Zinc in PDB 1wur: Structure of Gtp Cyclohydrolase I Complexed with 8-Oxo-Dgtp

All present enzymatic activity of Structure of Gtp Cyclohydrolase I Complexed with 8-Oxo-Dgtp:
3.5.4.16;

The structure of Structure of Gtp Cyclohydrolase I Complexed with 8-Oxo-Dgtp, PDB code: 1wur was solved by Y.Tanaka, N.Nakagawa, R.Masui, S.Yokoyama, S.Kuramitsu, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.69 / 1.82
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	160.570, 110.560, 70.530, 90.00, 105.78, 90.00
R / Rfree (%)	20.6 / 23.7

The binding sites of Zinc atom in the Structure of Gtp Cyclohydrolase I Complexed with 8-Oxo-Dgtp (pdb code 1wur). 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 Complexed with 8-Oxo-Dgtp, PDB code: 1wur:
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 Complexed with 8-Oxo-Dgtp


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 Complexed with 8-Oxo-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:22.2 occ:1.00 O8 A:8DG821 2.0 23.5 1.0 ND1 A:HIS111 2.2 21.3 1.0 SG A:CYS179 2.3 18.4 1.0 SG A:CYS108 2.3 20.3 1.0 CB A:CYS179 3.0 18.2 1.0 C8 A:8DG821 3.1 25.9 1.0 CE1 A:HIS111 3.1 24.0 1.0 CG A:HIS111 3.2 22.4 1.0 O A:HOH1038 3.3 35.2 1.0 CB A:CYS108 3.3 16.1 1.0 CB A:HIS111 3.5 19.6 1.0 N7 A:8DG821 3.6 23.7 1.0 N A:HIS111 3.8 18.9 1.0 O A:HOH1004 4.0 16.3 1.0 CB A:HIS110 4.1 18.1 1.0 NE2 A:HIS111 4.2 23.5 1.0 O A:HOH1060 4.2 33.3 1.0 N9 A:8DG821 4.2 27.3 1.0 CD2 A:HIS111 4.3 20.4 1.0 CA A:HIS111 4.3 20.0 1.0 CA A:CYS179 4.5 17.4 1.0 C A:HIS110 4.5 19.1 1.0 C2' A:8DG821 4.6 26.2 1.0 CA A:HIS110 4.7 18.0 1.0 CA A:CYS108 4.7 12.8 1.0 C1' A:8DG821 4.8 28.9 1.0 N A:HIS110 4.8 15.4 1.0 O4' A:8DG821 4.8 30.8 1.0 C5 A:8DG821 4.9 24.7 1.0 N A:CYS179 5.0 16.4 1.0

Zinc binding site 2 out of 5 in the Structure of Gtp Cyclohydrolase I Complexed with 8-Oxo-Dgtp


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 Complexed with 8-Oxo-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:25.4 occ:1.00 O8 C:8DG822 2.0 29.9 1.0 ND1 B:HIS111 2.3 18.6 1.0 SG B:CYS179 2.3 21.0 1.0 SG B:CYS108 2.3 22.7 1.0 CB B:CYS179 3.0 20.6 1.0 C8 C:8DG822 3.1 33.6 1.0 CE1 B:HIS111 3.1 22.3 1.0 CG B:HIS111 3.3 20.4 1.0 CB B:CYS108 3.3 21.2 1.0 N7 C:8DG822 3.6 30.3 1.0 CB B:HIS111 3.6 18.3 1.0 N B:HIS111 3.9 20.8 1.0 O B:HOH1015 4.0 18.4 1.0 CB B:HIS110 4.1 20.9 1.0 NE2 B:HIS111 4.2 24.4 1.0 N9 C:8DG822 4.3 34.0 1.0 CD2 B:HIS111 4.3 19.2 1.0 CA B:HIS111 4.4 19.0 1.0 CA B:CYS179 4.5 20.7 1.0 C B:HIS110 4.5 22.1 1.0 C2' C:8DG822 4.7 35.1 1.0 CA B:CYS108 4.7 19.4 1.0 CA B:HIS110 4.7 19.7 1.0 C1' C:8DG822 4.8 33.7 1.0 N B:HIS110 4.9 18.4 1.0 O4' C:8DG822 4.9 35.6 1.0 C5 C:8DG822 4.9 31.2 1.0

Zinc binding site 3 out of 5 in the Structure of Gtp Cyclohydrolase I Complexed with 8-Oxo-Dgtp


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 Complexed with 8-Oxo-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1003 b:34.3 occ:1.00 O8 D:8DG823 2.0 37.1 1.0 SG C:CYS108 2.3 31.6 1.0 ND1 C:HIS111 2.4 30.2 1.0 SG C:CYS179 2.4 27.6 1.0 CB C:CYS179 2.9 25.6 1.0 C8 D:8DG823 3.1 37.5 1.0 O C:HOH1019 3.2 42.8 1.0 CB C:CYS108 3.3 25.4 1.0 CG C:HIS111 3.3 28.4 1.0 CE1 C:HIS111 3.3 31.7 1.0 CB C:HIS111 3.5 29.5 1.0 N7 D:8DG823 3.6 34.2 1.0 N C:HIS111 3.9 30.3 1.0 O C:HOH1022 4.0 25.4 1.0 O D:HOH1050 4.1 32.1 1.0 CB C:HIS110 4.2 35.0 1.0 N9 D:8DG823 4.3 37.3 1.0 CA C:HIS111 4.3 29.4 1.0 CD2 C:HIS111 4.4 29.1 1.0 NE2 C:HIS111 4.4 30.9 1.0 CA C:CYS179 4.4 25.5 1.0 C C:HIS110 4.6 32.4 1.0 C2' D:8DG823 4.6 38.9 1.0 CA C:CYS108 4.7 26.8 1.0 CA C:HIS110 4.8 31.9 1.0 C1' D:8DG823 4.9 39.6 1.0 C5 D:8DG823 4.9 35.8 1.0 O4' D:8DG823 5.0 40.7 1.0 N C:HIS110 5.0 30.4 1.0

Zinc binding site 4 out of 5 in the Structure of Gtp Cyclohydrolase I Complexed with 8-Oxo-Dgtp


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 Complexed with 8-Oxo-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1004 b:24.7 occ:1.00 O8 D:8DG824 2.0 28.2 1.0 ND1 D:HIS111 2.2 22.0 1.0 SG D:CYS179 2.3 19.9 1.0 SG D:CYS108 2.4 25.7 1.0 CB D:CYS179 2.9 15.9 1.0 C8 D:8DG824 3.0 28.4 1.0 CE1 D:HIS111 3.1 22.8 1.0 CG D:HIS111 3.2 20.4 1.0 CB D:CYS108 3.4 22.0 1.0 CB D:HIS111 3.5 21.2 1.0 N7 D:8DG824 3.6 25.8 1.0 N D:HIS111 3.8 22.3 1.0 O D:HOH1030 4.0 22.1 1.0 CB D:HIS110 4.1 24.0 1.0 O D:HOH1052 4.1 32.8 1.0 N9 D:8DG824 4.2 29.0 1.0 NE2 D:HIS111 4.3 23.9 1.0 CD2 D:HIS111 4.3 21.1 1.0 CA D:HIS111 4.3 20.9 1.0 CA D:CYS179 4.4 15.3 1.0 C D:HIS110 4.6 22.9 1.0 C2' D:8DG824 4.7 30.2 1.0 CA D:HIS110 4.8 22.0 1.0 ND1 D:HIS110 4.8 33.5 1.0 CA D:CYS108 4.8 20.5 1.0 C1' D:8DG824 4.8 30.3 1.0 O4' D:8DG824 4.8 31.6 1.0 C5 D:8DG824 4.9 28.9 1.0 CG D:HIS110 4.9 29.1 1.0 N D:HIS110 4.9 21.1 1.0 N D:CYS179 5.0 17.1 1.0

Zinc binding site 5 out of 5 in the Structure of Gtp Cyclohydrolase I Complexed with 8-Oxo-Dgtp


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 Complexed with 8-Oxo-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1005 b:22.5 occ:1.00 O8 A:8DG825 2.0 29.1 1.0 ND1 E:HIS111 2.2 18.2 1.0 SG E:CYS179 2.4 18.9 1.0 SG E:CYS108 2.5 22.6 1.0 CB E:CYS179 2.9 18.0 1.0 C8 A:8DG825 3.1 30.3 1.0 CE1 E:HIS111 3.1 19.0 1.0 CG E:HIS111 3.2 17.1 1.0 CB E:CYS108 3.3 18.5 1.0 O E:HOH1023 3.3 38.6 1.0 CB E:HIS111 3.6 16.9 1.0 N7 A:8DG825 3.7 26.4 1.0 N E:HIS111 3.8 17.8 1.0 O E:HOH1018 3.9 22.9 1.0 CB E:HIS110 4.0 18.1 1.0 O A:HOH1039 4.1 27.8 1.0 NE2 E:HIS111 4.2 18.7 1.0 N9 A:8DG825 4.3 31.9 1.0 CD2 E:HIS111 4.3 18.5 1.0 CA E:HIS111 4.3 17.0 1.0 CA E:CYS179 4.5 15.0 1.0 C2' A:8DG825 4.5 31.1 1.0 C E:HIS110 4.6 18.4 1.0 ND1 E:HIS110 4.7 33.0 1.0 CA E:HIS110 4.7 17.0 1.0 CA E:CYS108 4.8 15.7 1.0 C1' A:8DG825 4.8 32.7 1.0 CG E:HIS110 4.8 24.7 1.0 O4' A:8DG825 4.9 31.3 1.0 N E:HIS110 4.9 15.8 1.0 C5 A:8DG825 5.0 28.1 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