Atomistry » Zinc » PDB 5h6b-5ho1 » 5hlv
Atomistry »
  Zinc »
    PDB 5h6b-5ho1 »
      5hlv »

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

Go back to Zinc Binding Sites List in 5hlv
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

Go back to Zinc Binding Sites List in 5hlv
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

Go back to Zinc Binding Sites List in 5hlv
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

Go back to Zinc Binding Sites List in 5hlv
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

Go back to Zinc Binding Sites List in 5hlv
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

Go back to Zinc Binding Sites List in 5hlv
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

Go back to Zinc Binding Sites List in 5hlv
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy