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Sodium in PDB 2gsi: Crystal Structure of A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease

Enzymatic activity of Crystal Structure of A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease

All present enzymatic activity of Crystal Structure of A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease:
3.1.31.1;

Protein crystallography data

The structure of Crystal Structure of A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease, PDB code: 2gsi was solved by A.A.Armstrong, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.74 / 2.81
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 105.739, 131.040, 291.340, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 29.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease (pdb code 2gsi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease, PDB code: 2gsi:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 2gsi

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Sodium binding site 1 out of 7 in the Crystal Structure of A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease


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 A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na229

b:22.1
occ:1.00
 OE1 B:GLU46 2.4 47.9 1.0
O B:GLY44 2.5 47.1 1.0
N B:ARG40 3.1 43.0 1.0
CD B:GLU46 3.2 46.5 1.0
CD B:ARG40 3.4 45.3 1.0
O B:LYS38 3.4 35.8 1.0
CB B:ARG40 3.5 44.6 1.0
CG B:ARG40 3.5 43.7 1.0
CG B:GLU46 3.6 45.2 1.0
C B:GLY44 3.7 47.7 1.0
CA B:ARG40 3.9 44.7 1.0
C B:LYS38 4.0 35.6 1.0
CA B:LEU39 4.0 38.9 1.0
C B:LEU39 4.1 41.0 1.0
N B:GLU46 4.1 45.3 1.0
OE2 B:GLU46 4.1 47.5 1.0
CB B:GLU46 4.3 44.9 1.0
N B:GLY44 4.3 50.5 1.0
CG B:LYS38 4.3 32.4 1.0
N B:LEU39 4.4 37.5 1.0
CA B:GLY44 4.5 48.9 1.0
N B:LEU45 4.6 46.7 1.0
C B:LEU45 4.6 45.8 1.0
CA B:LEU45 4.6 46.1 1.0
O B:ARG40 4.7 45.8 1.0
CB B:GLN43 4.7 52.3 1.0
OE1 B:GLN43 4.7 53.5 1.0
CE B:LYS38 4.8 30.9 1.0
C B:ARG40 4.8 46.5 1.0
NE B:ARG40 4.8 47.4 1.0
CA B:GLU46 4.8 44.7 1.0
CB B:LYS38 4.9 33.5 1.0
C B:GLN43 4.9 51.6 1.0

Sodium binding site 2 out of 7 in 2gsi

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Sodium binding site 2 out of 7 in the Crystal Structure of A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease


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 A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na229

b:26.9
occ:1.00
 N D:GLY65 2.4 41.3 1.0
O D:VAL67 2.7 34.2 1.0
CA D:GLY65 3.2 40.9 1.0
C D:GLN64 3.2 41.7 1.0
CA D:GLN64 3.3 42.1 1.0
N D:LYS66 3.5 38.7 1.0
N D:VAL67 3.5 35.9 1.0
O D:PHE63 3.5 40.3 1.0
C D:GLY65 3.6 40.4 1.0
CD1 D:TYR59 3.7 32.9 1.0
CE1 D:TYR59 3.7 32.7 1.0
C D:VAL67 3.7 34.3 1.0
CG D:GLN64 4.0 45.3 1.0
CB D:GLN64 4.1 42.5 1.0
CA D:VAL67 4.1 35.3 1.0
CG2 D:VAL67 4.2 35.7 1.0
N D:GLN64 4.3 41.1 1.0
C D:PHE63 4.3 40.1 1.0
O D:GLN64 4.3 41.3 1.0
CG D:TYR59 4.4 33.1 1.0
C D:LYS66 4.5 36.8 1.0
CZ D:TYR59 4.5 33.8 1.0
CA D:LYS66 4.6 37.5 1.0
O D:GLY65 4.6 40.9 1.0
CB D:VAL67 4.8 35.6 1.0
N D:THR68 5.0 32.7 1.0

Sodium binding site 3 out of 7 in 2gsi

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Sodium binding site 3 out of 7 in the Crystal Structure of A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease


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 A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na212

b:29.7
occ:1.00
 O E:ILE91 2.5 33.1 1.0
C E:ILE91 3.4 33.6 1.0
N E:LEU94 3.7 36.7 1.0
NE E:ARG96 3.8 33.4 1.0
C E:GLU93 3.8 36.8 1.0
CG E:ARG96 3.9 31.0 1.0
N E:GLU93 4.0 35.8 1.0
CE Y:LYS5 4.0 45.0 1.0
CG2 Y:VAL8 4.1 45.7 1.0
CA E:ILE91 4.1 33.5 1.0
O E:GLU93 4.2 36.4 1.0
CA E:GLU93 4.2 37.3 1.0
CA E:LEU94 4.3 36.1 1.0
CD E:ARG96 4.3 31.6 1.0
C E:ARG92 4.3 35.0 1.0
N E:ARG92 4.4 34.6 1.0
CB E:ILE91 4.5 34.6 1.0
CB E:LEU94 4.6 35.7 1.0
NZ Y:LYS5 4.7 41.8 1.0
CZ E:ARG96 4.8 35.2 1.0
O E:ARG92 4.8 35.0 1.0
CA E:ARG92 4.8 34.8 1.0
NH2 E:ARG96 4.9 35.7 1.0

Sodium binding site 4 out of 7 in 2gsi

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Sodium binding site 4 out of 7 in the Crystal Structure of A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease


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 A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na229

b:28.6
occ:1.00
 O F:VAL109 2.4 32.6 1.0
C F:VAL109 3.0 32.3 1.0
OG1 F:THR110 3.1 36.0 1.0
N F:VAL109 3.4 31.6 1.0
O F:ALA88 3.5 28.6 1.0
N F:THR110 3.6 33.0 1.0
N F:ALA88 3.7 28.8 1.0
CA F:VAL109 3.8 31.7 1.0
CG2 F:THR87 3.9 27.7 1.0
CA F:THR110 3.9 33.7 1.0
C F:ALA88 3.9 27.9 1.0
O F:HOH230 4.0 26.0 1.0
OG1 F:THR108 4.0 36.8 1.0
C F:THR108 4.0 31.7 1.0
CB F:THR110 4.1 34.1 1.0
CA F:ALA88 4.3 28.3 1.0
C F:THR87 4.4 29.7 1.0
CA F:THR108 4.5 31.7 1.0
CB F:THR108 4.5 32.3 1.0
N F:VAL89 4.7 27.1 1.0
CA F:THR87 4.7 29.5 1.0
O F:THR108 4.8 32.2 1.0
CB F:THR87 4.9 28.7 1.0
CB F:VAL109 4.9 31.9 1.0
CG2 F:VAL89 4.9 24.9 1.0

Sodium binding site 5 out of 7 in 2gsi

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Sodium binding site 5 out of 7 in the Crystal Structure of A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease


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 A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na212

b:29.1
occ:1.00
 OD1 G:ASP34 2.3 40.4 1.0
N G:LEU50 2.5 29.6 1.0
CA G:LEU50 3.3 30.2 1.0
CG G:ASP34 3.4 36.4 1.0
CB G:TYR49 3.4 27.3 1.0
C G:TYR49 3.4 29.1 1.0
CA G:TYR49 3.5 28.1 1.0
OD2 G:ASP34 3.7 31.2 1.0
O G:MET33 3.7 38.2 1.0
CG G:LEU50 3.7 28.6 1.0
CA G:TYR32 3.8 37.8 1.0
C G:TYR32 3.9 38.1 1.0
CB G:LEU50 4.0 29.3 1.0
CD2 G:LEU50 4.1 25.8 1.0
N G:MET33 4.2 37.9 1.0
O G:TYR32 4.2 38.6 1.0
CB G:TYR32 4.3 37.5 1.0
C G:MET33 4.3 37.5 1.0
CD1 H:ILE97 4.4 37.6 1.0
CG G:TYR49 4.4 25.8 1.0
CD1 G:TYR49 4.4 23.6 1.0
CD2 G:TYR32 4.4 35.1 1.0
O G:TYR49 4.6 29.6 1.0
C G:LEU50 4.7 30.9 1.0
O G:SER31 4.7 38.0 1.0
CB G:ASP34 4.7 36.6 1.0
CG1 H:ILE97 4.8 38.0 1.0
CG G:TYR32 4.9 36.9 1.0
N G:VAL51 4.9 31.9 1.0
N G:ASP34 4.9 36.9 1.0
N G:TYR49 4.9 28.1 1.0
CA G:MET33 4.9 37.9 1.0
CA G:ASP34 5.0 36.6 1.0
CD1 G:LEU50 5.0 27.0 1.0

Sodium binding site 6 out of 7 in 2gsi

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Sodium binding site 6 out of 7 in the Crystal Structure of A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease


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 A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na213

b:37.8
occ:1.00
 O H:GLN105 2.6 24.0 1.0
N G:PRO43 3.4 35.8 1.0
CD G:PRO43 3.5 36.0 1.0
OH H:TYR91 3.5 26.5 1.0
C H:GLN105 3.6 25.2 1.0
O G:GLY41 3.6 38.6 1.0
C G:GLN42 3.7 36.0 1.0
CB G:PRO43 3.8 36.0 1.0
CG G:PRO43 3.8 36.9 1.0
CA G:PRO43 3.8 35.9 1.0
CE2 H:TYR91 3.8 25.1 1.0
O G:GLN42 4.0 36.7 1.0
CZ H:TYR91 4.1 25.7 1.0
CA H:GLN105 4.2 25.7 1.0
CA G:GLN42 4.3 36.1 1.0
C G:GLY41 4.5 37.5 1.0
N H:GLY106 4.6 24.7 1.0
CB H:GLN105 4.7 25.0 1.0
N G:GLN42 4.9 36.5 1.0
CA H:GLY106 4.9 25.7 1.0

Sodium binding site 7 out of 7 in 2gsi

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Sodium binding site 7 out of 7 in the Crystal Structure of A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease


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 A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Na77

b:26.6
occ:1.00
 O W:TYR11 2.5 45.5 1.0
OXT W:TYR11 3.1 45.1 1.0
C W:TYR11 3.1 45.2 1.0
O W:HOH61 3.2 45.0 1.0
CA W:TYR11 4.3 45.3 1.0
CB W:TYR11 4.4 45.5 1.0

Reference:

A.A.Armstrong, L.M.Amzel. Crystal Structure of A Murine Fab in Complex with An 11 Residue Peptide Derived From Staphylococcal Nuclease To Be Published.
Page generated: Mon Oct 7 02:39:56 2024

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