Nickel in PDB 5mx1: Crystal Structure of Human Chondroadherin

The structure of Crystal Structure of Human Chondroadherin, PDB code: 5mx1 was solved by P.Paracuellos, E.Hohenester, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.35 / 2.17
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	215.450, 60.700, 57.660, 90.00, 100.60, 90.00
R / Rfree (%)	18.8 / 24

The structure of Crystal Structure of Human Chondroadherin also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Nickel atom in the Crystal Structure of Human Chondroadherin (pdb code 5mx1). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Human Chondroadherin, PDB code: 5mx1:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Human Chondroadherin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Human Chondroadherin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:61.1 occ:1.00 ND1 A:HIS30 2.1 53.5 1.0 OD1 B:ASP172 2.3 46.5 1.0 HB3 A:HIS30 2.5 47.3 1.0 CG A:HIS30 2.9 48.4 1.0 HD22 B:ASN148 2.9 40.6 1.0 CL A:CL403 3.0 53.9 1.0 CB A:HIS30 3.1 39.4 1.0 CE1 A:HIS30 3.1 55.9 1.0 ND2 B:ASN148 3.2 33.8 1.0 HD21 B:ASN148 3.3 40.6 1.0 CG B:ASP172 3.4 41.0 1.0 HE1 A:HIS30 3.4 67.1 1.0 O A:HOH643 3.7 35.1 1.0 HA B:ASN148 3.8 29.8 1.0 CG B:ASN148 3.8 35.6 1.0 OD2 B:ASP172 3.8 40.5 1.0 HB2 A:HIS30 3.8 47.3 1.0 HA A:HIS30 3.8 38.5 1.0 CD2 A:HIS30 4.0 52.3 1.0 NE2 A:HIS30 4.1 55.2 1.0 CA A:HIS30 4.1 32.1 1.0 HE3 B:LYS171 4.1 93.5 1.0 OD1 B:ASN148 4.1 42.7 1.0 O B:VAL147 4.2 32.2 1.0 H A:SER31 4.5 44.2 1.0 HZ1 B:LYS171 4.6 93.8 1.0 CB B:ASP172 4.6 34.9 1.0 CA B:ASN148 4.6 24.8 1.0 CB B:ASN148 4.7 29.2 1.0 HB3 B:ASP172 4.7 41.9 1.0 HB2 B:ASP172 4.7 41.9 1.0 O A:CYS29 4.8 32.3 1.0 HD2 A:HIS30 4.8 62.7 1.0 HE1 A:HIS28 4.9 78.1 1.0 HB3 B:ASN148 4.9 35.0 1.0 HE2 A:HIS30 4.9 66.2 1.0 CE B:LYS171 4.9 77.9 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Human Chondroadherin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Human Chondroadherin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni403 b:87.2 occ:1.00 ND1 B:HIS30 2.3 0.4 1.0 OD1 A:ASP172 2.4 87.9 1.0 HB3 B:HIS30 2.4 0.4 1.0 CG B:HIS30 3.1 0.7 1.0 CB B:HIS30 3.2 0.8 1.0 CE1 B:HIS30 3.4 0.6 1.0 OD1 A:ASN148 3.5 48.7 1.0 CG A:ASP172 3.6 81.7 1.0 HE1 B:HIS30 3.7 0.8 1.0 HB2 B:HIS30 3.8 0.4 1.0 HA B:HIS30 4.0 82.8 1.0 HA A:ASN148 4.0 42.8 1.0 CG A:ASN148 4.1 44.0 1.0 CA B:HIS30 4.2 69.0 1.0 O A:VAL147 4.2 41.1 1.0 HD21 A:ASN148 4.2 50.3 1.0 CD2 B:HIS30 4.3 0.1 1.0 OD2 A:ASP172 4.3 86.2 1.0 NE2 B:HIS30 4.4 0.4 1.0 ND2 A:ASN148 4.4 41.9 1.0 HB2 A:ASP172 4.5 80.6 1.0 H B:SER31 4.6 92.1 1.0 CB A:ASP172 4.7 67.2 1.0 HE2 A:PHE150 4.8 63.0 1.0 CA A:ASN148 4.9 35.7 1.0 HG23 A:VAL147 5.0 49.6 1.0 HB3 A:ASP172 5.0 80.6 1.0 O A:HOH597 5.0 43.7 1.0

P.Paracuellos, S.Kalamajski, A.Bonna, D.Bihan, R.W.Farndale, E.Hohenester. Structural and Functional Analysis of Two Small Leucine-Rich Repeat Proteoglycans, Fibromodulin and Chondroadherin. Matrix Biol. V. 63 106 2017.
ISSN: ISSN 1569-1802
PubMed: 28215822
DOI: 10.1016/J.MATBIO.2017.02.002