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Gold in PDB 3odm: Archaeal-Type Phosphoenolpyruvate Carboxylase

Enzymatic activity of Archaeal-Type Phosphoenolpyruvate Carboxylase

All present enzymatic activity of Archaeal-Type Phosphoenolpyruvate Carboxylase:
4.1.1.31;

Protein crystallography data

The structure of Archaeal-Type Phosphoenolpyruvate Carboxylase, PDB code: 3odm was solved by P.W.Dunten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.84 / 2.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 121.420, 161.580, 279.980, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.3

Gold Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Gold atom in the Archaeal-Type Phosphoenolpyruvate Carboxylase (pdb code 3odm). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 36 binding sites of Gold where determined in the Archaeal-Type Phosphoenolpyruvate Carboxylase, PDB code: 3odm:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Gold binding site 1 out of 36 in 3odm

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Gold binding site 1 out of 36 in the Archaeal-Type Phosphoenolpyruvate Carboxylase


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Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Archaeal-Type Phosphoenolpyruvate Carboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au607

b:67.5
occ:0.99
AU A:AUC607 0.0 67.5 1.0
C2 A:AUC607 1.8 65.8 1.0
C1 A:AUC607 1.8 66.3 1.0
N2 A:AUC607 3.0 65.3 1.0
N1 A:AUC607 3.0 66.1 1.0
OD2 A:ASP48 3.6 49.0 1.0
NE2 A:HIS11 3.6 43.9 1.0
CD2 A:HIS11 3.7 43.5 1.0
CE1 A:HIS11 3.7 42.8 1.0
CG A:HIS11 3.8 41.3 1.0
ND1 A:HIS11 3.8 41.9 1.0
CG A:ASP48 3.9 45.5 1.0
NH1 A:ARG82 4.1 40.5 1.0
CA A:HIS11 4.1 40.8 1.0
CZ A:ARG82 4.2 42.0 1.0
N A:HIS11 4.2 40.2 1.0
CB A:ASP48 4.2 42.0 1.0
NH2 A:ARG344 4.3 57.9 1.0
NE A:ARG82 4.3 40.9 1.0
C A:GLN10 4.3 40.4 1.0
CD A:ARG82 4.4 38.8 1.0
OD1 A:ASP48 4.4 48.8 1.0
O A:GLN10 4.4 41.0 1.0
O A:HOH762 4.5 30.6 1.0
CB A:HIS11 4.6 41.0 1.0
NH2 A:ARG82 4.7 44.4 1.0
O8 A:MLI901 4.9 41.5 0.7
N A:GLN10 4.9 39.5 1.0
CD A:PRO12 4.9 42.2 1.0

Gold binding site 2 out of 36 in 3odm

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Gold binding site 2 out of 36 in the Archaeal-Type Phosphoenolpyruvate Carboxylase


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Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Archaeal-Type Phosphoenolpyruvate Carboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au608

b:74.7
occ:1.00
SG A:CYS5 1.5 58.6 1.0
CB A:CYS5 3.1 57.0 1.0
N A:CYS5 3.4 55.9 1.0
CA A:CYS5 3.8 55.1 1.0
CG2 A:ILE293 3.8 62.4 1.0
CG A:LYS290 4.0 61.8 1.0
OE1 A:GLU43 4.1 63.2 1.0
CA A:LYS290 4.1 61.3 1.0
CB A:LYS290 4.4 62.2 1.0
CD A:LYS290 4.4 66.0 1.0
C A:PRO4 4.5 55.2 1.0
CB A:ILE293 4.6 60.2 1.0
O A:LYS290 4.6 64.5 1.0
CG1 A:ILE293 4.8 58.5 1.0
CA A:PRO4 4.8 56.3 1.0
C A:LYS290 4.9 63.7 1.0
N A:LYS290 5.0 59.5 1.0
C A:CYS5 5.0 53.0 1.0

Gold binding site 3 out of 36 in 3odm

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Gold binding site 3 out of 36 in the Archaeal-Type Phosphoenolpyruvate Carboxylase


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Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of Archaeal-Type Phosphoenolpyruvate Carboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au624

b:71.8
occ:0.24
OE2 A:GLU279 2.9 74.2 1.0
CD A:GLU279 3.1 72.4 1.0
OE1 A:GLU279 3.1 72.8 1.0
CD2 A:LEU40 3.4 52.3 1.0
O A:GLY38 3.5 65.1 1.0
CG A:LEU40 3.7 51.8 1.0
C A:GLY39 4.0 59.2 1.0
N A:LEU40 4.1 56.1 1.0
CG A:GLU279 4.2 69.0 1.0
CA A:GLY39 4.3 60.6 1.0
O A:GLY39 4.3 61.3 1.0
NZ A:LYS30 4.3 68.8 1.0
CG A:LYS30 4.3 57.2 1.0
C A:GLY38 4.4 65.8 1.0
NZ A:LYS283 4.5 66.4 1.0
CE A:LYS30 4.5 67.5 1.0
CA A:LEU40 4.5 54.6 1.0
CD A:LYS283 4.7 61.7 1.0
CB A:GLU279 4.7 67.8 1.0
CB A:LEU40 4.7 52.4 1.0
N A:GLY39 4.8 64.4 1.0
CD1 A:LEU40 4.8 49.6 1.0
CD A:LYS30 5.0 63.9 1.0

Gold binding site 4 out of 36 in 3odm

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Gold binding site 4 out of 36 in the Archaeal-Type Phosphoenolpyruvate Carboxylase


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Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of Archaeal-Type Phosphoenolpyruvate Carboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au631

b:59.9
occ:0.14
AU A:AUC631 0.0 59.9 0.1
C2 A:AUC631 1.8 58.7 0.2
C1 A:AUC631 1.8 58.5 0.2
O A:ASP36 2.8 79.7 1.0
N2 A:AUC631 3.0 58.5 0.2
N1 A:AUC631 3.0 57.9 0.2
C A:ASP36 3.9 76.6 1.0
CA A:LYS37 4.0 73.7 1.0
CG A:LYS37 4.0 75.5 1.0
N A:LYS37 4.4 73.8 1.0
CB A:LYS37 4.5 72.6 1.0
CE A:LYS37 4.8 81.8 1.0

Gold binding site 5 out of 36 in 3odm

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Gold binding site 5 out of 36 in the Archaeal-Type Phosphoenolpyruvate Carboxylase


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Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 5 of Archaeal-Type Phosphoenolpyruvate Carboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au630

b:0.1
occ:0.23
CE H:MET144 2.5 70.7 1.0
CE B:MET144 3.1 76.5 1.0
SD H:MET144 3.1 73.5 0.0
SD B:MET144 3.3 76.4 1.0
CG H:MET144 4.4 74.1 1.0
CG B:MET144 4.4 70.8 1.0
CD1 H:LEU95 4.5 57.1 1.0

Gold binding site 6 out of 36 in 3odm

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Gold binding site 6 out of 36 in the Archaeal-Type Phosphoenolpyruvate Carboxylase


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Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 6 of Archaeal-Type Phosphoenolpyruvate Carboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au609

b:79.6
occ:1.00
SG B:CYS5 1.6 63.0 1.0
CB B:CYS5 3.2 61.6 1.0
CG B:LYS290 3.5 69.8 1.0
N B:CYS5 3.6 60.6 1.0
OE1 B:GLU43 3.6 64.1 1.0
CG2 B:ILE293 3.9 72.4 1.0
CA B:LYS290 3.9 70.4 1.0
CA B:CYS5 4.0 60.7 1.0
CB B:LYS290 4.3 70.2 1.0
O B:LYS290 4.4 73.3 1.0
C B:PRO4 4.6 60.5 1.0
CD B:GLU43 4.6 62.6 1.0
C B:LYS290 4.6 72.3 1.0
CB B:ILE293 4.7 71.4 1.0
N B:LYS290 4.8 69.3 1.0
CD B:LYS290 4.8 69.2 1.0
OE2 B:GLU43 4.8 64.5 1.0
CE B:LYS290 4.9 67.5 1.0
CA B:PRO4 4.9 60.0 1.0
O B:ILE3 5.0 64.3 1.0

Gold binding site 7 out of 36 in 3odm

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Gold binding site 7 out of 36 in the Archaeal-Type Phosphoenolpyruvate Carboxylase


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Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 7 of Archaeal-Type Phosphoenolpyruvate Carboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au610

b:86.9
occ:0.51
AU B:AUC610 0.0 86.9 0.5
C2 B:AUC610 1.8 84.0 0.6
C1 B:AUC610 1.8 84.1 0.6
N2 B:AUC610 3.0 83.2 0.6
N1 B:AUC610 3.0 82.4 0.6
OD2 B:ASP48 3.1 66.1 1.0
NH1 B:ARG82 3.1 60.1 1.0
CG B:ASP48 3.5 61.0 1.0
NE2 B:HIS11 3.7 60.8 1.0
CD2 B:HIS11 3.7 59.6 1.0
NH2 B:ARG344 3.8 78.5 1.0
NH1 B:ARG344 3.8 74.9 1.0
CE1 B:HIS11 3.9 59.2 1.0
CG B:HIS11 3.9 56.8 1.0
CZ B:ARG82 4.0 60.5 1.0
ND1 B:HIS11 4.0 57.2 1.0
OD1 B:ASP48 4.0 63.8 1.0
CZ B:ARG344 4.2 76.2 1.0
CB B:ASP48 4.2 56.2 1.0
CA B:HIS11 4.2 54.0 1.0
N B:HIS11 4.3 52.4 1.0
O B:GLN10 4.3 53.3 1.0
C B:GLN10 4.4 52.0 1.0
NH2 B:ARG82 4.5 62.7 1.0
CB B:HIS11 4.7 55.2 1.0
AU B:AUC640 4.8 93.8 0.3
NE B:ARG82 4.9 59.2 1.0

Gold binding site 8 out of 36 in 3odm

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Gold binding site 8 out of 36 in the Archaeal-Type Phosphoenolpyruvate Carboxylase


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 8 of Archaeal-Type Phosphoenolpyruvate Carboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au622

b:69.8
occ:0.27
OE1 B:GLU279 2.5 68.9 1.0
CD2 B:LEU40 2.6 51.3 1.0
CD B:GLU279 3.1 65.5 1.0
O B:GLY38 3.4 56.7 1.0
CD B:LYS30 3.5 56.5 1.0
OE2 B:GLU279 3.7 65.5 1.0
CG B:LEU40 3.8 50.3 1.0
NZ B:LYS30 3.8 63.0 1.0
CE B:LYS30 3.9 60.2 1.0
CG B:GLU279 3.9 61.6 1.0
C B:GLY39 4.2 54.0 1.0
N B:LEU40 4.3 52.3 1.0
CA B:GLY39 4.4 54.3 1.0
CB B:GLU279 4.5 59.3 1.0
CG B:LYS30 4.5 53.9 1.0
C B:GLY38 4.5 56.9 1.0
O B:GLY39 4.5 55.3 1.0
CA B:LEU40 4.7 51.7 1.0
CB B:LEU40 4.8 51.0 1.0
CD1 B:LEU40 4.8 49.0 1.0
N B:GLY39 5.0 56.1 1.0

Gold binding site 9 out of 36 in 3odm

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Gold binding site 9 out of 36 in the Archaeal-Type Phosphoenolpyruvate Carboxylase


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Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 9 of Archaeal-Type Phosphoenolpyruvate Carboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au638

b:86.5
occ:0.19
ND1 B:HIS284 3.4 65.4 1.0
CE1 B:HIS284 3.5 67.3 1.0
CG B:GLU251 3.7 61.5 1.0
CB B:GLU251 4.0 60.6 1.0
CG B:HIS284 4.0 63.8 1.0
NE2 B:HIS284 4.1 67.9 1.0
O B:GLU251 4.2 63.3 1.0
O B:HOH845 4.3 52.3 1.0
C B:GLU251 4.3 62.7 1.0
CD2 B:HIS284 4.4 66.7 1.0
N B:GLU252 4.6 64.2 1.0
CB B:HIS284 4.7 60.8 1.0
CA B:GLU251 4.8 60.7 1.0
CA B:GLU252 4.8 66.7 1.0

Gold binding site 10 out of 36 in 3odm

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Gold binding site 10 out of 36 in the Archaeal-Type Phosphoenolpyruvate Carboxylase


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Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 10 of Archaeal-Type Phosphoenolpyruvate Carboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au640

b:93.8
occ:0.34
NH1 B:ARG82 2.7 60.1 1.0
NH2 B:ARG82 3.2 62.7 1.0
CZ B:ARG82 3.2 60.5 1.0
CE B:MET197 3.3 57.2 1.0
NE2 B:HIS11 3.4 60.8 1.0
CE1 B:HIS11 3.4 59.2 1.0
NE B:ARG82 4.2 59.2 1.0
CD2 B:LEU163 4.4 63.4 1.0
SD B:MET46 4.4 65.3 1.0
CE B:MET46 4.6 64.0 1.0
SD B:MET197 4.7 56.6 1.0
ND1 B:HIS11 4.7 57.2 1.0
CD2 B:HIS11 4.8 59.6 1.0
AU B:AUC610 4.8 86.9 0.5
CD B:ARG82 4.9 56.4 1.0

Reference:

L.Dharmarajan, J.L.Kraszewski, B.Mukhopadhyay, P.W.Dunten. Structure of An Archaeal-Type Phosphoenolpyruvate Carboxylase Sensitive to Inhibition By Aspartate. Proteins V. 79 1820 2011.
ISSN: ISSN 0887-3585
PubMed: 21491491
DOI: 10.1002/PROT.23006
Page generated: Sat Dec 12 01:53:48 2020

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