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Zinc in PDB 6z86: Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp

Enzymatic activity of Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp

All present enzymatic activity of Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp:
3.5.4.16;

Protein crystallography data

The structure of Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp, PDB code: 6z86 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) 162.99 / 2.21
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 87.861, 88.595, 163.567, 85.22, 88.91, 83.55
R / Rfree (%) 18.3 / 20.8

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Zinc atom in the Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp (pdb code 6z86). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 20 binding sites of Zinc where determined in the Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp, PDB code: 6z86:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 20 in 6z86

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Zinc binding site 1 out of 20 in the Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp


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 in Complex with 7-Deaza-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:51.6
occ:1.00
 SG A:CYS141 2.3 37.6 1.0
ND1 A:HIS144 2.3 40.2 1.0
SG A:CYS212 2.4 48.5 1.0
O A:HOH431 2.7 35.1 1.0
CB A:CYS212 3.0 40.8 1.0
CE1 A:HIS144 3.3 40.6 1.0
CG A:HIS144 3.3 38.4 1.0
CB A:CYS141 3.5 33.4 1.0
C4 C:QBQ302 3.6 37.6 1.0
CB A:HIS144 3.6 36.4 1.0
N A:HIS144 4.0 35.0 1.0
C3 C:QBQ302 4.1 36.8 1.0
CB A:HIS143 4.4 37.6 1.0
CA A:HIS144 4.4 35.1 1.0
NE2 A:HIS144 4.4 40.6 1.0
CD2 A:HIS144 4.5 39.6 1.0
CA A:CYS212 4.5 38.9 1.0
C9 C:QBQ302 4.7 40.7 1.0
C A:HIS143 4.7 35.8 1.0
N2 C:QBQ302 4.8 38.3 1.0
CA A:CYS141 4.8 32.9 1.0
CA A:HIS143 4.9 36.1 1.0
N A:CYS212 5.0 38.3 1.0
N A:HIS143 5.0 35.5 1.0
O12 C:QBQ302 5.0 41.5 1.0

Zinc binding site 2 out of 20 in 6z86

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Zinc binding site 2 out of 20 in the Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp


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 in Complex with 7-Deaza-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:54.7
occ:1.00
 SG B:CYS212 2.2 49.6 1.0
SG B:CYS141 2.3 34.8 1.0
ND1 B:HIS144 2.4 32.9 1.0
O O:HOH424 2.5 31.6 1.0
CB B:CYS212 2.8 43.2 1.0
CE1 B:HIS144 3.3 32.8 1.0
CG B:HIS144 3.4 31.2 1.0
CB B:CYS141 3.4 30.0 1.0
CB B:HIS144 3.6 29.2 1.0
C4 O:QBQ302 3.7 38.7 1.0
N B:HIS144 4.0 30.2 1.0
O B:HOH413 4.1 35.6 1.0
C3 O:QBQ302 4.2 38.7 1.0
CA B:CYS212 4.3 41.6 1.0
CA B:HIS144 4.4 29.5 1.0
NE2 B:HIS144 4.5 32.6 1.0
CB B:HIS143 4.5 34.0 1.0
CD2 B:HIS144 4.5 31.9 1.0
C9 O:QBQ302 4.7 39.3 1.0
C B:HIS143 4.8 31.8 1.0
CA B:CYS141 4.8 29.4 1.0
N2 O:QBQ302 4.8 38.9 1.0
N B:CYS212 4.9 41.3 1.0
CA B:HIS143 5.0 32.8 1.0

Zinc binding site 3 out of 20 in 6z86

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Zinc binding site 3 out of 20 in the Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp


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 in Complex with 7-Deaza-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:55.3
occ:1.00
 ND1 C:HIS144 2.3 43.3 1.0
SG C:CYS212 2.3 55.2 1.0
SG C:CYS141 2.3 40.6 1.0
O P:HOH418 2.6 44.9 1.0
CB C:CYS212 2.8 44.5 1.0
CE1 C:HIS144 3.2 43.4 1.0
CG C:HIS144 3.3 41.8 1.0
CB C:CYS141 3.4 36.6 1.0
CB C:HIS144 3.5 39.8 1.0
C4 P:QBQ302 3.7 43.1 1.0
N C:HIS144 4.0 38.0 1.0
O C:HOH408 4.3 53.5 1.0
C3 P:QBQ302 4.3 42.7 1.0
CA C:CYS212 4.3 42.3 1.0
NE2 C:HIS144 4.4 43.6 1.0
CA C:HIS144 4.4 38.6 1.0
CD2 C:HIS144 4.4 42.9 1.0
CB C:HIS143 4.5 40.2 1.0
C C:HIS143 4.7 39.1 1.0
C9 P:QBQ302 4.7 44.8 1.0
CA C:CYS141 4.8 36.0 1.0
N C:CYS212 4.9 41.8 1.0
N2 P:QBQ302 4.9 43.2 1.0
CA C:HIS143 4.9 39.0 1.0

Zinc binding site 4 out of 20 in 6z86

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Zinc binding site 4 out of 20 in the Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp


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 in Complex with 7-Deaza-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:51.6
occ:1.00
 ND1 D:HIS144 2.3 35.4 1.0
SG D:CYS212 2.3 43.5 1.0
SG D:CYS141 2.4 34.2 1.0
O B:HOH441 2.5 28.7 1.0
CB D:CYS212 2.8 36.3 1.0
CE1 D:HIS144 3.2 35.5 1.0
CG D:HIS144 3.3 35.0 1.0
CB D:CYS141 3.5 32.2 1.0
CB D:HIS144 3.6 34.3 1.0
C4 B:QBQ302 3.7 35.1 1.0
N D:HIS144 4.0 33.8 1.0
C3 B:QBQ302 4.2 34.3 1.0
O D:HOH412 4.3 33.5 1.0
CA D:CYS212 4.3 34.8 1.0
NE2 D:HIS144 4.4 36.8 1.0
CB D:HIS143 4.4 35.0 1.0
CA D:HIS144 4.4 34.2 1.0
CD2 D:HIS144 4.4 36.0 1.0
C9 B:QBQ302 4.6 37.4 1.0
C D:HIS143 4.7 34.2 1.0
N2 B:QBQ302 4.8 35.8 1.0
O12 B:QBQ302 4.8 37.0 1.0
N D:CYS212 4.9 34.7 1.0
CA D:HIS143 4.9 33.8 1.0
CA D:CYS141 4.9 32.3 1.0

Zinc binding site 5 out of 20 in 6z86

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Zinc binding site 5 out of 20 in the Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp


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 in Complex with 7-Deaza-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:53.6
occ:1.00
 SG E:CYS212 2.3 52.2 1.0
ND1 E:HIS144 2.3 36.8 1.0
SG E:CYS141 2.4 40.1 1.0
O N:HOH430 2.5 34.4 1.0
CB E:CYS212 2.8 44.3 1.0
CE1 E:HIS144 3.2 36.6 1.0
CG E:HIS144 3.3 35.8 1.0
CB E:CYS141 3.4 35.1 1.0
CB E:HIS144 3.6 35.5 1.0
C4 N:QBQ302 3.8 41.8 1.0
N E:HIS144 4.0 36.2 1.0
O E:HOH416 4.1 37.0 1.0
C3 N:QBQ302 4.3 41.6 1.0
CA E:CYS212 4.3 42.5 1.0
NE2 E:HIS144 4.4 37.3 1.0
CA E:HIS144 4.4 36.0 1.0
CD2 E:HIS144 4.4 36.3 1.0
CB E:HIS143 4.5 39.6 1.0
C9 N:QBQ302 4.7 42.4 1.0
C E:HIS143 4.8 36.8 1.0
N E:CYS212 4.9 41.6 1.0
CA E:CYS141 4.9 35.1 1.0
N2 N:QBQ302 5.0 41.9 1.0
CA E:HIS143 5.0 37.9 1.0

Zinc binding site 6 out of 20 in 6z86

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Zinc binding site 6 out of 20 in the Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:45.7
occ:1.00
 ND1 F:HIS144 2.2 31.7 1.0
SG F:CYS212 2.3 52.5 1.0
SG F:CYS141 2.3 37.8 1.0
O K:HOH430 2.6 28.2 1.0
CB F:CYS212 2.9 40.4 1.0
CG F:HIS144 3.2 30.5 1.0
CE1 F:HIS144 3.2 31.6 1.0
CB F:CYS141 3.4 30.2 1.0
CB F:HIS144 3.4 30.2 1.0
C4 K:QBQ302 3.8 32.1 1.0
N F:HIS144 3.9 30.6 1.0
CA F:HIS144 4.3 30.6 1.0
CD2 F:HIS144 4.3 31.1 1.0
CA F:CYS212 4.3 38.0 1.0
NE2 F:HIS144 4.3 31.8 1.0
C3 K:QBQ302 4.4 31.0 1.0
CB F:HIS143 4.5 31.2 1.0
C F:HIS143 4.7 31.6 1.0
C9 K:QBQ302 4.8 34.1 1.0
CA F:CYS141 4.8 30.6 1.0
N F:CYS212 4.9 38.2 1.0
CA F:HIS143 4.9 31.5 1.0
N2 K:QBQ302 5.0 32.2 1.0
N F:HIS143 5.0 31.7 1.0

Zinc binding site 7 out of 20 in 6z86

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Zinc binding site 7 out of 20 in the Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn301

b:52.7
occ:1.00
 SG G:CYS212 2.1 45.7 1.0
ND1 G:HIS144 2.3 36.2 1.0
SG G:CYS141 2.4 41.3 1.0
O G:HOH433 2.9 35.6 1.0
CB G:CYS212 2.9 37.8 1.0
CG G:HIS144 3.3 34.5 1.0
CE1 G:HIS144 3.3 36.5 1.0
CB G:CYS141 3.5 31.5 1.0
CB G:HIS144 3.5 32.2 1.0
C4 H:QBQ302 3.8 35.7 1.0
N G:HIS144 3.9 30.6 1.0
CA G:HIS144 4.3 30.9 1.0
O H:HOH401 4.3 36.5 1.0
C3 H:QBQ302 4.4 35.4 1.0
CA G:CYS212 4.4 36.1 1.0
CB G:HIS143 4.4 32.0 1.0
NE2 G:HIS144 4.4 37.0 1.0
CD2 G:HIS144 4.4 36.0 1.0
C G:HIS143 4.6 31.3 1.0
C9 H:QBQ302 4.9 36.0 1.0
CA G:CYS141 4.9 29.6 1.0
CA G:HIS143 4.9 31.4 1.0
N G:CYS212 5.0 35.4 1.0
N G:HIS143 5.0 31.3 1.0

Zinc binding site 8 out of 20 in 6z86

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Zinc binding site 8 out of 20 in the Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn301

b:56.7
occ:1.00
 ND1 H:HIS144 2.1 35.5 1.0
SG H:CYS212 2.3 50.2 1.0
SG H:CYS141 2.4 41.2 1.0
O J:HOH431 2.6 34.9 1.0
CB H:CYS212 2.7 40.0 1.0
CE1 H:HIS144 3.1 35.2 1.0
CG H:HIS144 3.1 34.0 1.0
CB H:HIS144 3.4 32.2 1.0
CB H:CYS141 3.6 32.2 1.0
C4 J:QBQ302 3.7 35.5 1.0
N H:HIS144 4.0 31.6 1.0
O J:HOH402 4.0 39.4 1.0
NE2 H:HIS144 4.2 35.5 1.0
CD2 H:HIS144 4.2 34.7 1.0
CA H:CYS212 4.2 38.4 1.0
C3 J:QBQ302 4.3 35.1 1.0
CA H:HIS144 4.3 31.9 1.0
CB H:HIS143 4.4 34.4 1.0
C H:HIS143 4.7 31.9 1.0
C9 J:QBQ302 4.8 37.1 1.0
N H:CYS212 4.9 37.8 1.0
N2 J:QBQ302 4.9 36.1 1.0
CA H:HIS143 5.0 32.9 1.0
CA H:CYS141 5.0 31.5 1.0

Zinc binding site 9 out of 20 in 6z86

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Zinc binding site 9 out of 20 in the Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn301

b:53.7
occ:1.00
 SG I:CYS212 2.2 56.5 1.0
ND1 I:HIS144 2.3 40.1 1.0
SG I:CYS141 2.3 42.5 1.0
O L:HOH422 2.6 22.8 1.0
CB I:CYS212 2.8 48.0 1.0
CE1 I:HIS144 3.2 40.5 1.0
CG I:HIS144 3.3 39.1 1.0
CB I:CYS141 3.4 36.9 1.0
CB I:HIS144 3.6 37.1 1.0
C4 L:QBQ302 3.8 45.2 1.0
O I:HOH425 4.0 42.5 1.0
N I:HIS144 4.0 37.2 1.0
CA I:CYS212 4.3 45.5 1.0
NE2 I:HIS144 4.4 41.5 1.0
C3 L:QBQ302 4.4 44.7 1.0
CA I:HIS144 4.4 36.6 1.0
CD2 I:HIS144 4.4 40.2 1.0
CB I:HIS143 4.4 39.8 1.0
C9 L:QBQ302 4.7 47.2 1.0
C I:HIS143 4.7 38.2 1.0
CA I:CYS141 4.8 36.0 1.0
O12 L:QBQ302 4.9 47.4 1.0
N I:CYS212 4.9 44.9 1.0
CA I:HIS143 5.0 38.4 1.0

Zinc binding site 10 out of 20 in 6z86

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Zinc binding site 10 out of 20 in the Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Human Gtp Cyclohydrolase I in Complex with 7-Deaza-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn301

b:54.0
occ:1.00
 SG J:CYS212 2.3 50.9 1.0
ND1 J:HIS144 2.3 36.6 1.0
SG J:CYS141 2.3 44.2 1.0
O E:HOH431 2.6 30.6 1.0
CB J:CYS212 2.8 43.1 1.0
CE1 J:HIS144 3.2 36.1 1.0
CG J:HIS144 3.3 35.5 1.0
CB J:CYS141 3.4 38.0 1.0
CB J:HIS144 3.5 36.6 1.0
C4 E:QBQ302 3.8 36.5 1.0
N J:HIS144 4.0 37.3 1.0
O J:HOH408 4.3 32.4 1.0
CA J:CYS212 4.3 41.0 1.0
C3 E:QBQ302 4.3 35.5 1.0
NE2 J:HIS144 4.3 36.6 1.0
CD2 J:HIS144 4.4 35.9 1.0
CA J:HIS144 4.4 37.6 1.0
CB J:HIS143 4.5 38.4 1.0
C9 E:QBQ302 4.7 39.2 1.0
C J:HIS143 4.7 37.9 1.0
CA J:CYS141 4.9 37.3 1.0
N J:CYS212 4.9 40.6 1.0
N2 E:QBQ302 4.9 36.7 1.0
O12 E:QBQ302 5.0 38.9 1.0
CA J:HIS143 5.0 37.7 1.0

Reference:

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
Page generated: Tue Oct 29 15:33:11 2024

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