Zinc in PDB 1wm9: Structure of Gtp Cyclohydrolase I From Thermus Thermophilus HB8

All present enzymatic activity of Structure of Gtp Cyclohydrolase I From Thermus Thermophilus HB8:
3.5.4.16;

The structure of Structure of Gtp Cyclohydrolase I From Thermus Thermophilus HB8, PDB code: 1wm9 was solved by Y.Tanaka, Riken Structural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	160.220, 110.477, 70.650, 90.00, 105.27, 90.00
R / Rfree (%)	20.8 / 26.1

The binding sites of Zinc atom in the Structure of Gtp Cyclohydrolase I From Thermus Thermophilus HB8 (pdb code 1wm9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Structure of Gtp Cyclohydrolase I From Thermus Thermophilus HB8, PDB code: 1wm9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Structure of Gtp Cyclohydrolase I From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Gtp Cyclohydrolase I From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:45.8 occ:1.00 SG A:CYS179 2.3 41.1 1.0 ND1 A:HIS111 2.5 32.6 1.0 SG A:CYS108 2.6 41.1 1.0 CB A:CYS179 3.1 30.2 1.0 O A:HOH1011 3.2 36.1 1.0 CE1 A:HIS111 3.3 29.9 1.0 CB A:CYS108 3.4 30.0 1.0 CG A:HIS111 3.5 30.3 1.0 CB A:HIS111 3.8 29.7 1.0 O A:HOH1023 3.9 30.6 1.0 N A:HIS111 3.9 29.9 1.0 CB A:HIS110 4.0 25.9 1.0 NE2 A:HIS111 4.4 34.3 1.0 CA A:HIS111 4.5 27.9 1.0 CD2 A:HIS111 4.5 31.3 1.0 C A:HIS110 4.5 30.7 1.0 CA A:CYS179 4.5 28.7 1.0 CA A:HIS110 4.6 29.4 1.0 N A:HIS110 4.8 29.5 1.0 CA A:CYS108 4.8 24.3 1.0 ND1 A:HIS110 4.8 32.8 1.0 CG A:HIS110 4.9 30.3 1.0

Zinc binding site 2 out of 5 in the Structure of Gtp Cyclohydrolase I From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Gtp Cyclohydrolase I From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:54.5 occ:1.00 SG B:CYS179 2.4 41.7 1.0 ND1 B:HIS111 2.4 27.8 1.0 SG B:CYS108 2.6 42.1 1.0 CB B:CYS179 2.9 35.6 1.0 CE1 B:HIS111 3.3 31.4 1.0 CG B:HIS111 3.4 28.7 1.0 CB B:CYS108 3.5 32.1 1.0 CB B:HIS111 3.7 27.5 1.0 N B:HIS111 3.9 29.3 1.0 O B:HOH1022 3.9 26.3 1.0 CB B:HIS110 3.9 26.9 1.0 CA B:HIS111 4.4 29.1 1.0 CA B:CYS179 4.4 36.2 1.0 NE2 B:HIS111 4.4 36.1 1.0 C B:HIS110 4.5 31.0 1.0 CD2 B:HIS111 4.5 32.1 1.0 CA B:HIS110 4.6 27.7 1.0 CG B:HIS110 4.8 34.6 1.0 ND1 B:HIS110 4.8 36.1 1.0 N B:HIS110 4.9 26.3 1.0 CA B:CYS108 4.9 30.7 1.0

Zinc binding site 3 out of 5 in the Structure of Gtp Cyclohydrolase I From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Gtp Cyclohydrolase I From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1003 b:57.4 occ:1.00 SG C:CYS108 2.4 46.4 1.0 SG C:CYS179 2.5 46.0 1.0 ND1 C:HIS111 2.6 42.8 1.0 O C:HOH1018 3.1 49.0 1.0 CB C:CYS179 3.1 36.5 1.0 CG C:HIS111 3.5 41.9 1.0 CE1 C:HIS111 3.5 47.0 1.0 CB C:CYS108 3.6 38.5 1.0 O D:HOH1012 3.6 45.7 1.0 CB C:HIS111 3.7 37.5 1.0 N C:HIS111 3.9 38.0 1.0 O C:HOH1012 4.0 29.3 1.0 CB C:HIS110 4.1 41.7 1.0 CA C:HIS111 4.4 35.0 1.0 NE2 C:HIS111 4.6 47.6 1.0 C C:HIS110 4.6 40.0 1.0 CA C:CYS179 4.6 37.5 1.0 CD2 C:HIS111 4.6 44.7 1.0 CA C:HIS110 4.8 38.2 1.0 ND1 C:HIS110 4.8 45.3 1.0 CG C:HIS110 4.9 45.2 1.0 N C:HIS110 4.9 36.8 1.0 CA C:CYS108 5.0 38.1 1.0

Zinc binding site 4 out of 5 in the Structure of Gtp Cyclohydrolase I From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Gtp Cyclohydrolase I From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1004 b:51.3 occ:1.00 ND1 D:HIS111 2.3 32.6 1.0 SG D:CYS179 2.5 38.6 1.0 SG D:CYS108 2.7 53.6 1.0 CB D:CYS179 3.0 31.5 1.0 O D:HOH1011 3.1 43.4 1.0 CE1 D:HIS111 3.1 34.4 1.0 CG D:HIS111 3.3 31.4 1.0 CB D:CYS108 3.3 33.1 1.0 O D:HOH1014 3.6 47.7 1.0 CB D:HIS111 3.7 29.9 1.0 N D:HIS111 3.9 29.5 1.0 CB D:HIS110 4.1 32.5 1.0 NE2 D:HIS111 4.3 35.3 1.0 CD2 D:HIS111 4.4 33.3 1.0 CA D:HIS111 4.4 28.4 1.0 CA D:CYS179 4.5 32.9 1.0 ND1 D:HIS110 4.6 36.5 1.0 C D:HIS110 4.6 31.8 1.0 CA D:CYS108 4.8 31.7 1.0 CA D:HIS110 4.8 32.4 1.0 CG D:HIS110 4.8 37.8 1.0 N D:HIS110 4.9 31.6 1.0

Zinc binding site 5 out of 5 in the Structure of Gtp Cyclohydrolase I From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Gtp Cyclohydrolase I From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1005 b:46.7 occ:1.00 SG E:CYS179 2.5 40.2 1.0 SG E:CYS108 2.5 44.4 1.0 ND1 E:HIS111 2.6 28.3 1.0 CB E:CYS179 3.1 27.8 1.0 O E:HOH1052 3.2 43.3 1.0 CB E:CYS108 3.4 30.3 1.0 CE1 E:HIS111 3.5 31.7 1.0 CG E:HIS111 3.5 27.8 1.0 CB E:HIS111 3.7 28.8 1.0 N E:HIS111 3.9 29.6 1.0 CB E:HIS110 4.0 30.5 1.0 O E:HOH1019 4.0 31.5 1.0 CA E:HIS111 4.4 27.2 1.0 C E:HIS110 4.5 31.4 1.0 CA E:CYS179 4.6 31.7 1.0 NE2 E:HIS111 4.6 32.6 1.0 CD2 E:HIS111 4.6 30.8 1.0 CA E:HIS110 4.6 28.7 1.0 ND1 E:HIS110 4.8 31.1 1.0 N E:HIS110 4.8 28.7 1.0 CG E:HIS110 4.8 33.0 1.0 CA E:CYS108 4.9 27.7 1.0

Y.Tanaka, N.Nakagawa, S.Kuramitsu, S.Yokoyama, R.Masui. Novel Reaction Mechanism of Gtp Cyclohydrolase I. High-Resolution X-Ray Crystallography of Thermus Thermophilus HB8 Enzyme Complexed with A Transition State Analogue, the 8-Oxoguanine Derivative. J.Biochem.(Tokyo) V. 138 263 2005.
ISSN: ISSN 0021-924X
PubMed: 16169877
DOI: 10.1093/JB/MVI120