25.3 1.0

Sodium binding site 6 out of 8 in 6dwh

Go back to Sodium Binding Sites List in 6dwh
Sodium binding site 6 out of 8 in the Crystal Structure of Complex of Bbki and Bovine Trypsin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Complex of Bbki and Bovine Trypsin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na201

b:38.4
occ:1.00
 N J:ALA40 3.9 56.0 1.0
NH1 J:ARG43 3.9 41.2 1.0
CB J:ALA40 4.1 57.2 1.0
NH2 J:ARG43 4.2 42.0 1.0
CZ J:ARG43 4.4 40.9 1.0
CA J:GLU39 4.6 56.5 1.0
CA J:ALA40 4.6 56.5 1.0
C J:GLU39 4.7 55.8 1.0
N J:GLU41 4.8 53.3 1.0
CB J:GLU39 4.9 55.6 1.0

Sodium binding site 7 out of 8 in 6dwh

Go back to Sodium Binding Sites List in 6dwh
Sodium binding site 7 out of 8 in the Crystal Structure of Complex of Bbki and Bovine Trypsin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Complex of Bbki and Bovine Trypsin within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na201

b:22.8
occ:1.00
 O L:LEU147 2.7 24.4 1.0
O L:VAL100 2.8 22.5 1.0
O L:VAL45 3.1 27.2 1.0
N L:VAL100 3.5 21.7 1.0
N L:LEU147 3.7 27.1 1.0
CB L:ALA44 3.7 29.1 1.0
C L:LEU147 3.7 24.8 1.0
CB L:ALA99 3.8 22.0 1.0
C L:VAL100 3.8 22.1 1.0
N L:VAL45 3.8 27.0 1.0
CD2 L:TYR146 3.9 30.0 1.0
CB L:TYR146 4.0 30.1 1.0
CA L:VAL100 4.1 21.7 1.0
C L:VAL45 4.1 27.0 1.0
C L:ALA99 4.1 21.5 1.0
CA L:ALA99 4.1 21.6 1.0
C L:TYR146 4.1 28.5 1.0
CA L:ALA44 4.1 29.1 1.0
CA L:LEU147 4.2 25.7 1.0
C L:ALA44 4.2 27.9 1.0
CA L:TYR146 4.2 30.2 1.0
CG L:TYR146 4.4 30.6 1.0
CB L:VAL100 4.4 21.4 1.0
CG2 L:ILE96 4.5 25.1 1.0
CA L:VAL45 4.5 26.5 1.0
CB L:LEU147 4.6 25.3 1.0
N L:ALA148 4.9 24.2 1.0
CE2 L:TYR146 4.9 30.5 1.0
O L:TYR146 4.9 28.6 1.0
N L:LYS101 5.0 22.0 1.0

Sodium binding site 8 out of 8 in 6dwh

Go back to Sodium Binding Sites List in 6dwh
Sodium binding site 8 out of 8 in the Crystal Structure of Complex of Bbki and Bovine Trypsin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Complex of Bbki and Bovine Trypsin within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na202

b:42.7
occ:1.00
 N F:GLY148 3.8 42.4 1.0
OG F:SER147 3.9 46.7 1.0
OG L:SER82 4.0 39.5 1.0
CB L:PRO80 4.1 30.1 1.0
N L:SER81 4.1 30.9 1.0
CA F:GLY148 4.3 42.1 1.0
N L:SER82 4.4 35.1 1.0
CB F:SER147 4.4 45.4 1.0
CB L:SER81 4.6 32.2 1.0
C F:SER147 4.6 43.2 1.0
CA L:PRO80 4.8 29.5 1.0
CB L:SER82 4.8 38.4 1.0
CA L:SER81 4.8 31.8 1.0
C L:PRO80 4.9 29.8 1.0
CA F:SER147 4.9 43.2 1.0

Reference:

M.Li, J.Srp, A.Gustchina, Z.Dauter, M.Mares, A.Wlodawer. Crystal Structures of the Complex of A Kallikrein Inhibitor From Bauhinia Bauhinioides with Trypsin and Modeling of Kallikrein Complexes. Acta Crystallogr D Struct V. 75 56 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 30644845
DOI: 10.1107/S2059798318016492
Page generated: Tue Oct 8 08:11:12 2024

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