Zinc in PDB 6z87: Human Gtp Cyclohydrolase I

All present enzymatic activity of Human Gtp Cyclohydrolase I:
3.5.4.16;

The structure of Human Gtp Cyclohydrolase I, PDB code: 6z87 was solved by R.Ebenhoch, H.Nar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	95.16 / 2.56
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	109.877, 109.877, 387.247, 90.00, 90.00, 120.00
R / Rfree (%)	22.7 / 24.6

The binding sites of Zinc atom in the Human Gtp Cyclohydrolase I (pdb code 6z87). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Human Gtp Cyclohydrolase I, PDB code: 6z87:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Human Gtp Cyclohydrolase I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Gtp Cyclohydrolase I within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:69.0 occ:1.00 ND1 A:HIS144 2.2 46.1 1.0 SG A:CYS141 2.2 60.4 1.0 SG A:CYS212 2.3 80.5 1.0 O A:HOH423 2.9 24.7 1.0 CE1 A:HIS144 3.1 46.7 1.0 CB A:CYS212 3.1 73.0 1.0 CG A:HIS144 3.3 44.4 1.0 CB A:CYS141 3.6 50.8 1.0 CB A:HIS144 3.6 43.0 1.0 N A:HIS144 4.0 42.4 1.0 NE2 A:HIS144 4.2 46.5 1.0 CB A:HIS143 4.3 44.0 1.0 CD2 A:HIS144 4.3 45.5 1.0 CA A:HIS144 4.4 42.6 1.0 CA A:CYS212 4.6 71.0 1.0 C A:HIS143 4.8 43.2 1.0 ND1 A:HIS143 4.8 48.6 1.0 CA A:HIS143 4.9 43.7 1.0 CA A:CYS141 4.9 48.1 1.0 N A:HIS143 4.9 44.2 1.0

Zinc binding site 2 out of 5 in the Human Gtp Cyclohydrolase I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Gtp Cyclohydrolase I within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn300 b:78.5 occ:1.00 ND1 B:HIS144 2.1 56.5 1.0 SG B:CYS141 2.3 67.8 1.0 SG B:CYS212 2.4 85.9 1.0 CE1 B:HIS144 3.1 57.2 1.0 CB B:CYS212 3.1 78.0 1.0 CG B:HIS144 3.2 54.1 1.0 CB B:CYS141 3.3 56.4 1.0 CB B:HIS144 3.5 49.9 1.0 N B:HIS144 3.8 49.0 1.0 CA B:HIS144 4.3 48.4 1.0 NE2 B:HIS144 4.3 57.3 1.0 CB B:HIS143 4.3 52.9 1.0 CD2 B:HIS144 4.3 56.1 1.0 CA B:CYS212 4.6 76.2 1.0 C B:HIS143 4.6 50.1 1.0 CA B:CYS141 4.7 53.0 1.0 CA B:HIS143 4.8 51.1 1.0 N B:HIS143 4.8 51.2 1.0 ND1 B:HIS143 4.9 59.9 1.0

Zinc binding site 3 out of 5 in the Human Gtp Cyclohydrolase I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Gtp Cyclohydrolase I within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn300 b:78.0 occ:1.00 ND1 C:HIS144 2.2 51.3 1.0 SG C:CYS141 2.2 62.6 1.0 SG C:CYS212 2.4 86.5 1.0 CE1 C:HIS144 3.0 51.9 1.0 O C:HOH424 3.1 26.7 1.0 CB C:CYS212 3.1 80.9 1.0 CG C:HIS144 3.3 49.2 1.0 CB C:CYS141 3.6 52.7 1.0 CB C:HIS144 3.7 47.1 1.0 O D:HOH407 3.8 29.8 1.0 N C:HIS144 4.0 46.6 1.0 NE2 C:HIS144 4.2 51.3 1.0 CB C:HIS143 4.2 48.4 1.0 CD2 C:HIS144 4.3 50.3 1.0 CA C:HIS144 4.5 46.4 1.0 CA C:CYS212 4.6 79.5 1.0 C C:HIS143 4.8 47.2 1.0 ND1 C:HIS143 4.8 53.6 1.0 CA C:HIS143 4.9 47.3 1.0 CA C:CYS141 4.9 49.9 1.0 N C:HIS143 4.9 47.0 1.0

Zinc binding site 4 out of 5 in the Human Gtp Cyclohydrolase I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Gtp Cyclohydrolase I within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn300 b:88.0 occ:1.00 ND1 D:HIS144 2.2 71.3 1.0 SG D:CYS212 2.3 91.4 1.0 SG D:CYS141 2.5 74.5 1.0 O D:HOH409 3.1 41.9 1.0 CE1 D:HIS144 3.1 72.1 1.0 CB D:CYS212 3.1 84.5 1.0 CG D:HIS144 3.3 69.0 1.0 CB D:CYS141 3.5 68.2 1.0 CB D:HIS144 3.7 65.5 1.0 O E:HOH413 3.9 30.3 1.0 N D:HIS144 4.0 65.1 1.0 NE2 D:HIS144 4.2 72.0 1.0 CB D:HIS143 4.3 68.6 1.0 CD2 D:HIS144 4.4 70.6 1.0 CA D:HIS144 4.5 64.3 1.0 CA D:CYS212 4.6 82.6 1.0 C D:HIS143 4.8 66.2 1.0 ND1 D:HIS143 4.8 75.0 1.0 CA D:CYS141 4.9 66.3 1.0 CA D:HIS143 4.9 67.1 1.0 N D:HIS143 5.0 67.0 1.0

Zinc binding site 5 out of 5 in the Human Gtp Cyclohydrolase I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Gtp Cyclohydrolase I within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn300 b:96.3 occ:1.00 ND1 E:HIS144 2.3 56.2 1.0 SG E:CYS212 2.4 83.9 1.0 SG E:CYS141 2.4 57.8 1.0 CE1 E:HIS144 3.0 56.9 1.0 O E:HOH415 3.2 21.1 1.0 CB E:CYS212 3.3 78.7 1.0 CG E:HIS144 3.5 53.9 1.0 O E:HOH414 3.8 47.2 1.0 CB E:CYS141 3.8 51.2 1.0 O A:HOH416 3.9 45.3 1.0 CB E:HIS144 4.1 50.3 1.0 NE2 E:HIS144 4.2 56.7 1.0 N E:HIS144 4.4 49.1 1.0 CB E:HIS143 4.4 51.0 1.0 CD2 E:HIS144 4.5 55.2 1.0 ND1 E:HIS143 4.7 58.1 1.0 CA E:CYS212 4.8 77.5 1.0 CA E:HIS144 4.9 48.9 1.0

R.Ebenhoch, S.Prinz, S.Kaltwasser, D.J.Mills, R.Meinecke, M.Rubbelke, D.Reinert, M.Bauer, L.Weixler, M.Zeeb, J.Vonck, H.Nar. A Hybrid Approach Reveals the Allosteric Regulation of Gtp Cyclohydrolase I. Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
PubMed: 33229582
DOI: 10.1073/PNAS.2013473117