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Zinc in PDB 2iv0: Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers

Enzymatic activity of Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers

All present enzymatic activity of Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers:
1.1.1.42;

Protein crystallography data

The structure of Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers, PDB code: 2iv0 was solved by R.Stokke, M.Karlstrom, N.Yang, I.Leiros, R.Ladenstein, N.K.Birkeland, I.H.Steen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 86.71 / 2.5
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.611, 65.405, 87.181, 90.00, 95.28, 90.00
R / Rfree (%) 19.6 / 25.4

Other elements in 2iv0:

The structure of Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers (pdb code 2iv0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers, PDB code: 2iv0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 2iv0

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Zinc binding site 1 out of 9 in the Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1413

b:11.6
occ:1.00
 O A:HOH2066 2.0 2.0 1.0
OD2 A:ASP26 2.0 13.9 1.0
CG A:ASP26 2.9 10.1 1.0
OD1 A:ASP26 3.0 9.6 1.0
O A:GLY58 4.3 12.4 1.0
CB A:ASP26 4.3 9.5 1.0
CE A:LYS59 4.5 13.2 1.0
O A:HOH2010 4.7 17.4 1.0
NZ A:LYS59 4.9 6.3 1.0

Zinc binding site 2 out of 9 in 2iv0

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Zinc binding site 2 out of 9 in the Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1414

b:34.4
occ:1.00
 O A:GLY393 2.0 19.9 1.0
NE2 A:HIS388 2.4 21.5 1.0
C A:GLY393 3.2 19.5 1.0
CE1 A:HIS388 3.3 22.1 1.0
CD2 A:HIS388 3.4 21.4 1.0
N A:GLY393 4.0 20.8 1.0
N A:LYS395 4.1 18.6 1.0
N A:THR394 4.1 19.1 1.0
CA A:THR394 4.2 19.4 1.0
CA A:GLY393 4.2 19.7 1.0
ND1 A:HIS388 4.5 21.4 1.0
CG A:HIS388 4.6 21.2 1.0
C A:THR394 4.6 18.9 1.0
C A:GLY392 4.8 21.9 1.0
CB A:LYS395 5.0 18.9 1.0

Zinc binding site 3 out of 9 in 2iv0

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Zinc binding site 3 out of 9 in the Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1415

b:15.1
occ:1.00
 OD2 B:ASP277 1.8 15.5 1.0
OD1 A:ASP301 2.0 18.4 1.0
OD2 A:ASP305 2.1 22.5 1.0
CL A:CL1418 2.8 20.5 1.0
CG B:ASP277 2.9 14.6 1.0
CG A:ASP301 3.0 16.2 1.0
CG A:ASP305 3.0 16.4 1.0
OD2 A:ASP301 3.3 16.8 1.0
OD1 A:ASP305 3.4 16.6 1.0
CB B:ASP277 3.5 12.8 1.0
O A:ASP301 4.0 13.5 1.0
OD1 B:ASP277 4.0 15.6 1.0
CB A:ASP301 4.3 15.4 1.0
CB A:ASP305 4.4 12.0 1.0
NH2 A:ARG125 4.4 30.0 1.0
C A:ASP301 4.4 14.7 1.0
CA A:ASP301 4.6 15.4 1.0
NZ B:LYS223 4.8 11.0 1.0
CA B:ASP277 4.8 13.2 1.0
O B:ASP277 4.9 14.3 1.0
C B:ASP277 4.9 13.7 1.0

Zinc binding site 4 out of 9 in 2iv0

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Zinc binding site 4 out of 9 in the Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1416

b:53.9
occ:1.00
 OE2 A:GLU196 2.6 22.2 1.0
CD A:GLU196 3.0 20.3 1.0
OE1 A:GLU196 3.0 23.2 1.0
NZ A:LYS200 3.7 8.5 1.0
OE1 A:GLU240 3.7 17.8 1.0
CG A:GLU196 4.2 16.6 1.0
NH1 B:ARG163 4.3 6.9 1.0
NH2 B:ARG163 4.6 10.4 1.0
NE1 A:TRP237 4.7 7.8 1.0
CD A:GLU240 4.8 18.1 1.0
CZ B:ARG163 4.9 9.5 1.0
CD1 A:TRP237 4.9 6.9 1.0
O B:HOH2009 4.9 2.2 1.0

Zinc binding site 5 out of 9 in 2iv0

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Zinc binding site 5 out of 9 in the Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1413

b:24.1
occ:1.00
 OE2 B:GLU400 1.9 4.2 1.0
O B:HOH2028 2.5 4.7 1.0
CD B:GLU400 3.0 5.1 1.0
OE1 B:GLU400 3.4 3.7 1.0
NH1 B:ARG399 3.5 15.4 1.0
O B:HOH2026 3.6 4.6 1.0
ND2 B:ASN343 3.9 2.0 1.0
CG B:GLU400 4.2 5.7 1.0
CZ B:ARG399 4.7 12.6 1.0

Zinc binding site 6 out of 9 in 2iv0

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Zinc binding site 6 out of 9 in the Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1414

b:10.7
occ:1.00
 OD2 B:ASP305 1.9 9.2 1.0
OD2 A:ASP277 2.0 14.4 1.0
OD1 B:ASP301 2.1 15.3 1.0
CL B:CL1418 2.7 20.9 1.0
CG B:ASP301 2.9 12.9 1.0
CG B:ASP305 3.0 10.0 1.0
CG A:ASP277 3.1 13.3 1.0
OD2 B:ASP301 3.1 11.8 1.0
OD1 B:ASP305 3.4 10.9 1.0
O A:HOH2040 3.5 17.3 1.0
CB A:ASP277 3.5 12.3 1.0
O B:ASP301 4.1 13.4 1.0
OD1 A:ASP277 4.2 14.8 1.0
CB B:ASP305 4.3 7.3 1.0
CB B:ASP301 4.3 12.7 1.0
NZ A:LYS223 4.5 21.0 1.0
C B:ASP301 4.6 12.3 1.0
NH1 B:ARG125 4.7 29.2 1.0
CA B:ASP301 4.7 12.2 1.0
O B:HOH2023 4.8 4.7 1.0
CA A:ASP277 4.9 12.2 1.0

Zinc binding site 7 out of 9 in 2iv0

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Zinc binding site 7 out of 9 in the Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1415

b:49.6
occ:1.00
 OE2 B:GLU240 2.7 17.8 1.0
OE1 B:GLU240 2.8 20.4 1.0
CD B:GLU240 3.0 14.2 1.0
CG B:GLU240 4.4 13.3 1.0
OE1 B:GLN244 4.6 15.5 1.0
NZ B:LYS200 4.6 2.0 1.0
NE2 B:GLN244 4.7 16.1 1.0
OE2 B:GLU196 4.7 24.9 1.0

Zinc binding site 8 out of 9 in 2iv0

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Zinc binding site 8 out of 9 in the Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1416

b:34.5
occ:1.00
 OE1 B:GLU196 2.4 22.1 1.0
OE2 B:GLU196 2.5 24.9 1.0
CD B:GLU196 2.8 20.1 1.0
NZ B:LYS200 3.5 2.0 1.0
NH2 A:ARG163 4.0 8.8 1.0
CG B:GLU196 4.3 14.2 1.0
CE B:LYS200 4.8 4.8 1.0

Zinc binding site 9 out of 9 in 2iv0

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Zinc binding site 9 out of 9 in the Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1417

b:19.8
occ:1.00
 OE2 B:GLU141 2.0 13.0 1.0
ND1 B:HIS139 2.0 3.1 1.0
CD B:GLU141 2.8 11.7 1.0
CE1 B:HIS139 2.8 2.0 1.0
OE1 B:GLU141 3.0 13.8 1.0
CG B:HIS139 3.1 2.1 1.0
CB B:HIS139 3.5 2.3 1.0
NZ B:LYS142 3.7 18.9 1.0
CA B:HIS139 3.7 3.0 1.0
O B:LYS138 3.8 2.3 1.0
NE2 B:HIS139 4.0 3.3 1.0
CD2 B:HIS139 4.1 2.0 1.0
CG B:GLU141 4.2 10.2 1.0
C B:LYS138 4.5 2.0 1.0
N B:HIS139 4.5 2.0 1.0
C B:HIS139 4.7 3.4 1.0

Reference:

R.Stokke, M.Karlstrom, N.Yang, I.Leiros, R.Ladenstein, N.K.Birkeland, I.H.Steen. Thermal Stability of Isocitrate Dehydrogenase From Archaeoglobus Fulgidus Studied By Crystal Structure Analysis and Engineering of Chimers Extremophiles V. 11 481 2007.
ISSN: ISSN 1431-0651
PubMed: 17401542
DOI: 10.1007/S00792-006-0060-Z
Page generated: Thu Oct 17 01:00:30 2024

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