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Zinc in PDB 1oi0: Crystal Structure of AF2198, A JAB1/Mpn Domain Protein From Archaeoglobus Fulgidus

Protein crystallography data

The structure of Crystal Structure of AF2198, A JAB1/Mpn Domain Protein From Archaeoglobus Fulgidus, PDB code: 1oi0 was solved by H.J.T.T.Tran, M.D.Allen, J.Lowe, M.Bycroft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 37.787, 87.081, 67.827, 90.00, 94.00, 90.00
R / Rfree (%) 21.3 / 24.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of AF2198, A JAB1/Mpn Domain Protein From Archaeoglobus Fulgidus (pdb code 1oi0). 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 AF2198, A JAB1/Mpn Domain Protein From Archaeoglobus Fulgidus, PDB code: 1oi0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1oi0

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Zinc binding site 1 out of 4 in the Crystal Structure of AF2198, A JAB1/Mpn Domain Protein From Archaeoglobus Fulgidus


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 AF2198, A JAB1/Mpn Domain Protein From Archaeoglobus Fulgidus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:17.9
occ:1.00
NE2 A:HIS72 2.1 18.5 1.0
OD2 A:ASP83 2.2 15.0 1.0
NE2 A:HIS70 2.2 17.6 1.0
O2 A:144202 2.3 19.1 1.0
OD1 A:ASP83 2.4 15.5 1.0
CG A:ASP83 2.6 15.6 1.0
C1 A:144202 2.6 16.5 1.0
C2 A:144202 2.9 23.6 1.0
CD2 A:HIS72 3.0 15.7 1.0
CE1 A:HIS72 3.0 17.6 1.0
CD2 A:HIS70 3.2 16.8 1.0
CE1 A:HIS70 3.2 15.1 1.0
N A:144202 3.3 24.6 1.0
C3 A:144202 3.9 26.1 1.0
CB A:ASP83 4.1 14.9 1.0
NH1 B:ARG89 4.1 16.4 1.0
ND1 A:HIS72 4.1 16.4 1.0
CG A:HIS72 4.2 14.4 1.0
ND1 A:HIS70 4.3 14.9 1.0
CG A:HIS70 4.3 16.7 1.0
OE1 A:GLU25 4.4 21.2 1.0
C4 A:144202 4.5 25.4 1.0
CD1 A:ILE96 4.5 19.0 1.0
OG A:SER80 4.6 19.1 1.0
NH2 B:ARG89 4.6 15.2 1.0
CZ B:ARG89 4.9 13.6 1.0
CA A:ASP83 5.0 18.1 1.0

Zinc binding site 2 out of 4 in 1oi0

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Zinc binding site 2 out of 4 in the Crystal Structure of AF2198, A JAB1/Mpn Domain Protein From Archaeoglobus Fulgidus


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 AF2198, A JAB1/Mpn Domain Protein From Archaeoglobus Fulgidus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:15.2
occ:1.00
OD2 B:ASP83 2.1 13.1 1.0
NE2 B:HIS72 2.1 17.3 1.0
NE2 B:HIS70 2.2 11.6 1.0
O B:HOH306 2.2 25.6 1.0
O B:HOH305 2.4 23.9 1.0
OD1 B:ASP83 2.6 14.7 1.0
CG B:ASP83 2.6 10.7 1.0
CD2 B:HIS72 3.0 14.3 1.0
CE1 B:HIS72 3.1 15.0 1.0
CD2 B:HIS70 3.1 13.9 1.0
CE1 B:HIS70 3.2 12.0 1.0
CB B:ASP83 4.1 13.7 1.0
CG B:HIS72 4.2 12.8 1.0
ND1 B:HIS72 4.2 13.4 1.0
OG B:SER80 4.2 16.3 1.0
NH1 A:ARG89 4.2 23.6 1.0
ND1 B:HIS70 4.3 15.3 1.0
CG B:HIS70 4.3 11.3 1.0
CD1 B:ILE96 4.5 14.5 1.0
OE1 B:GLU25 4.5 24.7 1.0
NH2 A:ARG89 4.7 21.3 1.0
N B:SER80 4.8 15.0 1.0
CB B:SER80 4.9 16.1 1.0
CZ A:ARG89 5.0 20.6 1.0
CG2 B:ILE96 5.0 13.9 1.0

Zinc binding site 3 out of 4 in 1oi0

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Zinc binding site 3 out of 4 in the Crystal Structure of AF2198, A JAB1/Mpn Domain Protein From Archaeoglobus Fulgidus


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 AF2198, A JAB1/Mpn Domain Protein From Archaeoglobus Fulgidus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:14.5
occ:1.00
NE2 C:HIS72 2.1 16.1 1.0
OD2 C:ASP83 2.1 14.2 1.0
NE2 C:HIS70 2.1 10.8 1.0
O D:HOH301 2.2 32.4 1.0
OD1 C:ASP83 2.6 13.5 1.0
CG C:ASP83 2.7 10.0 1.0
CD2 C:HIS72 3.0 15.2 1.0
CE1 C:HIS72 3.1 11.5 1.0
CD2 C:HIS70 3.1 12.4 1.0
CE1 C:HIS70 3.1 9.5 1.0
O B:HOH301 3.5 7.3 1.0
NH2 D:ARG89 3.5 43.0 1.0
O C:HOH332 4.1 22.4 1.0
CB C:ASP83 4.1 12.3 1.0
CG C:HIS72 4.1 14.2 1.0
O B:HOH312 4.2 26.0 1.0
ND1 C:HIS72 4.2 13.8 1.0
OG C:SER80 4.2 14.7 1.0
ND1 C:HIS70 4.2 13.0 1.0
CG C:HIS70 4.3 12.7 1.0
CD1 C:ILE96 4.4 14.7 1.0
OE1 C:GLU25 4.6 31.5 1.0
CZ D:ARG89 4.7 39.9 1.0
N C:SER80 4.8 17.1 1.0
CB C:SER80 4.9 17.5 1.0
CG1 C:ILE96 4.9 13.5 1.0
OE2 C:GLU25 4.9 31.3 1.0
CG2 C:ILE96 5.0 13.7 1.0
O D:HOH315 5.0 23.3 1.0
OE1 B:GLU16 5.0 24.2 1.0

Zinc binding site 4 out of 4 in 1oi0

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Zinc binding site 4 out of 4 in the Crystal Structure of AF2198, A JAB1/Mpn Domain Protein From Archaeoglobus Fulgidus


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 AF2198, A JAB1/Mpn Domain Protein From Archaeoglobus Fulgidus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:20.8
occ:1.00
NE2 D:HIS72 2.1 19.9 1.0
NE2 D:HIS70 2.2 20.6 1.0
OD2 D:ASP83 2.2 19.0 1.0
O2 D:144202 2.3 21.7 1.0
OD1 D:ASP83 2.4 20.0 1.0
CG D:ASP83 2.6 18.2 1.0
C1 D:144202 2.6 25.3 1.0
C2 D:144202 2.8 25.4 1.0
CE1 D:HIS72 3.0 15.2 1.0
CD2 D:HIS72 3.1 16.0 1.0
CD2 D:HIS70 3.1 17.2 1.0
CE1 D:HIS70 3.2 17.6 1.0
N D:144202 3.2 27.7 1.0
C3 D:144202 3.9 30.1 1.0
CB D:ASP83 4.1 16.6 1.0
NH1 C:ARG89 4.1 20.4 1.0
ND1 D:HIS72 4.1 16.8 1.0
CG D:HIS72 4.2 18.1 1.0
ND1 D:HIS70 4.3 18.4 1.0
CG D:HIS70 4.3 16.7 1.0
OE1 D:GLU25 4.4 21.5 1.0
CD1 D:ILE96 4.4 21.4 1.0
C4 D:144202 4.5 27.1 1.0
OG D:SER80 4.5 22.3 1.0
NH2 C:ARG89 4.7 17.6 1.0
CZ C:ARG89 4.9 20.3 1.0

Reference:

H.J.T.T.Tran, M.D.Allen, J.Lowe, M.Bycroft. The Structure of the JAB1/Mpn Domain and Its Implications For Proteasome Function Biochemistry V. 42 11460 2003.
ISSN: ISSN 0006-2960
PubMed: 14516197
DOI: 10.1021/BI035033G
Page generated: Wed Dec 16 02:59:47 2020

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