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Chlorine 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
Calcium (Ca) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group C2221, PDB code: 5hlo:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5hlo

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl107

b:33.2
occ:0.91
 O D:HOH435 2.8 51.0 1.0
O D:HOH420 2.9 38.3 1.0
N D:PHE26 3.1 27.2 1.0
ND1 A:HIS87 3.4 36.0 1.0
CE1 C:HIS27 3.5 24.7 1.0
CG A:HIS87 3.5 34.8 1.0
CB D:PHE26 3.7 24.7 1.0
CG D:ASN25 3.8 28.9 1.0
ND2 D:ASN25 3.8 32.7 1.0
OD1 D:ASN25 3.8 29.7 1.0
CE1 A:HIS87 3.9 34.8 1.0
CB A:HIS87 3.9 36.0 1.0
CA D:ASN25 3.9 27.0 1.0
CG D:PHE26 4.0 24.9 1.0
CA D:PHE26 4.0 24.6 1.0
C D:ASN25 4.0 23.3 1.0
O C:HOH223 4.0 35.1 1.0
CD2 A:HIS87 4.1 32.7 1.0
CD2 D:PHE26 4.1 25.9 1.0
NE2 A:HIS87 4.2 34.0 1.0
ND1 C:HIS27 4.3 26.8 1.0
NE2 C:HIS27 4.4 28.8 1.0
CB D:ASN25 4.4 25.0 1.0
N D:HIS27 4.7 28.5 1.0
CD1 D:PHE26 4.7 24.2 1.0
C D:PHE26 4.8 29.8 1.0
O D:GLY24 4.9 29.8 1.0

Chlorine binding site 2 out of 8 in 5hlo

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl108

b:64.9
occ:0.97
 ZN A:ZN104 2.3 62.3 0.9
O A:HOH252 2.4 65.7 1.0
O1 A:CAC105 3.5 0.6 1.0
C1 A:CAC105 3.5 30.5 1.0
NE2 A:HIS27 3.8 58.3 1.0
NE2 C:HIS91 3.8 78.0 1.0
AS A:CAC105 3.9 56.0 0.9
CB A:PHE26 4.0 46.3 1.0
CE1 A:HIS27 4.0 55.4 1.0
CE1 C:HIS91 4.2 81.0 1.0
C2 A:CAC105 4.3 0.3 1.0
CD2 A:LEU21 4.5 56.2 1.0
CD2 A:PHE26 4.5 62.1 1.0
CD2 A:HIS27 4.6 51.4 1.0
CG A:PHE26 4.7 53.1 1.0
ND1 A:HIS27 4.9 52.3 1.0
CD2 C:HIS91 4.9 78.3 1.0
O A:PHE26 5.0 45.0 1.0

Chlorine binding site 3 out of 8 in 5hlo

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl106

b:32.1
occ:0.91
 N C:PHE26 3.0 28.8 1.0
O C:HOH223 3.1 35.1 1.0
O C:HOH245 3.2 49.6 1.0
ND1 B:HIS87 3.4 36.5 1.0
CB C:PHE26 3.4 30.5 1.0
CG B:HIS87 3.5 35.2 1.0
CE1 D:HIS27 3.6 32.7 1.0
CG C:PHE26 3.7 26.5 1.0
ND2 C:ASN25 3.7 29.7 1.0
CA C:PHE26 3.8 29.8 1.0
CG C:ASN25 3.8 30.0 1.0
CB B:HIS87 3.8 33.7 1.0
CE1 B:HIS87 3.9 31.9 1.0
CD2 C:PHE26 3.9 30.2 1.0
CA C:ASN25 3.9 25.5 1.0
C C:ASN25 3.9 28.7 1.0
CD2 B:HIS87 3.9 30.8 1.0
OD1 C:ASN25 4.0 27.8 1.0
NE2 B:HIS87 4.1 30.5 1.0
ND1 D:HIS27 4.4 27.4 1.0
O C:HOH235 4.4 63.7 1.0
CB C:ASN25 4.5 25.5 1.0
O D:HOH420 4.5 38.3 1.0
CD1 C:PHE26 4.5 28.9 1.0
NE2 D:HIS27 4.5 34.6 1.0
N C:HIS27 4.7 23.4 1.0
C C:PHE26 4.7 29.4 1.0
CE2 C:PHE26 4.8 34.0 1.0
O C:GLY24 4.8 32.9 1.0
CA B:HIS87 5.0 36.5 1.0

Chlorine binding site 4 out of 8 in 5hlo

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl107

b:83.2
occ:1.00
 ZN B:ZN104 2.2 40.8 0.9
C1 B:CAC110 3.6 34.0 1.0
O1 B:CAC110 3.7 39.3 0.9
NE2 B:HIS27 3.7 43.9 1.0
NE2 D:HIS91 3.7 65.0 1.0
CE1 D:HIS91 4.0 69.8 1.0
AS B:CAC110 4.1 41.1 0.9
CE1 B:HIS27 4.1 42.8 1.0
CB B:PHE26 4.2 33.0 1.0
CD2 B:LEU21 4.3 51.2 1.0
CD2 B:HIS27 4.5 39.5 1.0
C2 B:CAC110 4.6 40.4 1.0
OG D:SER90 4.8 73.3 1.0
CD2 D:HIS91 4.8 64.8 1.0
CD2 B:PHE26 4.9 41.4 1.0
O B:PHE26 4.9 37.2 1.0
CG B:PHE26 5.0 35.0 1.0
ND1 B:HIS27 5.0 38.1 1.0

Chlorine binding site 5 out of 8 in 5hlo

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl104

b:33.8
occ:1.00
 ZN A:ZN103 2.2 36.5 1.0
NE2 C:HIS83 3.3 40.4 1.0
O A:HOH217 3.5 35.4 1.0
CD2 A:HIS27 3.5 51.4 1.0
CE2 A:TYR16 3.6 34.0 1.0
CA A:HIS27 3.6 40.3 1.0
NE2 A:HIS17 3.6 43.3 1.0
C1 A:CAC105 3.7 30.5 1.0
CB A:HIS27 3.7 37.9 1.0
O2 A:CAC105 3.7 83.1 0.9
CE1 C:HIS83 3.8 39.7 1.0
CD2 A:HIS17 3.8 36.4 1.0
CG A:HIS27 3.9 47.8 1.0
O A:PHE26 4.2 45.0 1.0
CD2 A:TYR16 4.2 31.6 1.0
AS A:CAC105 4.3 56.0 0.9
C A:HIS27 4.4 43.4 1.0
O A:HIS27 4.4 44.9 1.0
CZ A:TYR16 4.6 31.3 1.0
CD2 C:HIS83 4.6 33.3 1.0
OH A:TYR16 4.6 32.8 1.0
CB A:PHE68 4.7 30.0 1.0
N A:HIS27 4.7 45.3 1.0
OG A:SER20 4.7 36.5 1.0
NE2 A:HIS27 4.7 58.3 1.0
O1 A:CAC105 4.8 0.6 1.0
C A:PHE26 4.8 45.1 1.0
CE1 A:HIS17 4.9 44.6 1.0

Chlorine binding site 6 out of 8 in 5hlo

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl105

b:48.5
occ:1.00
 NZ C:LYS49 2.5 92.8 1.0
OE2 C:GLU57 3.0 46.7 1.0
CD C:LYS49 3.3 87.7 1.0
CE C:LYS49 3.4 94.0 1.0
CD C:GLU57 3.8 49.2 1.0
OE1 C:GLU57 3.9 54.9 1.0
CH2 C:TRP54 4.0 47.0 1.0
CZ2 C:TRP54 4.2 46.0 1.0
CZ3 C:TRP54 4.3 44.1 1.0
NZ C:LYS77 4.3 62.2 1.0
CE2 C:TRP54 4.7 43.8 1.0
CE3 C:TRP54 4.8 40.6 1.0
CG C:LYS49 4.8 81.0 1.0
CD2 C:TRP54 5.0 38.7 1.0

Chlorine binding site 7 out of 8 in 5hlo

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl104

b:28.6
occ:1.00
 ZN B:ZN103 2.2 32.0 1.0
NE2 D:HIS83 3.3 42.6 1.0
O B:HOH208 3.5 34.6 1.0
O2 B:CAC110 3.6 75.1 0.9
NE2 B:HIS17 3.6 33.2 1.0
CA B:HIS27 3.6 30.6 1.0
CB B:HIS27 3.6 26.2 1.0
C1 B:CAC110 3.7 34.0 1.0
CE2 B:TYR16 3.7 27.9 1.0
CD2 B:HIS27 3.7 39.5 1.0
CD2 B:HIS17 3.9 30.8 1.0
CE1 D:HIS83 3.9 44.4 1.0
CG B:HIS27 4.0 38.9 1.0
O B:HIS27 4.2 33.3 1.0
AS B:CAC110 4.2 41.1 0.9
C B:HIS27 4.3 33.1 1.0
CD2 B:TYR16 4.4 26.4 1.0
O B:PHE26 4.4 37.2 1.0
CD2 D:HIS83 4.5 34.9 1.0
OG B:SER20 4.6 34.0 1.0
CB B:PHE68 4.6 28.6 1.0
CZ B:TYR16 4.7 31.5 1.0
OH B:TYR16 4.7 32.2 1.0
N B:HIS27 4.8 33.1 1.0
CE1 B:HIS17 4.8 30.1 1.0
O1 B:CAC110 4.9 39.3 0.9

Chlorine binding site 8 out of 8 in 5hlo

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl105

b:49.2
occ:1.00
 OE2 D:GLU57 3.4 40.2 1.0
NZ D:LYS49 3.8 85.6 1.0
CH2 D:TRP54 3.8 39.2 1.0
OE1 D:GLU57 3.9 42.3 1.0
CZ2 D:TRP54 4.0 41.5 1.0
CD D:GLU57 4.0 39.7 1.0
CZ3 D:TRP54 4.2 43.2 1.0
CG D:LYS49 4.4 76.8 1.0
CE2 D:TRP54 4.5 40.2 1.0
NZ D:LYS77 4.6 61.6 1.0
CD D:LYS49 4.7 84.0 1.0
CE3 D:TRP54 4.7 40.2 1.0
CE D:LYS49 4.9 85.7 1.0
CD2 D:TRP54 4.9 39.0 1.0
CB D:LYS49 5.0 70.0 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 11:48:50 2020

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