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Zinc in PDB 5hlv: Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121

Protein crystallography data

The structure of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121, PDB code: 5hlv 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) 40.26 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.930, 85.090, 197.200, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.7

Other elements in 5hlv:

The structure of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 16 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121 (pdb code 5hlv). 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 P212121, PDB code: 5hlv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5hlv

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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 P212121


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 P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn103

b:23.1
occ:1.00
 NE2 A:HIS17 2.0 23.7 1.0
NE2 D:HIS87 2.0 22.9 1.0
NE2 D:HIS83 2.1 26.1 1.0
NE2 A:HIS27 2.1 37.1 1.0
CD2 D:HIS83 2.8 23.8 1.0
CE1 A:HIS17 2.9 26.2 1.0
CD2 D:HIS87 2.9 23.6 1.0
CD2 A:HIS27 3.0 31.0 1.0
CE1 A:HIS27 3.0 41.5 1.0
CE1 D:HIS87 3.1 24.4 1.0
CD2 A:HIS17 3.1 23.6 1.0
CE1 D:HIS83 3.2 24.4 1.0
ND1 A:HIS17 4.0 23.5 1.0
CG D:HIS83 4.0 26.6 1.0
CG D:HIS87 4.1 25.6 1.0
ND1 A:HIS27 4.1 38.9 1.0
ND1 D:HIS87 4.1 31.7 1.0
CG A:HIS27 4.1 33.4 1.0
CG A:HIS17 4.2 22.2 1.0
ND1 D:HIS83 4.2 25.3 1.0
O D:HOH218 4.8 46.3 1.0
OG D:SER86 5.0 30.7 1.0

Zinc binding site 2 out of 8 in 5hlv

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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 P212121


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 P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn104

b:23.5
occ:1.00
 NE2 A:HIS87 2.0 34.1 1.0
NE2 D:HIS27 2.0 31.6 1.0
NE2 D:HIS17 2.0 25.9 1.0
NE2 A:HIS83 2.0 27.1 1.0
CE1 D:HIS17 2.9 24.1 1.0
CD2 D:HIS27 2.9 20.5 1.0
CE1 A:HIS87 2.9 34.9 1.0
CD2 A:HIS83 2.9 21.1 1.0
CD2 A:HIS87 3.0 31.6 1.0
CE1 D:HIS27 3.0 30.4 1.0
CE1 A:HIS83 3.1 26.1 1.0
CD2 D:HIS17 3.1 25.4 1.0
ND1 A:HIS87 4.0 35.1 1.0
CG D:HIS27 4.0 21.2 1.0
ND1 D:HIS17 4.0 23.5 1.0
ND1 D:HIS27 4.0 20.2 1.0
CG A:HIS87 4.1 35.0 1.0
CG A:HIS83 4.1 29.5 1.0
ND1 A:HIS83 4.1 25.8 1.0
CG D:HIS17 4.2 25.0 1.0
O A:HOH238 4.7 27.3 1.0

Zinc binding site 3 out of 8 in 5hlv

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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 P212121


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 P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn103

b:23.9
occ:1.00
 NE2 H:HIS17 2.0 22.8 1.0
NE2 B:HIS87 2.0 29.6 1.0
NE2 B:HIS83 2.1 31.2 1.0
NE2 H:HIS27 2.1 28.3 1.0
CE1 H:HIS17 2.7 23.3 1.0
CD2 H:HIS27 2.9 25.7 1.0
CD2 B:HIS83 3.0 26.5 1.0
CE1 B:HIS87 3.0 30.7 1.0
CE1 B:HIS83 3.0 32.3 1.0
CD2 B:HIS87 3.1 28.7 1.0
CD2 H:HIS17 3.1 22.5 1.0
CE1 H:HIS27 3.2 29.8 1.0
ND1 H:HIS17 3.9 22.1 1.0
CG H:HIS27 4.0 29.3 1.0
ND1 B:HIS83 4.1 30.1 1.0
CG B:HIS83 4.1 26.7 1.0
ND1 B:HIS87 4.1 31.5 1.0
CG H:HIS17 4.1 21.5 1.0
ND1 H:HIS27 4.2 29.4 1.0
CG B:HIS87 4.2 30.3 1.0
O B:HOH219 4.8 24.5 1.0

Zinc binding site 4 out of 8 in 5hlv

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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 P212121


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 P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn105

b:30.4
occ:1.00
 NE2 B:HIS17 2.0 34.2 1.0
NE2 H:HIS87 2.0 63.2 1.0
NE2 H:HIS83 2.0 38.0 1.0
CL H:CL103 2.1 34.5 1.0
CE1 B:HIS17 2.9 39.4 1.0
CE1 H:HIS87 2.9 65.8 1.0
CD2 H:HIS83 2.9 36.8 1.0
CD2 H:HIS87 3.0 61.0 1.0
CD2 B:HIS17 3.0 33.8 1.0
CE1 H:HIS83 3.0 38.3 1.0
O B:HOH222 3.9 37.5 1.0
ND1 H:HIS87 4.0 63.6 1.0
ND1 B:HIS17 4.0 35.4 1.0
CG H:HIS87 4.1 62.2 1.0
CG H:HIS83 4.1 38.1 1.0
CG B:HIS17 4.1 32.5 1.0
ND1 H:HIS83 4.1 37.4 1.0
O C:HOH211 4.6 36.8 1.0
ND1 B:HIS27 4.7 51.2 1.0
OG H:SER86 4.8 53.6 1.0
CE2 B:TYR16 4.8 21.4 1.0
CD2 B:TYR16 4.8 22.4 1.0

Zinc binding site 5 out of 8 in 5hlv

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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 P212121


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 P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn103

b:33.6
occ:1.00
 NE2 C:HIS17 2.0 27.5 1.0
NE2 E:HIS87 2.1 70.8 1.0
NE2 C:HIS27 2.1 35.2 1.0
NE2 E:HIS83 2.1 40.2 1.0
CD2 E:HIS87 2.6 70.9 1.0
CE1 C:HIS17 2.8 32.1 1.0
CD2 E:HIS83 2.9 35.4 1.0
CD2 C:HIS27 3.0 28.4 1.0
CE1 C:HIS27 3.1 37.0 1.0
CE1 E:HIS83 3.2 40.5 1.0
CD2 C:HIS17 3.2 36.5 1.0
CE1 E:HIS87 3.3 73.8 1.0
CG E:HIS87 3.8 72.0 1.0
ND1 C:HIS17 4.0 33.5 1.0
CG E:HIS83 4.1 39.5 1.0
CG C:HIS27 4.1 29.9 1.0
ND1 E:HIS87 4.1 75.5 1.0
ND1 C:HIS27 4.1 33.1 1.0
ND1 E:HIS83 4.1 39.0 1.0
CG C:HIS17 4.2 33.6 1.0

Zinc binding site 6 out of 8 in 5hlv

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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 P212121


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 P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn104

b:22.8
occ:1.00
 NE2 E:HIS27 2.0 27.3 1.0
NE2 E:HIS17 2.0 18.4 1.0
NE2 C:HIS87 2.0 26.1 1.0
NE2 C:HIS83 2.1 24.1 1.0
CE1 E:HIS17 2.8 18.8 1.0
CD2 E:HIS27 2.8 22.2 1.0
CD2 C:HIS87 2.9 26.4 1.0
CD2 C:HIS83 2.9 22.3 1.0
CE1 E:HIS27 3.0 27.1 1.0
CE1 C:HIS87 3.1 27.5 1.0
CE1 C:HIS83 3.1 22.7 1.0
CD2 E:HIS17 3.1 18.9 1.0
ND1 E:HIS17 4.0 17.3 1.0
CG E:HIS27 4.0 22.6 1.0
CG C:HIS87 4.1 27.1 1.0
ND1 E:HIS27 4.1 23.9 1.0
CG C:HIS83 4.1 22.0 1.0
ND1 C:HIS83 4.1 21.9 1.0
ND1 C:HIS87 4.1 26.5 1.0
CG E:HIS17 4.2 21.9 1.0
O C:HOH232 4.8 35.2 1.0

Zinc binding site 7 out of 8 in 5hlv

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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 P212121


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 P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn103

b:22.6
occ:1.00
 NE2 G:HIS87 1.9 34.4 1.0
NE2 F:HIS17 2.0 17.7 1.0
NE2 F:HIS27 2.1 23.9 1.0
NE2 G:HIS83 2.1 22.3 1.0
CE1 G:HIS87 2.8 41.3 1.0
CD2 F:HIS27 2.8 20.8 1.0
CD2 G:HIS87 2.9 31.3 1.0
CD2 G:HIS83 2.9 21.7 1.0
CE1 F:HIS17 3.0 21.1 1.0
CD2 F:HIS17 3.0 21.6 1.0
CE1 G:HIS83 3.1 22.4 1.0
CE1 F:HIS27 3.2 27.7 1.0
ND1 G:HIS87 3.9 29.5 1.0
CG G:HIS87 4.0 29.0 1.0
CG F:HIS27 4.1 22.4 1.0
CG G:HIS83 4.1 21.9 1.0
ND1 F:HIS17 4.1 20.9 1.0
ND1 G:HIS83 4.1 22.0 1.0
CG F:HIS17 4.2 20.9 1.0
ND1 F:HIS27 4.2 25.0 1.0
O F:HOH228 4.7 44.8 1.0
CE2 F:TYR16 4.9 20.6 1.0
O G:HOH220 4.9 37.5 1.0
CD2 F:TYR16 4.9 20.9 1.0

Zinc binding site 8 out of 8 in 5hlv

Go back to Zinc Binding Sites List in 5hlv
Zinc binding site 8 out of 8 in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121


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 P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn104

b:38.6
occ:1.00
 NE2 F:HIS87 1.9 77.7 1.0
NE2 G:HIS17 2.0 35.9 1.0
NE2 F:HIS83 2.2 39.5 1.0
CE1 F:HIS87 2.3 79.7 1.0
CL F:CL105 2.3 49.5 1.0
CD2 G:HIS17 2.9 35.3 1.0
CE1 G:HIS17 3.0 41.0 1.0
CD2 F:HIS83 3.0 38.4 1.0
CD2 F:HIS87 3.2 81.7 1.0
CE1 F:HIS83 3.2 35.9 1.0
ND1 F:HIS87 3.6 77.8 1.0
CG F:HIS87 4.0 77.0 1.0
CG G:HIS17 4.1 38.4 1.0
ND1 G:HIS17 4.1 41.4 1.0
CG F:HIS83 4.2 38.5 1.0
ND1 F:HIS83 4.2 41.0 1.0
ND1 G:HIS27 4.7 63.9 1.0
CE2 G:TYR16 4.9 25.2 1.0
CD2 G:TYR16 4.9 27.4 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: Sun Oct 27 17:30:56 2024

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