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Manganese in PDB 4ywb: Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid

Enzymatic activity of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid

All present enzymatic activity of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid:
4.1.1.32;

Protein crystallography data

The structure of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid, PDB code: 4ywb was solved by M.D.Balan, T.A.Johnson, W.R.Lotosky, M.J.Mcleod, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.21 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.124, 118.732, 86.393, 90.00, 107.27, 90.00
R / Rfree (%) 17.3 / 21

Other elements in 4ywb:

The structure of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid (pdb code 4ywb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid, PDB code: 4ywb:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4ywb

Go back to Manganese Binding Sites List in 4ywb
Manganese binding site 1 out of 4 in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:13.3
occ:0.90
 OD1 A:ASP311 1.9 14.3 1.0
O6 A:OXD704 2.1 17.1 1.0
O5 A:OXD704 2.2 19.4 1.0
O A:HOH1086 2.2 19.7 1.0
NE2 A:HIS264 2.2 16.6 1.0
NZ A:LYS244 2.3 16.0 1.0
C2 A:OXD704 2.8 19.6 1.0
C1 A:OXD704 2.9 20.0 1.0
CG A:ASP311 3.0 14.5 1.0
CD2 A:HIS264 3.2 15.6 1.0
CE1 A:HIS264 3.2 15.5 1.0
OD2 A:ASP311 3.3 16.9 1.0
CE A:LYS244 3.3 14.6 1.0
O4 A:OXD704 4.0 25.2 1.0
NZ A:LYS290 4.1 27.4 1.0
O3 A:OXD704 4.1 24.9 1.0
O A:HOH1066 4.3 21.6 1.0
ND1 A:HIS264 4.3 13.7 1.0
OG A:SER286 4.3 25.2 1.0
O A:HOH1079 4.3 32.6 1.0
CG A:HIS264 4.3 14.6 1.0
O A:HOH923 4.4 26.7 1.0
CB A:ASP311 4.5 15.7 1.0
CD A:LYS244 4.6 14.6 1.0
CB A:SER286 4.8 26.2 1.0
CA A:SER286 4.9 26.6 1.0
O A:ASP311 4.9 16.0 1.0
CZ A:PHE485 4.9 14.4 1.0
CE A:LYS290 5.0 29.1 1.0
CA A:ASP311 5.0 15.2 1.0
CE2 A:PHE485 5.0 15.5 1.0

Manganese binding site 2 out of 4 in 4ywb

Go back to Manganese Binding Sites List in 4ywb
Manganese binding site 2 out of 4 in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn702

b:17.7
occ:0.70
 OE2 A:GLU607 2.1 22.5 1.0
O A:HOH1134 2.1 26.6 1.0
NE2 A:HIS502 2.2 20.8 1.0
O A:HOH1280 2.3 25.9 1.0
O A:HOH947 2.5 22.5 1.0
CD A:GLU607 3.0 22.1 1.0
CE1 A:HIS502 3.1 24.5 1.0
CD2 A:HIS502 3.3 21.1 1.0
OE1 A:GLU607 3.3 23.9 1.0
ND1 A:HIS502 4.3 22.6 1.0
CG A:HIS502 4.4 21.6 1.0
CG A:GLU607 4.4 19.9 1.0
O A:HOH1302 4.4 33.3 1.0
O A:HOH1410 4.5 29.2 1.0
NE2 A:GLN451 4.6 20.4 1.0
O A:LEU498 4.7 17.5 1.0

Manganese binding site 3 out of 4 in 4ywb

Go back to Manganese Binding Sites List in 4ywb
Manganese binding site 3 out of 4 in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn701

b:12.3
occ:0.85
 O6 C:OXD704 2.0 15.3 1.0
OD1 C:ASP311 2.1 16.6 1.0
O5 C:OXD704 2.2 19.2 1.0
O C:HOH1140 2.2 20.1 1.0
NE2 C:HIS264 2.2 15.1 1.0
NZ C:LYS244 2.3 16.3 1.0
C2 C:OXD704 2.8 22.9 1.0
C1 C:OXD704 2.8 19.2 1.0
CG C:ASP311 3.0 13.7 1.0
CE1 C:HIS264 3.2 15.4 1.0
CD2 C:HIS264 3.2 16.1 1.0
OD2 C:ASP311 3.3 15.7 1.0
CE C:LYS244 3.3 14.9 1.0
NZ C:LYS290 3.9 19.6 0.5
O4 C:OXD704 4.0 25.6 1.0
O3 C:OXD704 4.1 25.9 1.0
NZ C:LYS290 4.2 16.8 0.5
O C:HOH1083 4.3 31.6 1.0
ND1 C:HIS264 4.3 14.3 1.0
O C:HOH908 4.3 20.8 1.0
CG C:HIS264 4.3 14.9 1.0
O C:HOH935 4.4 24.6 1.0
OG C:SER286 4.4 26.1 1.0
CB C:ASP311 4.5 14.1 1.0
CE C:LYS290 4.6 18.9 0.5
CD C:LYS244 4.7 15.3 1.0
O C:ASP311 4.9 15.8 1.0
CB C:SER286 4.9 27.7 1.0
CE2 C:PHE485 4.9 16.9 1.0
CZ C:PHE485 4.9 16.4 1.0
CA C:SER286 5.0 27.9 1.0
CA C:ASP311 5.0 14.0 1.0

Manganese binding site 4 out of 4 in 4ywb

Go back to Manganese Binding Sites List in 4ywb
Manganese binding site 4 out of 4 in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn702

b:21.5
occ:0.80
 OE2 C:GLU607 2.0 26.5 1.0
O C:HOH1155 2.1 30.4 1.0
O C:HOH1269 2.2 24.5 1.0
NE2 C:HIS502 2.3 23.8 1.0
O C:HOH843 2.5 24.7 1.0
CD C:GLU607 3.0 26.5 1.0
CE1 C:HIS502 3.2 23.2 1.0
OE1 C:GLU607 3.3 27.7 1.0
CD2 C:HIS502 3.3 22.9 1.0
O C:HOH986 3.9 38.1 1.0
CG C:GLU607 4.3 22.1 1.0
ND1 C:HIS502 4.3 24.0 1.0
CG C:HIS502 4.4 22.9 1.0
O C:HOH1316 4.4 29.8 1.0
O C:HOH1406 4.5 33.2 1.0
NE2 C:GLN451 4.7 22.4 1.0
O C:LEU498 4.8 20.4 1.0

Reference:

M.D.Balan, M.J.Mcleod, W.R.Lotosky, M.Ghaly, T.Holyoak. Inhibition and Allosteric Regulation of Monomeric Phosphoenolpyruvate Carboxykinase By 3-Mercaptopicolinic Acid. Biochemistry V. 54 5878 2015.
ISSN: ISSN 0006-2960
PubMed: 26322521
DOI: 10.1021/ACS.BIOCHEM.5B00822
Page generated: Sat Aug 16 16:35:20 2025

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