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Magnesium in PDB 1xd3: Crystal Structure of UCHL3-Ubvme Complex

Enzymatic activity of Crystal Structure of UCHL3-Ubvme Complex

All present enzymatic activity of Crystal Structure of UCHL3-Ubvme Complex:
3.4.19.12;

Protein crystallography data

The structure of Crystal Structure of UCHL3-Ubvme Complex, PDB code: 1xd3 was solved by S.Misaghi, P.J.Galardy, W.J.N.Meester, H.Ovaa, H.L.Ploegh, R.Gaudet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.76 / 1.45
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.110, 49.290, 67.620, 86.12, 75.03, 76.78
R / Rfree (%) 16.6 / 19.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of UCHL3-Ubvme Complex (pdb code 1xd3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of UCHL3-Ubvme Complex, PDB code: 1xd3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 1xd3

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Magnesium binding site 1 out of 10 in the Crystal Structure of UCHL3-Ubvme Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of UCHL3-Ubvme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2006

b:44.6
occ:1.00
 OD1 A:ASP109 1.9 30.5 1.0
O A:HOH2346 2.0 38.2 1.0
CG A:ASP109 3.1 29.5 1.0
CA A:ASP109 3.3 13.7 1.0
N A:ASP109 3.4 14.1 1.0
CG A:LYS108 3.6 20.0 1.0
C A:LYS108 3.7 12.7 1.0
NZ A:LYS108 3.7 29.8 1.0
CB A:ASP109 3.8 18.1 1.0
O A:LYS108 3.8 12.5 1.0
CD A:LYS108 4.0 25.5 1.0
CB A:LYS108 4.0 12.4 1.0
OD2 A:ASP109 4.1 36.2 1.0
O A:HOH2097 4.2 24.3 1.0
CA A:LYS108 4.5 12.8 1.0
CE A:LYS108 4.5 24.9 1.0
O A:HOH2299 4.6 39.2 1.0
C A:ASP109 4.6 14.2 1.0
O A:HOH2120 4.7 26.4 1.0

Magnesium binding site 2 out of 10 in 1xd3

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Magnesium binding site 2 out of 10 in the Crystal Structure of UCHL3-Ubvme Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of UCHL3-Ubvme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2009

b:47.2
occ:1.00
 O A:HOH2264 2.2 35.4 1.0
O A:HOH2305 2.2 39.3 1.0
O A:HOH2047 3.9 16.1 1.0
O A:HOH2188 3.9 34.7 1.0
O A:HOH2227 4.1 28.6 1.0
CB A:PRO46 4.4 14.0 1.0
CG A:PRO46 4.8 15.1 1.0
CA A:PRO46 4.9 11.9 1.0

Magnesium binding site 3 out of 10 in 1xd3

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Magnesium binding site 3 out of 10 in the Crystal Structure of UCHL3-Ubvme Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of UCHL3-Ubvme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2010

b:45.9
occ:1.00
 OE2 A:GLU114 2.1 40.1 1.0
CD A:GLU114 2.8 28.5 1.0
O A:LYS21 2.8 12.9 1.0
O A:HOH2317 3.1 41.2 1.0
O A:LEU25 3.4 15.4 1.0
OE1 A:GLU114 3.4 32.4 1.0
CA A:GLY24 3.6 13.7 1.0
C A:GLY24 3.6 9.8 1.0
CG A:GLU114 3.6 17.8 1.0
C A:LYS21 3.7 13.5 1.0
N A:LEU25 3.8 10.1 1.0
CA A:LYS21 3.8 11.0 1.0
CG A:LYS21 3.9 16.5 1.0
C A:LEU25 3.9 12.3 1.0
O A:GLY24 4.1 11.5 1.0
N A:GLY24 4.1 11.4 1.0
O A:HOH2102 4.3 19.1 1.0
O C:HOH2204 4.4 37.2 1.0
CB A:LYS21 4.4 11.0 1.0
CA A:LEU25 4.5 9.9 1.0
N A:HIS26 4.6 11.3 1.0
CA A:HIS26 4.8 13.8 1.0
O A:LEU20 4.8 12.5 1.0
CB A:GLU114 4.9 14.1 1.0
N A:GLN22 5.0 12.5 1.0

Magnesium binding site 4 out of 10 in 1xd3

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Magnesium binding site 4 out of 10 in the Crystal Structure of UCHL3-Ubvme Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of UCHL3-Ubvme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2001

b:40.6
occ:1.00
 OD2 C:ASP163 2.1 34.8 1.0
O C:HOH2129 2.1 31.7 1.0
O C:HOH2193 2.2 25.2 1.0
O C:HOH2366 2.6 44.8 1.0
CG C:ASP163 3.0 33.1 1.0
OD1 C:ASP163 3.4 29.2 1.0
CB C:ASP163 4.4 26.4 1.0
O C:HOH2422 4.5 52.9 1.0
O C:HOH2143 4.7 27.6 1.0
CG2 C:ILE162 4.7 27.3 1.0
O C:HOH2274 4.8 37.2 1.0

Magnesium binding site 5 out of 10 in 1xd3

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Magnesium binding site 5 out of 10 in the Crystal Structure of UCHL3-Ubvme Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of UCHL3-Ubvme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2002

b:28.7
occ:1.00
 O C:HOH2281 2.0 32.2 1.0
O C:HOH2194 2.1 28.7 1.0
O C:HOH2150 2.2 28.0 1.0
O C:HOH2199 4.1 28.4 1.0
OD1 C:ASP109 4.4 24.0 1.0
O C:ASP109 4.4 19.3 1.0
O C:HOH2073 4.5 18.3 1.0
CA C:ASP109 4.9 13.9 1.0

Magnesium binding site 6 out of 10 in 1xd3

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Magnesium binding site 6 out of 10 in the Crystal Structure of UCHL3-Ubvme Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of UCHL3-Ubvme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2003

b:20.7
occ:1.00
 NE2 C:HIS179 2.1 18.7 1.0
O C:HOH2191 2.1 24.8 1.0
O C:HOH2185 2.1 25.3 1.0
CE1 C:HIS179 3.0 19.2 1.0
CD2 C:HIS179 3.2 12.9 1.0
O C:HOH2181 4.0 26.7 1.0
ND1 C:HIS179 4.1 22.5 1.0
O C:HOH2095 4.2 21.3 1.0
CG C:HIS179 4.3 12.8 1.0
OD2 C:ASP79 4.4 15.9 0.5

Magnesium binding site 7 out of 10 in 1xd3

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Magnesium binding site 7 out of 10 in the Crystal Structure of UCHL3-Ubvme Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of UCHL3-Ubvme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2004

b:26.2
occ:1.00
 O C:HOH2249 2.0 25.2 1.0
O C:HOH2169 2.1 20.8 1.0
O C:HOH2072 2.1 27.1 1.0
O C:HOH2397 2.1 33.0 1.0
O C:HOH2425 2.2 27.3 1.0
O C:HOH2229 3.6 44.1 1.0
O C:HOH2277 4.1 37.8 1.0
O C:HOH2353 4.3 39.9 1.0
O C:HOH2115 4.4 24.1 1.0
O C:ALA159 4.4 15.4 1.0
NE2 C:HIS153 4.9 24.3 1.0
CD2 C:HIS153 5.0 17.6 1.0

Magnesium binding site 8 out of 10 in 1xd3

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Magnesium binding site 8 out of 10 in the Crystal Structure of UCHL3-Ubvme Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of UCHL3-Ubvme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2005

b:40.4
occ:1.00
 OD1 C:ASP79 1.9 12.8 0.5
O C:HOH2190 2.1 24.7 1.0
O C:HOH2181 2.7 26.7 1.0
N C:ASP79 3.0 11.0 0.5
N C:ASP79 3.0 10.4 0.5
CG C:ASP79 3.2 13.6 0.5
O C:HOH2158 3.6 29.0 1.0
CA C:GLN78 3.6 8.9 1.0
O C:HOH2065 3.7 23.7 1.0
C C:GLN78 3.8 9.5 1.0
CB C:ASP79 3.8 18.1 0.5
CB C:GLN78 3.9 8.6 1.0
CB C:ASP79 4.0 14.6 0.5
CA C:ASP79 4.0 13.2 0.5
CA C:ASP79 4.0 11.8 0.5
OD2 C:ASP79 4.1 15.9 0.5
ND2 C:ASN192 4.1 13.3 1.0
O C:ASP79 4.3 14.1 0.5
O C:ASP79 4.3 11.7 0.5
CG C:ASN192 4.3 12.1 1.0
CB C:ASN192 4.4 10.4 1.0
O C:HOH2206 4.6 23.7 1.0
C C:ASP79 4.6 11.4 0.5
C C:ASP79 4.6 11.8 0.5
O C:HOH2191 4.7 24.8 1.0
O C:HOH2045 4.9 16.4 1.0
OD1 C:ASN192 4.9 13.8 1.0
N C:GLN78 4.9 8.4 1.0
O C:GLN78 5.0 10.2 1.0
CG C:GLN78 5.0 10.0 1.0

Magnesium binding site 9 out of 10 in 1xd3

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Magnesium binding site 9 out of 10 in the Crystal Structure of UCHL3-Ubvme Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of UCHL3-Ubvme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2007

b:43.0
occ:1.00
 OE1 C:GLU149 2.0 35.4 1.0
O C:HOH2069 2.9 22.4 1.0
CD C:GLU149 2.9 30.4 1.0
O C:HOH2433 2.9 31.8 1.0
O C:HOH2078 3.0 23.9 1.0
O C:HOH2282 3.2 45.8 1.0
OE2 C:GLU149 3.4 37.2 1.0
CG2 C:VAL146 3.8 18.2 1.0
CG C:GLU149 4.0 18.4 1.0
CA C:VAL146 4.1 12.9 1.0
CB C:GLU149 4.1 13.0 1.0
CG1 C:VAL146 4.1 18.8 1.0
O C:HOH2283 4.1 36.1 1.0
NH1 C:ARG145 4.2 21.8 1.0
CB C:VAL146 4.2 12.3 1.0
O C:VAL146 4.6 11.8 1.0
O C:HOH2052 4.8 22.0 1.0
C C:VAL146 4.9 10.7 1.0
N C:VAL146 5.0 10.9 1.0

Magnesium binding site 10 out of 10 in 1xd3

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Magnesium binding site 10 out of 10 in the Crystal Structure of UCHL3-Ubvme Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of UCHL3-Ubvme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2008

b:44.6
occ:1.00
 OD2 C:ASP79 1.9 26.3 0.5
OH C:TYR181 2.8 12.8 1.0
OD2 C:ASP79 2.8 15.9 0.5
CG C:ASP79 2.9 22.2 0.5
O C:HOH2022 3.3 17.1 1.0
N C:THR81 3.3 13.0 1.0
O C:HOH2103 3.4 25.9 1.0
O C:ASP79 3.5 14.1 0.5
CG C:ASP79 3.5 13.6 0.5
C C:ASP79 3.5 11.8 0.5
C C:ASP79 3.6 11.4 0.5
CB C:ASP79 3.6 18.1 0.5
O C:ASP79 3.6 11.7 0.5
CB C:ASP79 3.6 14.6 0.5
N C:VAL80 3.7 12.5 1.0
C C:VAL80 3.8 13.0 1.0
ND2 C:ASN192 3.9 13.3 1.0
OD1 C:ASP79 3.9 23.2 0.5
CA C:VAL80 3.9 9.8 1.0
ND1 C:HIS179 4.0 22.5 1.0
CA C:THR81 4.0 15.6 1.0
CB C:THR81 4.1 20.9 1.0
CZ C:TYR181 4.1 12.4 1.0
CA C:ASP79 4.2 13.2 0.5
CA C:ASP79 4.2 11.8 0.5
O C:HOH2335 4.3 43.2 1.0
CE1 C:HIS179 4.3 19.2 1.0
OD1 C:ASP79 4.5 12.8 0.5
CG C:HIS179 4.5 12.8 1.0
O C:HOH2319 4.7 38.1 1.0
O C:VAL80 4.7 15.3 1.0
CG2 C:THR81 4.7 17.6 1.0
CE1 C:TYR181 4.8 10.6 1.0
NE2 C:HIS179 5.0 18.7 1.0
O C:HOH2136 5.0 28.8 1.0

Reference:

S.Misaghi, P.J.Galardy, W.J.N.Meester, H.Ovaa, H.L.Ploegh, R.Gaudet. Structure of the Ubiquitin Hydrolase Uch-L3 Complexed with A Suicide Substrate J.Biol.Chem. V. 280 1512 2005.
ISSN: ISSN 0021-9258
PubMed: 15531586
DOI: 10.1074/JBC.M410770200
Page generated: Tue Aug 13 17:30:52 2024

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