Zinc in PDB 2hf8: Crystal Structure of Hypb From Methanocaldococcus Jannaschii in the Triphosphate Form, in Complex with Zinc

The structure of Crystal Structure of Hypb From Methanocaldococcus Jannaschii in the Triphosphate Form, in Complex with Zinc, PDB code: 2hf8 was solved by R.Gasper, A.Scrima, A.Wittinghofer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.92 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.120, 68.130, 155.990, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.2

The structure of Crystal Structure of Hypb From Methanocaldococcus Jannaschii in the Triphosphate Form, in Complex with Zinc also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Hypb From Methanocaldococcus Jannaschii in the Triphosphate Form, in Complex with Zinc (pdb code 2hf8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Hypb From Methanocaldococcus Jannaschii in the Triphosphate Form, in Complex with Zinc, PDB code: 2hf8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Hypb From Methanocaldococcus Jannaschii in the Triphosphate Form, in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Hypb From Methanocaldococcus Jannaschii in the Triphosphate Form, in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:23.3 occ:0.80 SG A:CYS127 2.2 24.3 1.0 SG B:CYS95 2.2 32.1 1.0 SG A:CYS95 2.4 29.4 1.0 CB B:CYS95 3.3 29.8 1.0 CB A:CYS127 3.3 22.3 1.0 CB A:CYS95 3.5 27.0 1.0 O B:HOH462 3.5 31.3 1.0 ZN B:ZN402 3.7 22.5 0.7 O A:HOH463 3.8 34.6 1.0 CA A:CYS127 4.5 22.4 1.0 CA B:CYS95 4.6 29.6 1.0 SG B:CYS127 4.7 28.0 1.0 N B:CYS95 4.8 30.4 1.0 CA A:CYS95 4.8 26.9 1.0 ND2 A:ASN124 4.8 21.3 1.0 ND1 A:HIS96 4.8 25.6 1.0 O A:CYS95 4.9 26.0 1.0 N A:CYS127 4.9 21.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Hypb From Methanocaldococcus Jannaschii in the Triphosphate Form, in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Hypb From Methanocaldococcus Jannaschii in the Triphosphate Form, in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:15.5 occ:0.50 NE2 A:HIS104 1.8 17.8 1.0 NE2 A:HIS100 2.3 15.5 1.0 CE1 A:HIS104 2.8 17.1 1.0 CD2 A:HIS104 2.9 16.2 1.0 CD2 A:HIS100 3.1 15.6 1.0 CE1 A:HIS100 3.4 16.2 1.0 ND1 A:HIS104 3.9 16.2 1.0 CG A:HIS104 4.0 14.9 1.0 CG A:HIS100 4.3 15.3 1.0 ND1 A:HIS100 4.4 16.4 1.0 O A:HOH431 4.5 12.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Hypb From Methanocaldococcus Jannaschii in the Triphosphate Form, in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Hypb From Methanocaldococcus Jannaschii in the Triphosphate Form, in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:22.5 occ:0.70 SG B:CYS95 2.1 32.1 1.0 ND1 B:HIS96 2.2 26.4 1.0 O B:HOH462 2.2 31.3 1.0 SG B:CYS127 2.3 28.0 1.0 CE1 B:HIS96 3.0 26.8 1.0 CB B:CYS95 3.1 29.8 1.0 CB B:CYS127 3.3 25.5 1.0 CG B:HIS96 3.3 25.9 1.0 C B:CYS95 3.5 28.3 1.0 CA B:CYS95 3.7 29.6 1.0 ZN A:ZN401 3.7 23.3 0.8 CB B:HIS96 3.8 25.6 1.0 N B:HIS96 3.8 26.9 1.0 O B:CYS95 3.8 28.2 1.0 N B:CYS95 3.9 30.4 1.0 NE2 B:HIS96 4.2 26.3 1.0 SG A:CYS95 4.3 29.4 1.0 CD2 B:HIS96 4.4 26.2 1.0 CA B:HIS96 4.5 25.6 1.0 CA B:CYS127 4.7 25.4 1.0 OE2 B:GLU94 4.8 37.8 1.0 ND2 B:ASN124 4.9 22.5 1.0 CB A:CYS95 5.0 27.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Hypb From Methanocaldococcus Jannaschii in the Triphosphate Form, in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Hypb From Methanocaldococcus Jannaschii in the Triphosphate Form, in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:19.9 occ:0.50 NE2 B:HIS104 2.1 18.4 1.0 NE2 B:HIS100 2.1 16.4 1.0 CD2 B:HIS104 2.9 18.4 1.0 CE1 B:HIS104 3.1 18.9 1.0 CE1 B:HIS100 3.1 17.2 1.0 CD2 B:HIS100 3.1 15.8 1.0 CG B:HIS104 4.1 18.5 1.0 ND1 B:HIS104 4.1 19.0 1.0 ND1 B:HIS100 4.2 16.6 1.0 CG B:HIS100 4.3 16.0 1.0

R.Gasper, A.Scrima, A.Wittinghofer. Structural Insights Into Hypb, A Gtp-Binding Protein That Regulates Metal Binding. J.Biol.Chem. V. 281 27492 2006.
ISSN: ISSN 0021-9258
PubMed: 16807243
DOI: 10.1074/JBC.M600809200