Atomistry » Gold » PDB 3l47-5ix6 » 3odm
Atomistry »
  Gold »
    PDB 3l47-5ix6 »
      3odm »

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

Go back to Gold Binding Sites List in 3odm
Gold binding site 1 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 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

Go back to Gold Binding Sites List in 3odm
Gold binding site 2 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 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

Go back to Gold Binding Sites List in 3odm
Gold binding site 3 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 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

Go back to Gold Binding Sites List in 3odm
Gold binding site 4 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 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

Go back to Gold Binding Sites List in 3odm
Gold binding site 5 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 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

Go back to Gold Binding Sites List in 3odm
Gold binding site 6 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 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

Go back to Gold Binding Sites List in 3odm
Gold binding site 7 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 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

Go back to Gold Binding Sites List in 3odm
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

Go back to Gold Binding Sites List in 3odm
Gold binding site 9 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 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

Go back to Gold Binding Sites List in 3odm
Gold binding site 10 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 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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy