Zinc in PDB 2ycb: Structure of the Archaeal Beta-Casp Protein with N-Terminal Kh Domains From Methanothermobacter Thermautotrophicus

The structure of Structure of the Archaeal Beta-Casp Protein with N-Terminal Kh Domains From Methanothermobacter Thermautotrophicus, PDB code: 2ycb was solved by A.P.G.Silva, M.Chechik, R.T.Byrne, D.G.Waterman, C.L.Ng, E.J.Dodson, E.V.Koonin, A.A.Antson, C.Smits, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.10
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	112.027, 112.027, 400.608, 90.00, 90.00, 90.00
R / Rfree (%)	21.462 / 25.081

The structure of Structure of the Archaeal Beta-Casp Protein with N-Terminal Kh Domains From Methanothermobacter Thermautotrophicus also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Zinc atom in the Structure of the Archaeal Beta-Casp Protein with N-Terminal Kh Domains From Methanothermobacter Thermautotrophicus (pdb code 2ycb). 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 the Archaeal Beta-Casp Protein with N-Terminal Kh Domains From Methanothermobacter Thermautotrophicus, PDB code: 2ycb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Structure of the Archaeal Beta-Casp Protein with N-Terminal Kh Domains From Methanothermobacter Thermautotrophicus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Archaeal Beta-Casp Protein with N-Terminal Kh Domains From Methanothermobacter Thermautotrophicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1637 b:70.4 occ:1.00 NE2 A:HIS247 2.1 80.5 1.0 NE2 A:HIS603 2.1 86.9 1.0 O2 A:PO41639 2.1 77.7 1.0 O3 A:PO41639 2.1 76.8 1.0 OD2 A:ASP352 2.1 82.8 1.0 P A:PO41639 2.6 82.2 1.0 CD2 A:HIS247 2.8 77.0 1.0 CG A:ASP352 2.8 76.7 1.0 OD1 A:ASP352 2.9 76.6 1.0 CE1 A:HIS603 2.9 86.0 1.0 OD2 A:ASP246 3.0 92.3 1.0 CD2 A:HIS603 3.1 84.0 1.0 CE1 A:HIS247 3.2 76.3 1.0 CB A:ASP246 3.4 83.0 1.0 ZN A:ZN1638 3.5 65.6 1.0 O1 A:PO41639 3.6 78.6 1.0 CG A:ASP246 3.7 89.5 1.0 O4 A:PO41639 3.8 81.8 1.0 CG A:HIS247 4.0 73.2 1.0 ND1 A:HIS603 4.0 84.9 1.0 CG A:HIS603 4.2 83.7 1.0 ND1 A:HIS247 4.2 73.2 1.0 NE2 A:HIS242 4.2 76.0 1.0 CB A:ASP352 4.3 75.1 1.0 CE1 A:HIS242 4.3 72.2 1.0 CE1 A:HIS579 4.3 80.3 1.0 CA A:ASP246 4.9 80.4 1.0 NE2 A:HIS579 4.9 82.1 1.0 OD1 A:ASP246 4.9 93.8 1.0

Zinc binding site 2 out of 5 in the Structure of the Archaeal Beta-Casp Protein with N-Terminal Kh Domains From Methanothermobacter Thermautotrophicus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Archaeal Beta-Casp Protein with N-Terminal Kh Domains From Methanothermobacter Thermautotrophicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1638 b:65.6 occ:1.00 O1 A:PO41639 2.1 78.6 1.0 O3 A:PO41639 2.1 76.8 1.0 OD2 A:ASP352 2.1 82.8 1.0 ND1 A:HIS244 2.1 75.8 1.0 NE2 A:HIS242 2.1 76.0 1.0 NE2 A:HIS329 2.2 77.1 1.0 P A:PO41639 2.6 82.2 1.0 CD2 A:HIS242 3.0 72.9 1.0 CE1 A:HIS244 3.0 75.3 1.0 CE1 A:HIS329 3.1 76.4 1.0 CE1 A:HIS242 3.1 72.2 1.0 CG A:ASP352 3.1 76.7 1.0 CD2 A:HIS329 3.1 72.0 1.0 CG A:HIS244 3.2 74.2 1.0 CB A:ASP352 3.4 75.1 1.0 ZN A:ZN1637 3.5 70.4 1.0 CB A:HIS244 3.6 73.9 1.0 O4 A:PO41639 3.6 81.8 1.0 O2 A:PO41639 3.7 77.7 1.0 CG A:HIS242 4.1 70.8 1.0 ND1 A:HIS242 4.1 70.8 1.0 NE2 A:HIS244 4.1 76.3 1.0 ND1 A:HIS329 4.1 74.3 1.0 NE2 A:HIS247 4.2 80.5 1.0 CG A:HIS329 4.2 71.6 1.0 OD1 A:ASP352 4.2 76.6 1.0 CD2 A:HIS244 4.2 75.4 1.0 CD2 A:HIS247 4.2 77.0 1.0 CE1 A:HIS579 4.6 80.3 1.0 NE2 A:HIS579 4.7 82.1 1.0 CA A:ASP352 4.9 73.4 1.0 CA A:HIS244 5.0 73.7 1.0 CE1 A:HIS247 5.0 76.3 1.0

Zinc binding site 3 out of 5 in the Structure of the Archaeal Beta-Casp Protein with N-Terminal Kh Domains From Methanothermobacter Thermautotrophicus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Archaeal Beta-Casp Protein with N-Terminal Kh Domains From Methanothermobacter Thermautotrophicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1642 b:93.4 occ:1.00 O2 A:PO41640 2.0 95.7 1.0 O3 A:PO41641 2.0 97.8 1.0 OD1 A:ASP468 2.0 0.0 1.0 O4 A:PO41641 2.6 98.5 1.0 P A:PO41640 2.7 93.3 1.0 P A:PO41641 2.7 95.2 1.0 O1 A:PO41640 2.9 92.9 1.0 O4 A:PO41640 2.9 93.3 1.0 CG A:ASP468 3.1 0.7 1.0 O1 A:PO41641 3.5 94.7 1.0 OD2 A:ASP468 3.6 0.2 1.0 NE2 A:HIS472 3.6 0.0 1.0 NZ A:LYS464 3.9 98.4 1.0 CD2 A:HIS472 3.9 0.4 1.0 O2 A:PO41641 4.0 93.4 1.0 O3 A:PO41640 4.1 91.9 1.0 NE A:ARG467 4.2 84.0 1.0 CB A:ASP468 4.4 0.4 1.0 CA A:ASP468 4.6 98.1 1.0 CE1 A:HIS472 4.7 1.0 1.0 CG A:ARG467 4.8 82.5 1.0 N A:ASP468 4.8 93.2 1.0 CD A:ARG467 4.8 82.0 1.0 NH2 A:ARG467 4.9 86.8 1.0 CZ A:ARG467 5.0 83.9 1.0

Zinc binding site 4 out of 5 in the Structure of the Archaeal Beta-Casp Protein with N-Terminal Kh Domains From Methanothermobacter Thermautotrophicus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Archaeal Beta-Casp Protein with N-Terminal Kh Domains From Methanothermobacter Thermautotrophicus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1637 b:71.6 occ:1.00 O4 B:PO41639 2.0 86.0 1.0 OD2 B:ASP352 2.1 94.2 1.0 NE2 B:HIS603 2.1 89.2 1.0 OD2 B:ASP246 2.1 94.5 1.0 NE2 B:HIS247 2.1 86.2 1.0 O1 B:PO41639 2.5 93.6 1.0 P B:PO41639 2.7 89.9 1.0 CG B:ASP352 2.8 87.4 1.0 CE1 B:HIS603 2.8 87.1 1.0 CD2 B:HIS247 2.8 83.0 1.0 OD1 B:ASP352 2.9 86.0 1.0 CD2 B:HIS603 3.1 85.1 1.0 CG B:ASP246 3.2 91.9 1.0 CE1 B:HIS247 3.3 81.5 1.0 O3 B:PO41639 3.5 87.4 1.0 ZN B:ZN1638 3.5 72.4 1.0 OD1 B:ASP246 3.6 93.9 1.0 ND1 B:HIS603 3.9 85.6 1.0 O2 B:PO41639 4.0 90.2 1.0 CG B:HIS603 4.1 84.3 1.0 CG B:HIS247 4.1 80.4 1.0 NE2 B:HIS242 4.1 87.3 1.0 CE1 B:HIS579 4.2 85.3 1.0 ND1 B:HIS247 4.2 79.4 1.0 CE1 B:HIS242 4.2 83.0 1.0 CB B:ASP352 4.3 86.3 1.0 CB B:ASP246 4.5 90.7 1.0 NE2 B:HIS579 4.7 87.4 1.0 CG1 B:VAL191 4.8 89.9 1.0 ND1 B:HIS244 4.9 90.9 1.0

Zinc binding site 5 out of 5 in the Structure of the Archaeal Beta-Casp Protein with N-Terminal Kh Domains From Methanothermobacter Thermautotrophicus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Archaeal Beta-Casp Protein with N-Terminal Kh Domains From Methanothermobacter Thermautotrophicus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1638 b:72.4 occ:1.00 O3 B:PO41639 2.0 87.4 1.0 ND1 B:HIS244 2.1 90.9 1.0 NE2 B:HIS242 2.1 87.3 1.0 NE2 B:HIS329 2.1 91.5 1.0 OD2 B:ASP352 2.1 94.2 1.0 O1 B:PO41639 2.2 93.6 1.0 P B:PO41639 2.6 89.9 1.0 CE1 B:HIS244 2.9 90.8 1.0 CD2 B:HIS242 2.9 84.9 1.0 CD2 B:HIS329 3.0 86.3 1.0 CE1 B:HIS329 3.0 90.0 1.0 CE1 B:HIS242 3.0 83.0 1.0 CG B:ASP352 3.1 87.4 1.0 CG B:HIS244 3.2 88.5 1.0 ZN B:ZN1637 3.5 71.6 1.0 CB B:ASP352 3.5 86.3 1.0 O4 B:PO41639 3.7 86.0 1.0 CB B:HIS244 3.7 85.4 1.0 O2 B:PO41639 3.8 90.2 1.0 CG B:HIS242 4.0 82.8 1.0 ND1 B:HIS242 4.0 81.7 1.0 NE2 B:HIS244 4.1 92.7 1.0 ND1 B:HIS329 4.1 87.7 1.0 CG B:HIS329 4.1 85.2 1.0 NE2 B:HIS247 4.1 86.2 1.0 CD2 B:HIS247 4.1 83.0 1.0 CD2 B:HIS244 4.2 91.3 1.0 OD1 B:ASP352 4.3 86.0 1.0 OD1 B:ASP246 4.5 93.9 1.0 CE1 B:HIS579 4.5 85.3 1.0 NE2 B:HIS579 4.6 87.4 1.0 OD2 B:ASP246 4.7 94.5 1.0 CA B:ASP352 5.0 83.7 1.0

A.P.G.Silva, M.Chechik, R.T.Byrne, D.G.Waterman, C.L.Ng, E.J.Dodson, E.V.Koonin, A.A.Antson, C.Smits. Structure and Activity of A Novel Archaeal Beta-Casp Protein with N-Terminal Kh Domains. Structure V. 19 622 2011.
ISSN: ISSN 0969-2126
PubMed: 21565697
DOI: 10.1016/J.STR.2011.03.002