Zinc in PDB 3eo3: Crystal Structure of the N-Acetylmannosamine Kinase Domain of Human Gne Protein

All present enzymatic activity of Crystal Structure of the N-Acetylmannosamine Kinase Domain of Human Gne Protein:
2.7.1.60; 5.1.3.14;

The structure of Crystal Structure of the N-Acetylmannosamine Kinase Domain of Human Gne Protein, PDB code: 3eo3 was solved by L.Nedyalkova, Y.Tong, W.M.Rabeh, B.Hong, W.Tempel, F.Mackenzie, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, A.Bochkarev, H.Park, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.84
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.946, 127.946, 127.247, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / 24.5

The binding sites of Zinc atom in the Crystal Structure of the N-Acetylmannosamine Kinase Domain of Human Gne Protein (pdb code 3eo3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the N-Acetylmannosamine Kinase Domain of Human Gne Protein, PDB code: 3eo3:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the N-Acetylmannosamine Kinase Domain of Human Gne Protein


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 N-Acetylmannosamine Kinase Domain of Human Gne Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:32.5 occ:1.00 ND1 A:HIS569 2.2 32.7 1.0 SG A:CYS586 2.3 29.9 1.0 SG A:CYS579 2.3 34.2 1.0 SG A:CYS581 2.3 31.4 1.0 CG A:HIS569 3.1 31.8 1.0 CE1 A:HIS569 3.1 32.8 1.0 CB A:CYS586 3.1 29.2 1.0 CB A:CYS581 3.2 31.4 1.0 CB A:HIS569 3.4 30.6 1.0 CB A:CYS579 3.4 33.9 1.0 CA A:HIS569 3.9 29.6 1.0 CD2 A:HIS569 4.1 32.4 1.0 NE2 A:HIS569 4.1 33.3 1.0 N A:CYS581 4.3 31.9 1.0 CA A:CYS581 4.4 31.6 1.0 CA A:CYS586 4.5 28.8 1.0 O A:GLY568 4.6 31.1 1.0 N A:HIS569 4.7 29.2 1.0 CA A:CYS579 4.7 33.5 1.0 CB A:SER583 4.9 31.6 1.0 C A:GLY568 5.0 30.3 1.0 C A:CYS579 5.0 32.1 1.0 C A:HIS569 5.0 29.0 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the N-Acetylmannosamine Kinase Domain of Human Gne Protein


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 N-Acetylmannosamine Kinase Domain of Human Gne Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:29.1 occ:1.00 ND1 B:HIS569 2.2 31.3 1.0 SG B:CYS579 2.3 29.8 1.0 SG B:CYS586 2.3 30.8 1.0 SG B:CYS581 2.3 30.0 1.0 CE1 B:HIS569 2.8 32.2 1.0 CG B:HIS569 3.2 30.3 1.0 CB B:CYS579 3.3 29.4 1.0 CB B:CYS586 3.3 29.7 1.0 CB B:CYS581 3.4 29.9 1.0 CB B:HIS569 3.8 29.0 1.0 NE2 B:HIS569 3.9 32.3 1.0 CD2 B:HIS569 4.1 31.0 1.0 CA B:HIS569 4.2 28.1 1.0 N B:CYS581 4.2 29.8 1.0 CA B:CYS581 4.4 29.7 1.0 CA B:CYS579 4.6 29.4 1.0 CA B:CYS586 4.7 29.2 1.0 O B:GLY568 4.7 28.2 1.0 C B:CYS579 4.9 29.2 1.0 N B:SER580 4.9 29.4 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the N-Acetylmannosamine Kinase Domain of Human Gne Protein


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 N-Acetylmannosamine Kinase Domain of Human Gne Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn801 b:29.2 occ:1.00 ND1 C:HIS569 2.2 31.3 1.0 SG C:CYS586 2.3 27.7 1.0 SG C:CYS581 2.3 31.0 1.0 SG C:CYS579 2.3 30.3 1.0 CE1 C:HIS569 3.0 32.1 1.0 CG C:HIS569 3.2 30.8 1.0 CB C:CYS586 3.2 28.9 1.0 CB C:CYS579 3.3 30.5 1.0 CB C:CYS581 3.3 30.4 1.0 CB C:HIS569 3.5 29.9 1.0 CA C:HIS569 4.0 29.6 1.0 NE2 C:HIS569 4.1 32.1 1.0 CD2 C:HIS569 4.2 31.6 1.0 N C:CYS581 4.3 30.0 1.0 CA C:CYS581 4.4 29.7 1.0 CA C:CYS586 4.6 28.9 1.0 CA C:CYS579 4.7 29.5 1.0 N C:HIS569 5.0 29.0 1.0 O C:GLY568 5.0 29.9 1.0

Y.Tong, W.Tempel, L.Nedyalkova, F.Mackenzie, H.W.Park. Crystal Structure of the N-Acetylmannosamine Kinase Domain of Gne. Plos One V. 4 E7165 2009.
ISSN: ESSN 1932-6203
PubMed: 19841673
DOI: 10.1371/JOURNAL.PONE.0007165