Zinc in PDB 4ybh: Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6

The structure of Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6, PDB code: 4ybh was solved by L.Yatime, G.R.Andersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.80 / 2.40
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	75.980, 112.530, 139.890, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.3

The structure of Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6 also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Calcium	(Ca)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6 (pdb code 4ybh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6, PDB code: 4ybh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6


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 the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:46.4 occ:0.99 OD2 A:ASP160 2.0 60.9 1.0 OD2 A:ASP201 2.0 67.1 1.0 CL A:CL407 2.1 77.1 1.0 CL A:CL406 2.1 40.7 1.0 CG A:ASP201 2.9 48.1 1.0 CG A:ASP160 3.0 44.0 1.0 CB A:ASP201 3.2 44.1 1.0 OD1 A:ASP160 3.4 35.7 1.0 O B:HOH206 4.0 44.9 1.0 O A:HOH640 4.1 57.7 1.0 OD1 A:ASP201 4.1 40.4 1.0 O A:HOH626 4.1 64.3 1.0 CB A:ASP160 4.2 35.0 1.0 O A:HOH510 4.3 30.1 1.0 O A:HOH548 4.4 63.6 1.0 CA A:PRO204 4.5 37.5 1.0 CA A:ASP201 4.7 41.4 1.0 CB A:PRO204 4.8 39.5 1.0 CD1 A:LEU159 4.9 37.0 1.0

Zinc binding site 2 out of 7 in the Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6


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 the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:37.3 occ:1.00 ND1 A:HIS180 2.0 52.0 1.0 OE1 A:GLU182 2.1 65.4 1.0 OE2 A:GLU182 2.1 73.6 1.0 CD A:GLU182 2.3 64.0 1.0 CE1 A:HIS180 2.9 54.1 1.0 CG A:HIS180 3.1 46.7 1.0 CB A:HIS180 3.5 37.2 1.0 CG A:GLU182 3.8 60.6 1.0 NH1 A:ARG178 4.0 69.1 1.0 O A:HOH511 4.1 32.3 1.0 NE2 A:HIS180 4.1 49.9 1.0 CD2 A:HIS180 4.2 47.5 1.0 CA A:HIS180 4.2 34.1 1.0 NH2 A:ARG178 4.6 68.8 1.0 CD A:PRO181 4.8 37.4 1.0 CB A:GLU182 4.8 52.9 1.0 CZ A:ARG178 4.8 65.2 1.0

Zinc binding site 3 out of 7 in the Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6


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 the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:0.2 occ:0.63 NE2 A:HIS217 2.0 0.9 1.0 O A:HOH550 2.1 41.8 1.0 CD2 A:HIS217 2.4 85.0 1.0 CE1 A:HIS217 3.1 88.2 1.0 CG A:HIS217 3.5 66.0 1.0 O A:HOH539 3.6 24.3 1.0 ND1 A:HIS217 3.8 67.9 1.0 CB A:HIS217 4.7 53.1 1.0

Zinc binding site 4 out of 7 in the Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6


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 the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:92.6 occ:1.00 ND1 A:HIS270 2.0 92.8 1.0 CL A:CL408 2.1 83.0 0.8 O A:HOH544 2.1 26.9 1.0 CE1 A:HIS270 3.0 86.4 1.0 CG A:HIS270 3.0 71.5 1.0 CB A:HIS270 3.4 52.5 1.0 O A:LEU280 3.9 60.5 1.0 NE2 A:HIS270 4.1 81.2 1.0 CD2 A:HIS270 4.1 75.3 1.0 CA A:HIS270 4.3 51.2 1.0 CG A:PRO282 4.5 52.0 1.0 CD A:PRO282 4.6 51.8 1.0 N A:PRO282 4.7 54.7 1.0

Zinc binding site 5 out of 7 in the Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6


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 the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn412 b:27.1 occ:0.88 ND1 B:HIS27 2.0 34.7 1.0 NE2 B:HIS17 2.0 35.7 1.0 OE1 A:GLU132 2.0 33.8 1.0 OE2 A:GLU132 2.1 36.5 1.0 CL A:CL405 2.1 38.3 1.0 CD A:GLU132 2.4 30.5 1.0 CE1 B:HIS27 2.7 31.4 1.0 CD2 B:HIS17 2.9 31.1 1.0 CE1 B:HIS17 3.0 27.8 1.0 CG B:HIS27 3.2 37.0 1.0 CB B:HIS27 3.8 38.2 1.0 CG A:GLU132 3.9 29.3 1.0 NE2 B:HIS27 3.9 32.1 1.0 CG B:HIS17 4.1 29.2 1.0 ND1 B:HIS17 4.1 31.1 1.0 CD2 B:HIS27 4.2 30.6 1.0 O A:HOH613 4.2 31.0 1.0 CA B:HIS27 4.5 34.7 1.0 O A:HOH661 4.6 56.1 1.0 CE2 B:PHE16 4.7 29.2 1.0 NH2 A:ARG228 4.7 25.6 1.0 CB A:GLU132 4.7 28.6 1.0 CD2 A:TRP230 4.7 31.0 1.0 CG A:TRP230 4.7 37.4 1.0 CB A:TRP230 4.8 36.5 1.0 CE3 A:TRP230 4.8 33.1 1.0 NE A:ARG228 4.9 37.8 1.0 CD2 B:PHE16 5.0 27.0 1.0

Zinc binding site 6 out of 7 in the Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6


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 the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:73.0 occ:0.86 SG B:CYS3 2.4 61.4 1.0 CB B:CYS3 3.4 69.6 1.0 CA B:CYS3 3.9 77.9 1.0 O B:HOH203 3.9 50.2 1.0 CD B:PRO4 3.9 73.2 1.0 N B:PRO4 4.5 72.1 1.0 C B:CYS3 4.5 71.7 1.0 CG B:PRO4 4.6 70.2 1.0 CD1 B:LEU5 4.6 61.6 1.0 CB B:LEU5 4.7 56.1 1.0 CG B:LEU5 4.7 59.2 1.0 N B:LEU5 4.8 56.6 1.0

Zinc binding site 7 out of 7 in the Crystal Structure of the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6


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 the Human Rage Ectodomain (VC1C2 Fragment) in Complex with Human S100A6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:0.0 occ:1.00 OE1 B:GLU41 2.0 0.2 1.0 OE2 B:GLU41 2.0 0.3 1.0 CL B:CL103 2.1 79.1 0.7 CD B:GLU41 2.3 0.7 1.0 CG B:GLU41 3.8 0.9 1.0 NZ B:LYS18 4.0 54.2 1.0 CB B:GLU41 4.6 98.7 1.0 CD1 B:ILE15 4.7 39.1 1.0 CG1 B:ILE15 4.9 38.7 1.0 O B:LYS40 5.0 60.1 1.0 CA B:GLU41 5.0 78.7 1.0

L.Yatime, C.Betzer, R.K.Jensen, S.Mortensen, P.H.Jensen, G.R.Andersen. The Structure of the Rage:S100A6 Complex Reveals A Unique Mode of Homodimerization For S100 Proteins. Structure V. 24 2043 2016.
ISSN: ISSN 1878-4186
PubMed: 27818100
DOI: 10.1016/J.STR.2016.09.011