Zinc in PDB 4b92: Crystal Structure of Truncated Human Crmp-5 Soaked with Zn

The structure of Crystal Structure of Truncated Human Crmp-5 Soaked with Zn, PDB code: 4b92 was solved by R.Ponnusamy, B.Lohkamp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.92 / 2.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.500, 89.500, 246.460, 90.00, 90.00, 90.00
R / Rfree (%)	19.077 / 25.009

The binding sites of Zinc atom in the Crystal Structure of Truncated Human Crmp-5 Soaked with Zn (pdb code 4b92). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Truncated Human Crmp-5 Soaked with Zn, PDB code: 4b92:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Truncated Human Crmp-5 Soaked with Zn


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 Truncated Human Crmp-5 Soaked with Zn within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1483 b:83.3 occ:1.00 OD2 A:ASP183 2.0 64.0 1.0 NE2 A:HIS179 2.2 66.8 1.0 O A:HOH2001 2.5 25.4 1.0 CE1 A:HIS179 2.9 62.8 1.0 CG A:ASP183 2.9 51.7 1.0 OD1 A:ASP183 3.0 49.3 1.0 CD2 A:HIS179 3.3 61.2 1.0 ND1 A:HIS179 4.0 56.4 1.0 CG A:HIS179 4.2 53.1 1.0 CB A:ASP183 4.3 47.0 1.0 NZ A:LYS182 5.0 71.2 1.0 O A:HIS179 5.0 39.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Truncated Human Crmp-5 Soaked with Zn


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 Truncated Human Crmp-5 Soaked with Zn within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1484 b:0.5 occ:0.64 ND1 A:HIS282 2.2 71.3 1.0 NE2 A:HIS290 2.2 73.5 1.0 CD2 A:HIS290 2.9 63.4 1.0 O A:HOH2002 3.0 27.4 1.0 CE1 A:HIS282 3.1 64.2 1.0 CG A:HIS282 3.2 64.5 1.0 CE1 A:HIS290 3.2 69.0 1.0 CD2 A:HIS285 3.6 95.9 1.0 CB A:HIS282 3.6 57.0 1.0 CA A:HIS282 3.8 57.5 1.0 CB A:HIS285 4.0 84.1 1.0 CG A:HIS285 4.0 88.8 1.0 CG A:HIS290 4.1 63.9 1.0 NE2 A:HIS282 4.1 62.7 1.0 ND1 A:HIS290 4.2 68.9 1.0 CD2 A:HIS282 4.2 64.5 1.0 O A:HIS282 4.5 56.3 1.0 OH A:TYR294 4.5 46.9 1.0 NE2 A:HIS285 4.6 94.2 1.0 CE1 A:TYR294 4.7 41.3 1.0 C A:HIS282 4.7 55.8 1.0 CZ A:TYR294 4.7 44.1 1.0 N A:HIS282 4.8 59.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Truncated Human Crmp-5 Soaked with Zn


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 Truncated Human Crmp-5 Soaked with Zn within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1483 b:91.7 occ:0.67 OD2 B:ASP183 2.0 57.7 1.0 NE2 B:HIS179 2.2 80.7 1.0 CG B:ASP183 2.9 51.8 1.0 CD2 B:HIS179 3.0 73.1 1.0 CE1 B:HIS179 3.1 72.9 1.0 OD1 B:ASP183 3.1 58.0 1.0 ND1 B:HIS179 4.1 70.4 1.0 CG B:HIS179 4.1 64.5 1.0 CB B:ASP183 4.4 48.3 1.0 CG2 A:THR147 4.6 46.9 1.0 OG1 A:THR147 4.7 47.6 1.0 O B:HIS179 4.9 46.5 1.0 CG1 A:VAL110 4.9 35.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Truncated Human Crmp-5 Soaked with Zn


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 Truncated Human Crmp-5 Soaked with Zn within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1484 b:98.6 occ:0.67 NE2 B:HIS290 2.2 80.6 1.0 ND1 B:HIS282 2.2 67.9 1.0 O B:HOH2001 2.9 52.5 1.0 CD2 B:HIS290 2.9 75.5 1.0 CE1 B:HIS282 3.0 64.9 1.0 CG B:HIS282 3.2 56.6 1.0 CE1 B:HIS290 3.2 80.1 1.0 CD2 B:HIS285 3.6 78.3 1.0 CB B:HIS282 3.6 55.1 1.0 CA B:HIS282 3.8 55.9 1.0 CB B:HIS285 4.0 86.7 1.0 CG B:HIS285 4.0 86.7 1.0 CG B:HIS290 4.1 69.5 1.0 NE2 B:HIS282 4.1 64.9 1.0 ND1 B:HIS290 4.1 74.7 1.0 CD2 B:HIS282 4.2 61.9 1.0 OH B:TYR294 4.4 38.5 1.0 O B:HIS282 4.5 53.8 1.0 CE1 B:TYR294 4.6 38.5 1.0 CZ B:TYR294 4.6 37.4 1.0 NE2 B:HIS285 4.6 69.7 1.0 C B:HIS282 4.7 52.8 1.0 N B:HIS282 4.9 57.6 1.0

R.Ponnusamy, B.Lohkamp. Insights Into the Oligomerization of Crmps: Crystal Structure of Human Collapsin Response Mediator Protein 5. J.Neurochem. V. 125 855 2013.
ISSN: ISSN 0022-3042
PubMed: 23373749
DOI: 10.1111/JNC.12188