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Sodium in PDB 4ag2: Human Chymase - Fynomer Complex

Enzymatic activity of Human Chymase - Fynomer Complex

All present enzymatic activity of Human Chymase - Fynomer Complex:
3.4.21.39;

Protein crystallography data

The structure of Human Chymase - Fynomer Complex, PDB code: 4ag2 was solved by D.Schlatter, S.Brack, D.W.Banner, S.Batey, J.Benz, J.Bertschinger, W.Huber, C.Joseph, A.Rufer, A.Van Der Kloosters, M.Weber, D.Grabulovski, M.Hennig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.75 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.937, 64.124, 174.987, 90.00, 90.00, 90.00
R / Rfree (%) 17.853 / 21.168

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Chymase - Fynomer Complex (pdb code 4ag2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Human Chymase - Fynomer Complex, PDB code: 4ag2:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4ag2

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Sodium binding site 1 out of 5 in the Human Chymase - Fynomer Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Chymase - Fynomer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1229

b:32.0
occ:1.00
 O A:HOH2058 2.3 33.5 1.0
OE1 A:GLU97 2.4 33.2 1.0
O A:LYS98 2.5 21.7 1.0
CD A:GLU97 3.4 35.4 1.0
C A:LYS98 3.6 25.0 1.0
CG A:GLU97 3.9 30.2 1.0
N A:LYS98 4.2 22.9 1.0
CA A:LYS98 4.3 22.7 1.0
OE2 A:GLU97 4.3 34.2 1.0
CB A:LYS98 4.4 23.1 1.0
C A:ALA99 4.5 28.7 1.0
OG A:SER100 4.5 29.6 1.0
N A:ALA99 4.6 23.8 1.0
CB A:GLU97 4.6 27.4 1.0
N A:SER100 4.6 26.4 1.0
O A:ALA99 4.7 28.2 1.0
CA A:ALA99 4.8 25.4 1.0
C A:GLU97 5.0 25.0 1.0

Sodium binding site 2 out of 5 in 4ag2

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Sodium binding site 2 out of 5 in the Human Chymase - Fynomer Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Chymase - Fynomer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1230

b:26.2
occ:1.00
 O A:HOH2114 2.1 34.5 1.0
O A:HOH2231 2.2 34.4 1.0
O A:HOH2232 2.4 30.9 1.0
CB A:SER84 3.8 20.9 1.0
OG A:SER84 3.9 24.6 1.0
O A:HOH2112 4.0 26.4 1.0
O A:HOH2048 4.1 48.7 1.0
O C:HOH2044 4.3 23.7 1.0
ND2 A:ASN82 4.7 28.1 1.0
CG2 A:THR85 5.0 20.1 1.0

Sodium binding site 3 out of 5 in 4ag2

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Sodium binding site 3 out of 5 in the Human Chymase - Fynomer Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Chymase - Fynomer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1231

b:19.9
occ:0.50
 O A:HOH2176 2.1 37.1 1.0
O A:HOH2180 2.2 36.7 1.0
O A:ARG158 2.3 18.1 1.0
O A:HOH2172 2.4 30.4 1.0
O A:PHE160 2.5 20.4 1.0
C A:ARG158 3.3 20.2 1.0
C A:PHE160 3.5 21.3 1.0
N A:PHE160 3.5 20.5 1.0
C A:ASP159 3.8 21.6 1.0
CA A:PHE160 4.0 19.8 1.0
N A:ASP159 4.1 20.3 1.0
O A:PHE157 4.1 17.9 1.0
CA A:ASP159 4.2 21.3 1.0
CA A:ARG158 4.3 16.8 1.0
CB A:PHE160 4.3 19.0 1.0
O A:ASP159 4.4 22.0 1.0
O A:HOH2178 4.5 48.1 1.0
O A:HOH2179 4.6 27.3 1.0
O A:HOH2079 4.7 59.7 1.0
N A:ASP161 4.7 19.3 1.0

Sodium binding site 4 out of 5 in 4ag2

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Sodium binding site 4 out of 5 in the Human Chymase - Fynomer Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human Chymase - Fynomer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1061

b:33.4
occ:1.00
 O C:THR48 2.3 22.4 1.0
O A:HOH2198 2.3 30.2 1.0
O A:HOH2197 2.3 39.0 1.0
O A:HOH2196 2.5 35.0 1.0
O C:HOH2053 2.6 59.8 1.0
O C:HOH2052 2.6 29.1 1.0
C C:THR48 3.5 22.3 1.0
NZ A:LYS179 3.8 26.0 1.0
N C:THR48 4.1 21.1 1.0
OE1 C:GLU47 4.1 27.4 1.0
O A:HOH2152 4.3 38.0 1.0
OG1 C:THR48 4.3 21.9 0.5
CA C:THR48 4.4 21.6 0.5
CA C:THR48 4.4 21.8 0.5
N C:GLY49 4.4 18.1 1.0
CA C:GLY49 4.5 17.1 1.0
O C:HOH2045 4.6 45.0 1.0
CD2 C:LEU19 4.7 27.6 1.0
O C:ASP18 4.7 19.4 1.0
O C:TRP16 4.8 17.2 0.7
CB C:GLU47 4.8 22.8 1.0
O C:TRP16 4.9 16.4 0.3
CB C:THR48 4.9 21.6 0.5
CB C:THR48 5.0 21.7 0.5

Sodium binding site 5 out of 5 in 4ag2

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Sodium binding site 5 out of 5 in the Human Chymase - Fynomer Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Human Chymase - Fynomer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1061

b:35.2
occ:1.00
 O D:HOH2028 2.2 28.0 1.0
O D:GLY32 2.3 26.5 1.0
O D:HOH2027 2.4 33.4 1.0
O D:GLY35 2.6 19.5 1.0
C D:GLY32 3.5 27.2 1.0
C D:GLY35 3.5 20.9 1.0
NE1 D:TRP38 3.6 21.8 1.0
N D:GLY35 3.8 26.5 1.0
CD1 D:TRP38 4.1 21.2 1.0
CA D:ASP33 4.1 29.7 1.0
CA D:GLY35 4.1 24.0 1.0
N D:ASP33 4.2 28.0 1.0
C D:ASP33 4.3 31.3 1.0
N D:SER34 4.4 26.9 1.0
OD1 D:ASP36 4.4 26.7 1.0
N D:ASP36 4.5 21.3 1.0
CA D:GLY32 4.6 26.1 1.0
CE2 D:TRP38 4.7 24.5 1.0
O D:HOH2023 4.7 21.6 1.0
CA D:ASP36 4.7 22.1 1.0
O D:ASP33 4.9 30.7 1.0
C D:SER34 5.0 26.2 1.0

Reference:

D.Schlatter, S.Brack, D.W.Banner, S.Batey, J.Benz, J.Bertschinger, W.Huber, C.Joseph, A.Rufer, A.Van Der Klooster, M.Weber, D.Grabulovski, M.Hennig. Generation, Characterization and Structural Data of Chymase Binding Proteins Based on the Human Fyn Kinase SH3 Domain. Mabs V. 4 497 2012.
ISSN: ISSN 1942-0862
PubMed: 22653218
DOI: 10.4161/MABS.20452
Page generated: Mon Oct 7 14:21:08 2024

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