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Calcium in PDB 5hlo: Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221

Protein crystallography data

The structure of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221, PDB code: 5hlo was solved by H.Lin, G.R.Andersen, L.Yatime, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.20 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 55.980, 90.030, 196.800, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 19.7

Other elements in 5hlo:

The structure of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221 also contains other interesting chemical elements:

Zinc (Zn) 8 atoms
Arsenic (As) 2 atoms
Chlorine (Cl) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221 (pdb code 5hlo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221, PDB code: 5hlo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5hlo

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Calcium binding site 1 out of 8 in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca101

b:26.0
occ:1.00
OD1 A:ASN61 2.4 30.1 1.0
OD1 A:ASP59 2.4 29.5 1.0
O A:ALA65 2.4 29.1 1.0
O A:HOH202 2.4 29.2 1.0
OE1 A:GLU70 2.4 26.6 1.0
OD1 A:ASP63 2.5 32.2 1.0
OE2 A:GLU70 2.6 25.8 1.0
CD A:GLU70 2.8 22.2 1.0
CG A:ASP63 3.1 33.0 1.0
OD2 A:ASP63 3.3 40.7 1.0
CG A:ASN61 3.4 31.1 1.0
CG A:ASP59 3.5 29.7 1.0
C A:ALA65 3.6 31.7 1.0
ND2 A:ASN61 4.0 29.9 1.0
CA A:ASP59 4.0 23.6 1.0
CB A:ASP59 4.2 24.8 1.0
N A:ASP63 4.3 33.8 1.0
CG A:GLU70 4.3 21.3 1.0
N A:ALA65 4.3 27.3 1.0
OD2 A:ASP59 4.4 32.1 1.0
CA A:VAL66 4.4 28.6 1.0
N A:VAL66 4.4 31.4 1.0
C A:ASP59 4.4 27.6 1.0
O A:HOH229 4.5 34.5 1.0
CB A:ASP63 4.5 34.2 1.0
N A:ASN67 4.5 24.0 1.0
N A:ASN61 4.5 25.3 1.0
CA A:ALA65 4.5 30.6 1.0
N A:ILE60 4.6 23.4 1.0
N A:THR62 4.7 27.2 1.0
CB A:ASN61 4.7 26.6 1.0
ND2 A:ASN67 4.8 35.2 1.0
CA A:ASP63 4.9 34.0 1.0
CG A:ASN67 4.9 33.4 1.0
C A:VAL66 4.9 28.0 1.0
CA A:ASN61 5.0 26.7 1.0

Calcium binding site 2 out of 8 in 5hlo

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Calcium binding site 2 out of 8 in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca102

b:58.9
occ:0.86
O A:SER20 2.4 39.1 1.0
O A:ALA28 2.4 34.8 1.0
O A:ASN25 2.4 34.8 1.0
O A:LYS23 2.5 38.5 1.0
O A:HOH203 2.5 30.9 1.0
C A:SER20 3.3 37.2 1.0
C A:ASN25 3.5 40.3 1.0
C A:ALA28 3.6 32.1 1.0
C A:LYS23 3.7 45.0 1.0
CE2 A:TYR30 3.7 39.4 1.0
CA A:SER20 3.8 37.4 1.0
N A:LYS23 4.0 45.8 1.0
CA A:PHE26 4.0 46.2 1.0
CD2 A:TYR30 4.1 41.4 1.0
N A:ALA28 4.2 41.4 1.0
N A:PHE26 4.2 43.4 1.0
N A:ASN25 4.3 38.2 1.0
CA A:ALA28 4.3 36.9 1.0
O A:TYR19 4.4 41.2 1.0
C A:GLY24 4.4 41.4 1.0
N A:LEU21 4.4 37.8 1.0
CA A:LYS23 4.5 50.0 1.0
C A:PHE26 4.5 45.1 1.0
CA A:ASN25 4.5 40.2 1.0
OD2 A:ASP33 4.5 48.7 1.0
CB A:SER20 4.5 33.2 1.0
N A:ILE22 4.5 43.9 1.0
CZ A:TYR30 4.6 38.4 1.0
CB A:ALA28 4.6 34.4 1.0
N A:VAL29 4.6 31.9 1.0
N A:GLY24 4.7 42.1 1.0
CD1 A:PHE26 4.7 52.5 1.0
O A:GLY24 4.7 43.6 1.0
OH A:TYR30 4.8 37.2 1.0
CA A:GLY24 4.8 41.1 1.0
CA A:VAL29 4.8 31.8 1.0
N A:HIS27 4.9 45.3 1.0
CA A:LEU21 4.9 44.2 1.0
N A:SER20 4.9 36.6 1.0
O A:PHE26 5.0 45.0 1.0
C A:LEU21 5.0 45.0 1.0

Calcium binding site 3 out of 8 in 5hlo

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Calcium binding site 3 out of 8 in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca101

b:52.4
occ:0.87
O B:ASN25 2.4 32.5 1.0
O B:LYS23 2.4 35.2 1.0
O B:SER20 2.4 35.0 1.0
O B:ALA28 2.5 30.6 1.0
O B:HOH209 2.5 30.6 1.0
C B:SER20 3.4 34.1 1.0
C B:ASN25 3.4 33.0 1.0
C B:ALA28 3.6 28.3 1.0
CE2 B:TYR30 3.6 39.7 1.0
C B:LYS23 3.6 41.1 1.0
CA B:SER20 3.8 34.0 1.0
CA B:PHE26 4.0 34.2 1.0
N B:LYS23 4.0 41.2 1.0
N B:ALA28 4.1 31.3 1.0
CD2 B:TYR30 4.1 34.8 1.0
N B:PHE26 4.1 33.8 1.0
N B:ASN25 4.3 32.4 1.0
CA B:ALA28 4.3 31.1 1.0
O B:TYR19 4.4 35.2 1.0
C B:GLY24 4.4 39.2 1.0
C B:PHE26 4.4 33.6 1.0
CA B:LYS23 4.4 41.6 1.0
CA B:ASN25 4.4 30.3 1.0
N B:LEU21 4.5 34.7 1.0
CZ B:TYR30 4.5 36.1 1.0
OD2 B:ASP33 4.5 51.2 1.0
CB B:SER20 4.5 31.5 1.0
N B:ILE22 4.6 43.2 1.0
N B:GLY24 4.6 37.8 1.0
CB B:ALA28 4.6 33.5 1.0
N B:VAL29 4.6 30.1 1.0
CD1 B:PHE26 4.7 40.8 1.0
N B:HIS27 4.7 33.1 1.0
OH B:TYR30 4.7 34.3 1.0
O B:GLY24 4.7 36.9 1.0
CA B:GLY24 4.8 39.2 1.0
CA B:VAL29 4.9 32.7 1.0
CA B:LEU21 4.9 40.3 1.0
O B:PHE26 5.0 37.2 1.0
N B:SER20 5.0 35.0 1.0

Calcium binding site 4 out of 8 in 5hlo

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Calcium binding site 4 out of 8 in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca102

b:26.4
occ:1.00
OD1 B:ASN61 2.3 34.6 1.0
OD1 B:ASP59 2.4 27.5 1.0
O B:ALA65 2.4 29.4 1.0
OE1 B:GLU70 2.4 24.2 1.0
O B:HOH207 2.4 31.1 1.0
OD1 B:ASP63 2.5 30.0 1.0
OE2 B:GLU70 2.6 23.7 1.0
CD B:GLU70 2.8 23.8 1.0
CG B:ASP63 3.2 28.2 1.0
OD2 B:ASP63 3.3 33.6 1.0
CG B:ASN61 3.4 27.4 1.0
CG B:ASP59 3.5 29.2 1.0
C B:ALA65 3.6 29.0 1.0
ND2 B:ASN61 3.9 23.3 1.0
CA B:ASP59 4.0 24.8 1.0
CB B:ASP59 4.2 26.0 1.0
N B:ASP63 4.2 26.3 1.0
CG B:GLU70 4.3 24.3 1.0
N B:ALA65 4.3 27.2 1.0
OD2 B:ASP59 4.4 28.5 1.0
C B:ASP59 4.4 26.2 1.0
CA B:VAL66 4.4 27.3 1.0
N B:VAL66 4.4 28.6 1.0
CB B:ASP63 4.5 28.1 1.0
N B:ASN61 4.5 26.2 1.0
CA B:ALA65 4.5 26.6 1.0
N B:ASN67 4.6 22.9 1.0
N B:ILE60 4.6 25.1 1.0
O B:HOH240 4.6 32.6 1.0
N B:THR62 4.6 29.1 1.0
CB B:ASN61 4.7 24.3 1.0
ND2 B:ASN67 4.7 35.7 1.0
CA B:ASP63 4.8 25.3 1.0
CG B:ASN67 4.9 30.6 1.0
N B:GLY64 4.9 28.1 1.0
CA B:ASN61 5.0 25.3 1.0
C B:VAL66 5.0 30.9 1.0
O B:LEU58 5.0 28.9 1.0

Calcium binding site 5 out of 8 in 5hlo

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Calcium binding site 5 out of 8 in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca101

b:51.1
occ:0.85
O C:SER20 2.4 26.4 1.0
O C:ALA28 2.4 30.0 1.0
O C:ASN25 2.4 27.2 1.0
O C:LYS23 2.4 28.1 1.0
O C:HOH210 2.5 25.9 1.0
C C:SER20 3.3 27.8 1.0
C C:ALA28 3.5 31.3 1.0
C C:ASN25 3.5 28.7 1.0
C C:LYS23 3.6 30.8 1.0
CE2 C:TYR30 3.6 28.7 1.0
CA C:SER20 3.8 27.8 1.0
N C:ALA28 4.0 27.4 1.0
N C:LYS23 4.0 32.6 1.0
CD2 C:TYR30 4.1 31.1 1.0
CA C:ALA28 4.1 29.2 1.0
N C:ASN25 4.1 29.4 1.0
C C:GLY24 4.3 30.3 1.0
CB C:ALA28 4.3 25.4 1.0
N C:LEU21 4.4 27.9 1.0
N C:PHE26 4.4 28.8 1.0
CA C:PHE26 4.4 29.8 1.0
CA C:ASN25 4.4 25.5 1.0
CA C:LYS23 4.5 33.0 1.0
O C:TYR19 4.5 36.2 1.0
OD2 C:ASP33 4.5 44.9 1.0
CB C:SER20 4.5 27.4 1.0
CZ C:TYR30 4.6 28.5 1.0
N C:GLY24 4.6 29.3 1.0
O C:GLY24 4.6 32.9 1.0
C C:PHE26 4.6 29.4 1.0
N C:ILE22 4.6 30.1 1.0
N C:VAL29 4.6 28.1 1.0
CA C:GLY24 4.7 30.0 1.0
OH C:TYR30 4.8 33.9 1.0
CA C:LEU21 4.8 30.1 1.0
CA C:VAL29 4.9 26.0 1.0
N C:HIS27 4.9 23.4 1.0
C C:LEU21 4.9 31.8 1.0
N C:SER20 5.0 27.2 1.0
O C:PHE26 5.0 26.8 1.0

Calcium binding site 6 out of 8 in 5hlo

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Calcium binding site 6 out of 8 in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca102

b:29.4
occ:1.00
OD1 C:ASN61 2.3 32.4 1.0
O C:ALA65 2.3 29.2 1.0
OD1 C:ASP59 2.4 34.9 1.0
OD1 C:ASP63 2.4 40.4 1.0
OE1 C:GLU70 2.5 26.7 1.0
O C:HOH205 2.5 32.7 1.0
OE2 C:GLU70 2.5 29.0 1.0
CD C:GLU70 2.8 30.3 1.0
CG C:ASP63 3.2 37.9 1.0
CG C:ASN61 3.4 36.9 1.0
C C:ALA65 3.5 30.9 1.0
OD2 C:ASP63 3.5 33.8 1.0
CG C:ASP59 3.6 41.6 1.0
ND2 C:ASN61 4.0 33.9 1.0
CA C:ASP59 4.1 36.5 1.0
N C:ASN61 4.3 30.1 1.0
N C:ASP63 4.3 41.0 1.0
N C:ALA65 4.3 29.9 1.0
CA C:VAL66 4.3 27.6 1.0
N C:ILE60 4.3 36.4 1.0
N C:VAL66 4.3 27.7 1.0
CG C:GLU70 4.3 29.0 1.0
CB C:ASP59 4.4 37.1 1.0
ND2 C:ASN67 4.4 30.7 1.0
C C:ASP59 4.4 36.7 1.0
N C:ASN67 4.4 26.4 1.0
CA C:ALA65 4.4 31.5 1.0
OD2 C:ASP59 4.5 45.4 1.0
CB C:ASP63 4.5 39.3 1.0
N C:THR62 4.6 42.9 1.0
CB C:ASN61 4.6 30.0 1.0
O C:HOH221 4.7 29.4 1.0
CA C:ASN61 4.8 32.7 1.0
CG C:ASN67 4.8 28.1 1.0
C C:ASN61 4.9 39.8 1.0
C C:VAL66 4.9 26.8 1.0
CA C:ASP63 4.9 40.2 1.0

Calcium binding site 7 out of 8 in 5hlo

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Calcium binding site 7 out of 8 in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca101

b:47.2
occ:0.86
O D:SER20 2.3 29.9 1.0
O D:ASN25 2.4 28.1 1.0
O D:ALA28 2.4 31.3 1.0
O D:LYS23 2.4 27.1 1.0
O D:HOH406 2.5 23.0 1.0
C D:SER20 3.2 25.9 1.0
C D:ASN25 3.5 23.3 1.0
C D:ALA28 3.5 26.8 1.0
C D:LYS23 3.6 29.7 1.0
CA D:SER20 3.7 27.5 1.0
CE2 D:TYR30 3.7 33.1 1.0
N D:ALA28 4.0 25.1 1.0
N D:LYS23 4.1 26.9 1.0
CA D:ALA28 4.1 25.7 1.0
N D:ASN25 4.1 23.6 1.0
C D:GLY24 4.2 32.8 1.0
CD2 D:TYR30 4.2 33.6 1.0
CB D:ALA28 4.3 22.4 1.0
CA D:PHE26 4.3 24.6 1.0
N D:PHE26 4.3 27.2 1.0
N D:LEU21 4.4 25.5 1.0
CB D:SER20 4.4 26.2 1.0
CA D:ASN25 4.4 27.0 1.0
O D:TYR19 4.4 30.9 1.0
C D:PHE26 4.5 29.8 1.0
CA D:LYS23 4.5 31.1 1.0
OD2 D:ASP33 4.5 37.3 1.0
N D:GLY24 4.6 29.4 1.0
O D:GLY24 4.6 29.8 1.0
N D:ILE22 4.6 26.1 1.0
N D:VAL29 4.6 23.7 1.0
CA D:GLY24 4.6 31.4 1.0
CZ D:TYR30 4.7 32.4 1.0
CA D:LEU21 4.8 27.9 1.0
N D:HIS27 4.8 28.5 1.0
OH D:TYR30 4.8 30.0 1.0
O D:PHE26 4.9 28.7 1.0
C D:LEU21 4.9 28.4 1.0
N D:SER20 4.9 27.2 1.0
CA D:VAL29 4.9 22.6 1.0

Calcium binding site 8 out of 8 in 5hlo

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Calcium binding site 8 out of 8 in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca102

b:27.4
occ:1.00
OD1 D:ASN61 2.3 31.4 1.0
O D:ALA65 2.3 27.4 1.0
OD1 D:ASP63 2.4 38.1 1.0
O D:HOH405 2.4 31.8 1.0
OD1 D:ASP59 2.4 36.2 1.0
OE1 D:GLU70 2.5 26.6 1.0
OE2 D:GLU70 2.5 23.6 1.0
CD D:GLU70 2.8 23.5 1.0
CG D:ASP63 3.2 41.3 1.0
CG D:ASN61 3.4 33.9 1.0
C D:ALA65 3.5 27.6 1.0
OD2 D:ASP63 3.6 41.7 1.0
CG D:ASP59 3.6 38.8 1.0
ND2 D:ASN61 4.0 31.5 1.0
CA D:ASP59 4.1 29.3 1.0
N D:ASP63 4.3 38.1 1.0
N D:ALA65 4.3 30.9 1.0
N D:ASN61 4.3 32.9 1.0
ND2 D:ASN67 4.3 30.1 1.0
N D:VAL66 4.3 23.0 1.0
CA D:VAL66 4.3 23.7 1.0
CG D:GLU70 4.3 24.5 1.0
N D:ILE60 4.4 24.7 1.0
CA D:ALA65 4.4 27.3 1.0
CB D:ASP59 4.4 37.6 1.0
N D:ASN67 4.4 25.6 1.0
C D:ASP59 4.4 28.5 1.0
OD2 D:ASP59 4.4 39.2 1.0
CB D:ASP63 4.5 39.5 1.0
N D:THR62 4.5 41.0 1.0
O D:HOH423 4.6 32.1 1.0
CB D:ASN61 4.6 29.6 1.0
CG D:ASN67 4.8 27.0 1.0
CA D:ASN61 4.8 34.8 1.0
CA D:ASP63 4.8 39.6 1.0
C D:VAL66 4.9 25.0 1.0
C D:ASN61 4.9 38.8 1.0
CB D:ALA65 4.9 25.6 1.0

Reference:

H.Lin, G.R.Andersen, L.Yatime. Crystal Structure of Human S100A8 in Complex with Zinc and Calcium. Bmc Struct.Biol. V. 16 8 2016.
ISSN: ESSN 1472-6807
PubMed: 27251136
DOI: 10.1186/S12900-016-0058-4
Page generated: Sat Dec 12 05:28:40 2020

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