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Sodium in PDB 5w1f: Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin

Protein crystallography data

The structure of Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin, PDB code: 5w1f was solved by T.G.Nakashige, C.L.Drennan, E.M.Nolan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.24 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.020, 77.611, 222.722, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 26.2

Other elements in 5w1f:

The structure of Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin also contains other interesting chemical elements:

Nickel (Ni) 6 atoms
Calcium (Ca) 10 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin (pdb code 5w1f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin, PDB code: 5w1f:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5w1f

Go back to Sodium Binding Sites List in 5w1f
Sodium binding site 1 out of 6 in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin


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 Ni(II)- and Ca(II)-Bound Human Calprotectin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na101

b:50.5
occ:1.00
 O A:ALA28 2.3 36.9 1.0
O A:LYS23 2.4 43.0 1.0
O A:SER20 2.4 39.4 1.0
O A:ASN25 2.5 39.7 1.0
O A:HOH201 2.5 37.3 1.0
C A:SER20 3.2 39.0 1.0
C A:ALA28 3.5 37.5 1.0
CA A:SER20 3.6 39.1 1.0
C A:LYS23 3.6 43.3 1.0
C A:ASN25 3.6 40.0 1.0
CE2 A:TYR30 3.7 38.2 1.0
N A:ASN25 4.0 41.7 1.0
N A:ALA28 4.1 36.6 1.0
N A:LYS23 4.1 42.5 1.0
C A:GLY24 4.2 42.5 1.0
CA A:ALA28 4.2 37.5 1.0
CD2 A:TYR30 4.2 38.2 1.0
CB A:SER20 4.3 38.6 1.0
N A:LEU21 4.3 37.9 1.0
O A:TYR19 4.4 42.3 1.0
CB A:ALA28 4.4 37.2 1.0
CA A:ASN25 4.4 41.1 1.0
CZ A:TYR30 4.5 37.6 1.0
CA A:GLY24 4.5 43.3 1.0
N A:GLY24 4.5 43.8 1.0
CA A:LYS23 4.5 43.2 1.0
O A:GLY24 4.6 42.1 1.0
N A:VAL29 4.6 38.0 1.0
OH A:TYR30 4.6 38.4 1.0
OD2 A:ASP33 4.6 46.9 1.0
N A:ILE22 4.6 39.3 1.0
N A:PHE26 4.6 39.2 1.0
CA A:PHE26 4.7 38.7 0.5
CA A:PHE26 4.8 38.7 0.5
N A:SER20 4.8 40.1 1.0
C A:PHE26 4.8 38.6 1.0
CA A:LEU21 4.8 37.5 1.0
CA A:VAL29 4.9 38.2 1.0

Sodium binding site 2 out of 6 in 5w1f

Go back to Sodium Binding Sites List in 5w1f
Sodium binding site 2 out of 6 in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin


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 Ni(II)- and Ca(II)-Bound Human Calprotectin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:31.6
occ:1.00
 O B:LEU26 2.3 57.4 1.0
O B:THR31 2.4 50.8 1.0
O B:SER23 2.5 44.4 1.0
O B:HOH312 2.5 62.7 1.0
OE1 B:GLU36 2.5 42.2 1.0
O B:HIS28 2.5 57.4 1.0
OE2 B:GLU36 2.8 42.9 1.0
CD B:GLU36 3.1 42.7 1.0
C B:SER23 3.4 45.0 1.0
C B:LEU26 3.6 57.4 1.0
C B:THR31 3.6 48.5 1.0
C B:HIS28 3.7 59.1 1.0
CA B:SER23 3.8 43.3 1.0
N B:HIS28 4.1 58.7 1.0
N B:LEU26 4.1 56.7 1.0
C B:GLY27 4.3 59.2 1.0
N B:THR31 4.4 49.6 1.0
CA B:LEU26 4.4 56.7 1.0
CA B:HIS28 4.4 58.8 1.0
CB B:SER23 4.4 42.7 1.0
N B:LEU32 4.4 47.9 1.0
CA B:LEU32 4.5 48.2 1.0
OG1 B:THR31 4.5 47.0 1.0
O B:TYR22 4.5 45.4 1.0
N B:GLY27 4.6 58.0 1.0
CA B:THR31 4.6 47.8 1.0
CG B:GLU36 4.6 43.6 1.0
N B:VAL24 4.6 46.8 1.0
N B:PRO29 4.6 61.7 1.0
CA B:PRO29 4.6 62.7 1.0
CA B:GLY27 4.7 57.9 1.0
ND2 B:ASN33 4.7 50.7 1.0
N B:ASN33 4.8 47.4 1.0
N B:LYS25 4.8 52.7 1.0
O B:GLY27 4.8 60.7 1.0
OE1 B:GLN73 4.9 50.3 1.0
CB B:LEU26 4.9 55.9 1.0
C B:PRO29 4.9 63.4 1.0
C B:LEU32 4.9 48.7 1.0
N B:SER23 5.0 42.5 1.0
CB B:HIS28 5.0 58.0 1.0

Sodium binding site 3 out of 6 in 5w1f

Go back to Sodium Binding Sites List in 5w1f
Sodium binding site 3 out of 6 in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin


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 Ni(II)- and Ca(II)-Bound Human Calprotectin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na102

b:34.2
occ:1.00
 O C:ALA28 2.3 19.9 1.0
O C:LYS23 2.4 30.8 1.0
O C:ASN25 2.4 22.9 1.0
O C:HOH209 2.5 27.6 1.0
O C:SER20 2.5 32.1 1.0
C C:ALA28 3.4 24.7 1.0
CE2 C:TYR30 3.4 27.2 1.0
C C:SER20 3.5 32.0 1.0
C C:ASN25 3.5 26.8 1.0
C C:LYS23 3.6 30.6 1.0
N C:ASN25 3.8 29.9 1.0
CA C:SER20 3.8 32.5 1.0
N C:ALA28 3.9 23.8 1.0
CA C:ALA28 4.0 24.3 1.0
CD2 C:TYR30 4.0 27.6 1.0
CB C:ALA28 4.0 20.7 1.0
C C:GLY24 4.0 30.3 1.0
CA C:ASN25 4.2 29.7 1.0
CZ C:TYR30 4.3 26.5 1.0
N C:LYS23 4.3 30.9 1.0
CA C:GLY24 4.4 30.0 1.0
CB C:SER20 4.4 31.7 1.0
OH C:TYR30 4.4 21.1 1.0
N C:GLY24 4.4 30.2 1.0
OD2 C:ASP33 4.5 32.0 1.0
O C:GLY24 4.5 30.9 1.0
N C:VAL29 4.5 25.1 1.0
N C:PHE26 4.6 28.4 1.0
CA C:LYS23 4.6 30.2 1.0
O C:TYR19 4.7 35.7 1.0
N C:LEU21 4.7 31.1 1.0
CB C:ASN25 4.7 31.8 1.0
C C:PHE26 4.7 28.7 1.0
CA C:PHE26 4.8 28.0 1.0
CA C:VAL29 4.9 24.8 1.0
O C:PHE26 5.0 28.9 1.0
N C:ILE22 5.0 31.9 1.0

Sodium binding site 4 out of 6 in 5w1f

Go back to Sodium Binding Sites List in 5w1f
Sodium binding site 4 out of 6 in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin


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 Ni(II)- and Ca(II)-Bound Human Calprotectin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na101

b:23.0
occ:1.00
 O G:LYS23 2.4 28.3 1.0
O G:SER20 2.4 30.7 1.0
O G:ALA28 2.4 30.3 1.0
O G:HOH203 2.5 22.2 1.0
O G:ASN25 2.5 34.1 1.0
C G:SER20 3.3 30.9 1.0
CE2 G:TYR30 3.5 28.3 1.0
C G:ALA28 3.6 30.2 1.0
C G:LYS23 3.6 29.6 1.0
C G:ASN25 3.6 35.0 1.0
CA G:SER20 3.7 30.9 1.0
N G:ASN25 4.0 36.9 1.0
CD2 G:TYR30 4.1 29.7 1.0
N G:ALA28 4.1 31.1 1.0
N G:LYS23 4.1 30.6 1.0
C G:GLY24 4.2 36.0 1.0
CA G:ALA28 4.2 30.6 1.0
CZ G:TYR30 4.3 27.1 1.0
O G:TYR19 4.4 32.2 1.0
N G:LEU21 4.4 30.7 1.0
CA G:ASN25 4.4 36.0 1.0
CB G:SER20 4.4 30.6 1.0
CB G:ALA28 4.4 30.2 1.0
OH G:TYR30 4.5 24.8 1.0
CA G:LYS23 4.5 30.9 1.0
OD2 G:ASP33 4.5 38.3 1.0
N G:GLY24 4.5 30.7 1.0
CA G:GLY24 4.6 32.7 1.0
O G:GLY24 4.6 37.6 1.0
N G:VAL29 4.7 29.4 1.0
N G:PHE26 4.7 36.1 1.0
N G:ILE22 4.7 29.2 1.0
C G:PHE26 4.7 34.9 1.0
CA G:PHE26 4.8 37.0 1.0
CA G:LEU21 4.9 28.9 1.0
N G:SER20 4.9 31.5 1.0
O G:PHE26 4.9 34.7 1.0
CA G:VAL29 4.9 29.9 1.0
CB G:ASN25 5.0 34.9 1.0
CG G:LYS23 5.0 30.7 1.0

Sodium binding site 5 out of 6 in 5w1f

Go back to Sodium Binding Sites List in 5w1f
Sodium binding site 5 out of 6 in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin


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 Ni(II)- and Ca(II)-Bound Human Calprotectin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na202

b:46.1
occ:1.00
 O H:LEU26 2.3 70.7 1.0
OE1 H:GLU36 2.4 54.0 1.0
O H:THR31 2.4 57.8 1.0
O H:HIS28 2.4 69.4 1.0
O H:SER23 2.4 57.5 1.0
O H:HOH309 2.5 56.5 1.0
OE2 H:GLU36 2.7 56.0 1.0
CD H:GLU36 2.9 54.4 1.0
C H:SER23 3.5 57.5 1.0
C H:LEU26 3.6 71.5 1.0
C H:HIS28 3.6 69.7 1.0
C H:THR31 3.6 57.8 1.0
CA H:SER23 3.9 56.3 1.0
N H:HIS28 3.9 70.8 1.0
C H:GLY27 4.2 72.2 1.0
ND2 H:ASN33 4.2 55.0 1.0
N H:LEU26 4.3 68.9 1.0
CA H:HIS28 4.3 70.2 1.0
N H:ASN33 4.3 54.1 1.0
OG1 H:THR31 4.4 62.4 1.0
CA H:LEU32 4.4 55.0 1.0
CG H:GLU36 4.4 54.7 1.0
N H:LEU32 4.4 55.9 1.0
CA H:GLY27 4.4 72.2 1.0
N H:GLY27 4.5 72.5 1.0
CB H:SER23 4.5 56.7 1.0
N H:THR31 4.5 61.5 1.0
CA H:LEU26 4.5 71.6 1.0
N H:PRO29 4.6 69.8 1.0
CA H:THR31 4.6 59.7 1.0
OE1 H:GLN73 4.6 62.5 1.0
N H:VAL24 4.7 58.8 1.0
CA H:PRO29 4.7 68.8 1.0
O H:GLY27 4.7 73.0 1.0
O H:TYR22 4.7 56.3 1.0
CG H:ASN33 4.7 54.7 1.0
C H:LEU32 4.7 54.4 1.0
C H:PRO29 4.8 66.2 1.0
N H:LYS25 4.9 62.2 1.0
CB H:HIS28 4.9 68.9 1.0

Sodium binding site 6 out of 6 in 5w1f

Go back to Sodium Binding Sites List in 5w1f
Sodium binding site 6 out of 6 in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin


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 Ni(II)- and Ca(II)-Bound Human Calprotectin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na102

b:33.9
occ:1.00
 O E:SER20 2.4 47.5 1.0
O E:HOH202 2.5 33.7 1.0
O E:ALA28 2.5 40.4 1.0
O E:LYS23 2.5 42.2 1.0
O E:ASN25 2.5 37.9 1.0
C E:SER20 3.3 45.8 1.0
CE2 E:TYR30 3.5 37.6 1.0
C E:ALA28 3.6 39.6 1.0
CA E:SER20 3.6 45.6 1.0
C E:ASN25 3.7 38.7 1.0
C E:LYS23 3.7 42.8 1.0
CD2 E:TYR30 4.0 37.0 1.0
N E:LYS23 4.1 43.9 1.0
N E:ASN25 4.2 41.2 1.0
N E:ALA28 4.2 40.4 1.0
C E:GLY24 4.3 42.3 1.0
O E:TYR19 4.3 46.6 1.0
CA E:ALA28 4.3 40.2 1.0
CZ E:TYR30 4.3 38.0 1.0
CB E:SER20 4.4 44.2 1.0
N E:LEU21 4.4 44.2 1.0
CA E:ASN25 4.5 39.4 1.0
CB E:ALA28 4.5 41.5 1.0
CA E:LYS23 4.5 43.8 1.0
OH E:TYR30 4.5 37.7 1.0
N E:ILE22 4.5 46.7 1.0
OD2 E:ASP33 4.6 42.5 1.0
N E:GLY24 4.6 43.3 1.0
O E:GLY24 4.6 41.8 1.0
N E:VAL29 4.6 37.9 1.0
N E:PHE26 4.6 39.0 1.0
CA E:GLY24 4.7 43.2 1.0
CA E:PHE26 4.7 38.5 0.5
CA E:PHE26 4.7 38.5 0.5
C E:PHE26 4.8 38.8 1.0
N E:SER20 4.8 45.4 1.0
CA E:LEU21 4.9 45.1 1.0
CA E:VAL29 4.9 36.3 1.0

Reference:

T.G.Nakashige, E.M.Zygiel, C.L.Drennan, E.M.Nolan. Nickel Sequestration By the Host-Defense Protein Human Calprotectin. J. Am. Chem. Soc. V. 139 8828 2017.
ISSN: ESSN 1520-5126
PubMed: 28573847
DOI: 10.1021/JACS.7B01212
Page generated: Tue Oct 8 00:58:41 2024

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