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

Enzymatic activity of Structure of Gtp Cyclohydrolase I Complexed with 8-Oxo-Gtp

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

Protein crystallography data

The structure of Structure of Gtp Cyclohydrolase I Complexed with 8-Oxo-Gtp, PDB code: 1wuq 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) 40.60 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 160.800, 110.957, 70.463, 90.00, 105.53, 90.00
R / Rfree (%) 20.7 / 23.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Gtp Cyclohydrolase I Complexed with 8-Oxo-Gtp (pdb code 1wuq). 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-Gtp, PDB code: 1wuq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 1wuq

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Zinc binding site 1 out of 5 in the Structure of Gtp Cyclohydrolase I Complexed with 8-Oxo-Gtp


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-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:34.4
occ:1.00
 O8 A:8GT811 2.0 27.3 1.0
SG A:CYS179 2.3 27.7 1.0
SG A:CYS108 2.4 29.4 1.0
ND1 A:HIS111 2.4 29.3 1.0
CB A:CYS179 3.0 24.2 1.0
C8 A:8GT811 3.1 33.7 1.0
CG A:HIS111 3.3 29.4 1.0
CB A:CYS108 3.4 25.5 1.0
CE1 A:HIS111 3.4 28.8 1.0
O A:HOH1006 3.4 31.2 1.0
CB A:HIS111 3.5 28.0 1.0
N7 A:8GT811 3.6 32.5 1.0
N A:HIS111 3.8 28.0 1.0
O A:HOH1014 4.0 23.7 1.0
CB A:HIS110 4.1 28.9 1.0
O A:HOH1003 4.2 30.4 1.0
N9 A:8GT811 4.3 34.3 1.0
CA A:HIS111 4.3 27.9 1.0
CD2 A:HIS111 4.4 26.0 1.0
NE2 A:HIS111 4.4 30.2 1.0
CA A:CYS179 4.5 23.5 1.0
C2' A:8GT811 4.5 36.1 1.0
C A:HIS110 4.5 26.7 1.0
CA A:HIS110 4.7 25.5 1.0
CA A:CYS108 4.8 22.9 1.0
C1' A:8GT811 4.8 37.6 1.0
ND1 A:HIS110 4.8 38.5 1.0
N A:HIS110 4.9 24.7 1.0
C5 A:8GT811 4.9 33.6 1.0
CG A:HIS110 4.9 34.6 1.0

Zinc binding site 2 out of 5 in 1wuq

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


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-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:40.2
occ:1.00
 O8 C:8GT812 2.1 37.6 1.0
SG B:CYS179 2.4 31.9 1.0
SG B:CYS108 2.4 32.7 1.0
ND1 B:HIS111 2.5 32.0 1.0
CB B:CYS179 3.0 29.3 1.0
C8 C:8GT812 3.1 40.1 1.0
O B:HOH1031 3.4 47.7 1.0
CB B:CYS108 3.4 29.4 1.0
CG B:HIS111 3.4 30.1 1.0
CE1 B:HIS111 3.4 32.8 1.0
CB B:HIS111 3.6 30.4 1.0
N7 C:8GT812 3.6 39.8 1.0
N B:HIS111 3.9 30.3 1.0
O B:HOH1011 4.0 28.3 1.0
CB B:HIS110 4.1 31.3 1.0
N9 C:8GT812 4.4 41.4 1.0
CA B:HIS111 4.4 29.9 1.0
CA B:CYS179 4.5 29.4 1.0
NE2 B:HIS111 4.5 35.6 1.0
CD2 B:HIS111 4.5 30.7 1.0
C B:HIS110 4.6 32.0 1.0
C2' C:8GT812 4.6 42.4 1.0
CA B:HIS110 4.7 30.0 1.0
ND1 B:HIS110 4.8 44.8 1.0
CA B:CYS108 4.8 28.4 1.0
CG B:HIS110 4.9 42.8 1.0
N B:HIS110 4.9 27.2 1.0
C1' C:8GT812 4.9 42.6 1.0
C5 C:8GT812 5.0 40.8 1.0

Zinc binding site 3 out of 5 in 1wuq

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


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-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1003

b:48.6
occ:1.00
 O8 C:8GT813 2.0 41.0 1.0
SG C:CYS108 2.4 42.4 1.0
ND1 C:HIS111 2.4 35.7 1.0
SG C:CYS179 2.5 39.3 1.0
CB C:CYS179 2.9 34.0 1.0
C8 C:8GT813 3.1 45.1 1.0
CB C:CYS108 3.3 36.8 1.0
CG C:HIS111 3.3 34.5 1.0
CE1 C:HIS111 3.3 38.8 1.0
CB C:HIS111 3.6 35.2 1.0
N7 C:8GT813 3.7 43.2 1.0
N C:HIS111 3.8 37.9 1.0
CB C:HIS110 4.0 44.5 1.0
O C:HOH1022 4.0 37.6 1.0
N9 C:8GT813 4.3 46.1 1.0
CA C:HIS111 4.3 35.5 1.0
CA C:CYS179 4.4 35.5 1.0
NE2 C:HIS111 4.4 36.7 1.0
CD2 C:HIS111 4.4 33.5 1.0
C2' C:8GT813 4.5 47.6 1.0
C C:HIS110 4.6 42.0 1.0
CA C:HIS110 4.7 41.0 1.0
CA C:CYS108 4.7 38.5 1.0
ND1 C:HIS110 4.7 50.7 1.0
C1' C:8GT813 4.8 48.5 1.0
CG C:HIS110 4.8 49.5 1.0
N C:HIS110 4.9 41.1 1.0
C5 C:8GT813 5.0 45.6 1.0

Zinc binding site 4 out of 5 in 1wuq

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


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-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1004

b:37.8
occ:1.00
 O8 D:8GT814 2.1 35.0 1.0
ND1 D:HIS111 2.2 25.7 1.0
SG D:CYS179 2.4 30.1 1.0
SG D:CYS108 2.4 35.6 1.0
CB D:CYS179 2.9 26.5 1.0
C8 D:8GT814 3.1 36.7 1.0
CE1 D:HIS111 3.1 27.1 1.0
CG D:HIS111 3.2 26.3 1.0
CB D:CYS108 3.4 31.5 1.0
O D:HOH1008 3.5 43.9 1.0
CB D:HIS111 3.6 28.4 1.0
N7 D:8GT814 3.6 35.4 1.0
N D:HIS111 3.8 29.6 1.0
CB D:HIS110 4.0 29.3 1.0
O D:HOH1017 4.1 26.6 1.0
O D:HOH1006 4.2 35.6 1.0
NE2 D:HIS111 4.3 26.8 1.0
N9 D:8GT814 4.3 37.2 1.0
CA D:HIS111 4.3 28.9 1.0
CD2 D:HIS111 4.3 26.9 1.0
CA D:CYS179 4.4 26.4 1.0
C D:HIS110 4.5 30.5 1.0
C2' D:8GT814 4.5 37.2 1.0
CA D:HIS110 4.7 25.1 1.0
ND1 D:HIS110 4.7 38.8 1.0
CA D:CYS108 4.8 29.8 1.0
CG D:HIS110 4.8 33.5 1.0
N D:HIS110 4.9 27.4 1.0
C1' D:8GT814 4.9 37.9 1.0
C5 D:8GT814 5.0 39.2 1.0

Zinc binding site 5 out of 5 in 1wuq

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


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-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1005

b:35.9
occ:1.00
 O8 A:8GT815 2.0 32.2 1.0
ND1 E:HIS111 2.3 28.4 1.0
SG E:CYS179 2.4 28.6 1.0
SG E:CYS108 2.5 32.2 1.0
CB E:CYS179 2.9 21.8 1.0
C8 A:8GT815 3.1 35.9 1.0
CE1 E:HIS111 3.3 26.9 1.0
CG E:HIS111 3.3 25.1 1.0
CB E:CYS108 3.3 26.6 1.0
O E:HOH1021 3.5 37.5 1.0
CB E:HIS111 3.6 27.5 1.0
N7 A:8GT815 3.6 34.3 1.0
N E:HIS111 3.8 28.8 1.0
O E:HOH1012 3.9 30.5 1.0
CB E:HIS110 4.0 29.8 1.0
O A:HOH1016 4.2 35.1 1.0
N9 A:8GT815 4.3 36.4 1.0
CA E:HIS111 4.4 27.7 1.0
NE2 E:HIS111 4.4 27.9 1.0
C2' A:8GT815 4.4 38.0 1.0
CD2 E:HIS111 4.4 26.0 1.0
CA E:CYS179 4.4 22.9 1.0
C E:HIS110 4.5 28.1 1.0
ND1 E:HIS110 4.6 39.6 1.0
CA E:HIS110 4.7 25.8 1.0
CG E:HIS110 4.7 34.6 1.0
CA E:CYS108 4.8 25.1 1.0
C1' A:8GT815 4.8 39.1 1.0
N E:HIS110 4.9 23.2 1.0
C5 A:8GT815 5.0 35.0 1.0
O2' A:8GT815 5.0 33.8 1.0

Reference:

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
Page generated: Wed Dec 16 03:10:29 2020

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