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Zinc 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:

Arsenic (As) 2 atoms
Calcium (Ca) 8 atoms
Chlorine (Cl) 8 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 5hlo

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Zinc 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 Zinc with other atoms in the Zn 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:Zn103

b:36.5
occ:1.00
NE2 A:HIS17 2.0 43.3 1.0
O2 A:CAC105 2.0 83.1 0.9
NE2 C:HIS83 2.1 40.4 1.0
CL C:CL104 2.2 33.8 1.0
CD2 C:HIS83 3.0 33.3 1.0
CD2 A:HIS17 3.0 36.4 1.0
CE1 A:HIS17 3.0 44.6 1.0
CE1 C:HIS83 3.1 39.7 1.0
AS A:CAC105 3.2 56.0 0.9
C1 A:CAC105 3.3 30.5 1.0
CG C:HIS83 4.1 40.5 1.0
ND1 A:HIS17 4.1 40.9 1.0
CG A:HIS17 4.1 39.5 1.0
ND1 C:HIS83 4.1 38.0 1.0
O1 A:CAC105 4.3 0.6 1.0
CD2 A:HIS27 4.6 51.4 1.0
C2 A:CAC105 4.6 0.3 1.0
CE2 A:TYR16 4.8 34.0 1.0
CD2 A:TYR16 4.8 31.6 1.0

Zinc binding site 2 out of 8 in 5hlo

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Zinc 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 Zinc with other atoms in the Zn 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:Zn104

b:62.3
occ:0.88
O1 A:CAC105 2.0 0.6 1.0
NE2 A:HIS27 2.1 58.3 1.0
NE2 C:HIS91 2.1 78.0 1.0
CL A:CL108 2.3 64.9 1.0
CE1 A:HIS27 2.8 55.4 1.0
CE1 C:HIS91 2.9 81.0 1.0
CD2 A:HIS27 3.2 51.4 1.0
CD2 C:HIS91 3.3 78.3 1.0
AS A:CAC105 3.3 56.0 0.9
ND1 C:HIS87 3.7 51.9 1.0
C1 A:CAC105 3.8 30.5 1.0
CE1 C:HIS87 3.8 58.8 1.0
ND1 A:HIS27 4.0 52.3 1.0
O A:HOH252 4.0 65.7 1.0
ND1 C:HIS91 4.1 84.5 1.0
CG A:HIS27 4.2 47.8 1.0
C2 A:CAC105 4.2 0.3 1.0
CG C:HIS91 4.3 83.9 1.0
O2 A:CAC105 4.7 83.1 0.9

Zinc binding site 3 out of 8 in 5hlo

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Zinc 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 Zinc with other atoms in the Zn 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
A:Zn106

b:27.7
occ:1.00
NE2 C:HIS17 2.0 21.1 1.0
NE2 A:HIS87 2.0 34.0 1.0
NE2 C:HIS27 2.1 28.8 1.0
NE2 A:HIS83 2.1 30.0 1.0
CD2 C:HIS27 2.9 23.6 1.0
CE1 C:HIS17 2.9 27.4 1.0
CD2 A:HIS83 2.9 27.9 1.0
CD2 A:HIS87 3.0 32.7 1.0
CE1 A:HIS87 3.0 34.8 1.0
CD2 C:HIS17 3.1 26.1 1.0
CE1 C:HIS27 3.1 24.7 1.0
CE1 A:HIS83 3.2 32.0 1.0
CG C:HIS27 4.0 28.2 1.0
ND1 C:HIS17 4.0 26.8 1.0
CG A:HIS83 4.1 28.7 1.0
CE2 D:PHE26 4.1 30.0 1.0
ND1 C:HIS27 4.1 26.8 1.0
ND1 A:HIS87 4.1 36.0 1.0
CG A:HIS87 4.1 34.8 1.0
CG C:HIS17 4.2 28.5 1.0
ND1 A:HIS83 4.2 27.3 1.0
CZ D:PHE26 4.5 31.9 1.0
O A:HOH225 4.8 29.2 1.0
CD2 D:PHE26 4.8 25.9 1.0

Zinc binding site 4 out of 8 in 5hlo

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Zinc 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 Zinc with other atoms in the Zn 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:Zn103

b:32.0
occ:0.99
O2 B:CAC110 2.0 75.1 0.9
NE2 B:HIS17 2.0 33.2 1.0
NE2 D:HIS83 2.1 42.6 1.0
CL D:CL104 2.2 28.6 1.0
CD2 D:HIS83 2.9 34.9 1.0
CE1 B:HIS17 3.0 30.1 1.0
CD2 B:HIS17 3.0 30.8 1.0
CE1 D:HIS83 3.2 44.4 1.0
AS B:CAC110 3.2 41.1 0.9
C1 B:CAC110 3.4 34.0 1.0
ND1 B:HIS17 4.1 32.5 1.0
CG D:HIS83 4.1 35.7 1.0
CG B:HIS17 4.1 33.2 1.0
ND1 D:HIS83 4.2 39.8 1.0
O1 B:CAC110 4.4 39.3 0.9
C2 B:CAC110 4.6 40.4 1.0
CE2 B:TYR16 4.7 27.9 1.0
CD2 B:TYR16 4.8 26.4 1.0
CD2 B:HIS27 4.8 39.5 1.0

Zinc binding site 5 out of 8 in 5hlo

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Zinc 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 Zinc with other atoms in the Zn 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
B:Zn104

b:40.8
occ:0.95
O1 B:CAC110 2.0 39.3 0.9
NE2 D:HIS91 2.0 65.0 1.0
NE2 B:HIS27 2.1 43.9 1.0
CL B:CL107 2.2 83.2 1.0
CE1 D:HIS91 2.6 69.8 1.0
CD2 B:HIS27 2.9 39.5 1.0
CE1 B:HIS27 3.0 42.8 1.0
CD2 D:HIS91 3.2 64.8 1.0
AS B:CAC110 3.2 41.1 0.9
C1 B:CAC110 3.5 34.0 1.0
ND1 D:HIS91 3.9 71.9 1.0
ND1 D:HIS87 3.9 45.9 1.0
ND1 B:HIS27 4.0 38.1 1.0
CG B:HIS27 4.0 38.9 1.0
CE1 D:HIS87 4.1 49.5 1.0
CG D:HIS91 4.1 71.7 1.0
C2 B:CAC110 4.3 40.4 1.0
O2 B:CAC110 4.6 75.1 0.9
OG D:SER90 4.9 73.3 1.0

Zinc binding site 6 out of 8 in 5hlo

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Zinc 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 Zinc with other atoms in the Zn 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
B:Zn105

b:28.8
occ:1.00
NE2 D:HIS17 2.0 25.4 1.0
NE2 B:HIS83 2.1 29.5 1.0
NE2 B:HIS87 2.1 30.5 1.0
NE2 D:HIS27 2.1 34.6 1.0
CE1 D:HIS17 2.8 27.8 1.0
CD2 B:HIS83 2.9 27.4 1.0
CD2 B:HIS87 3.0 30.8 1.0
CD2 D:HIS27 3.0 30.1 1.0
CE1 D:HIS27 3.0 32.7 1.0
CE1 B:HIS83 3.1 31.0 1.0
CE1 B:HIS87 3.1 31.9 1.0
CD2 D:HIS17 3.1 21.7 1.0
ND1 D:HIS17 4.0 23.8 1.0
ND1 D:HIS27 4.1 27.4 1.0
CG B:HIS83 4.1 31.9 1.0
CE2 C:PHE26 4.1 34.0 1.0
CG D:HIS27 4.1 30.4 1.0
ND1 B:HIS83 4.1 28.4 1.0
CG B:HIS87 4.1 35.2 1.0
ND1 B:HIS87 4.2 36.5 1.0
CG D:HIS17 4.2 24.0 1.0
CZ C:PHE26 4.5 35.5 1.0
O B:HOH232 4.7 36.4 1.0
CD2 C:PHE26 4.8 30.2 1.0

Zinc binding site 7 out of 8 in 5hlo

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Zinc 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 Zinc with other atoms in the Zn 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
C:Zn103

b:58.2
occ:0.94
OE2 C:GLU93 2.2 0.8 1.0
NE2 C:HIS87 2.3 62.8 1.0
CD C:GLU93 3.0 0.1 1.0
CD2 C:HIS87 3.1 57.0 1.0
OE1 C:GLU93 3.2 0.3 1.0
CE1 C:HIS87 3.2 58.8 1.0
CG C:HIS87 4.3 53.2 1.0
ND1 C:HIS87 4.3 51.9 1.0
CG C:GLU93 4.4 0.4 1.0

Zinc binding site 8 out of 8 in 5hlo

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Zinc 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 Zinc with other atoms in the Zn 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:Zn103

b:46.8
occ:0.93
OE2 D:GLU93 2.1 80.1 1.0
NE2 D:HIS87 2.1 54.2 1.0
OE1 D:GLU93 2.7 77.5 1.0
CD D:GLU93 2.7 80.7 1.0
CE1 D:HIS87 3.1 49.5 1.0
CD2 D:HIS87 3.1 50.2 1.0
ND1 D:HIS87 4.1 45.9 1.0
CG D:HIS87 4.2 46.5 1.0
CG D:GLU93 4.2 85.3 1.0
CG D:HIS91 4.7 71.7 1.0
CD2 D:HIS91 4.8 64.8 1.0
CB D:HIS91 4.9 73.9 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: Wed Dec 16 06:20:25 2020

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