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Manganese in PDB 4ox2: I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp

Enzymatic activity of I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp

All present enzymatic activity of I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp:
4.1.1.32;

Protein crystallography data

The structure of I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp, PDB code: 4ox2 was solved by T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.13 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.924, 119.252, 87.397, 90.00, 106.92, 90.00
R / Rfree (%) 18.9 / 23.3

Other elements in 4ox2:

The structure of I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp (pdb code 4ox2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp, PDB code: 4ox2:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 4ox2

Go back to Manganese Binding Sites List in 4ox2
Manganese binding site 1 out of 6 in the I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:23.8
occ:1.00
 OD1 A:ASP311 2.1 19.2 1.0
O2 A:SPV704 2.1 27.2 1.0
O1 A:SPV704 2.2 28.4 1.0
O3G A:GTP703 2.2 24.8 1.0
NE2 A:HIS264 2.3 22.7 1.0
NZ A:LYS244 2.4 23.7 1.0
C2 A:SPV704 2.9 27.9 1.0
C1 A:SPV704 3.0 28.4 1.0
CG A:ASP311 3.0 21.9 1.0
CE1 A:HIS264 3.2 24.1 1.0
CD2 A:HIS264 3.2 24.0 1.0
OD2 A:ASP311 3.2 24.8 1.0
PG A:GTP703 3.3 27.1 1.0
CE A:LYS244 3.4 23.9 1.0
O2G A:GTP703 3.8 26.2 1.0
NZ A:LYS290 3.9 25.9 1.0
O1G A:GTP703 3.9 28.3 1.0
CE A:LYS290 4.2 26.5 1.0
O2' A:SPV704 4.2 28.9 1.0
O A:HOH868 4.2 25.9 1.0
ND1 A:HIS264 4.3 23.7 1.0
CG A:HIS264 4.4 24.4 1.0
C3 A:SPV704 4.4 27.8 1.0
O A:HOH1002 4.4 34.8 1.0
CB A:ASP311 4.4 23.1 1.0
OG A:SER286 4.5 32.4 1.0
O3B A:GTP703 4.7 28.8 1.0
CD A:LYS244 4.8 24.6 1.0
CB A:SER286 4.9 31.4 1.0
O A:ASP311 4.9 24.6 1.0
CZ A:PHE485 4.9 26.0 1.0

Manganese binding site 2 out of 6 in 4ox2

Go back to Manganese Binding Sites List in 4ox2
Manganese binding site 2 out of 6 in the I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn702

b:31.2
occ:1.00
 O A:HOH868 1.9 25.9 1.0
O1G A:GTP703 2.0 28.3 1.0
O1B A:GTP703 2.2 30.5 1.0
O A:HOH1004 2.2 27.9 1.0
O A:HOH893 2.2 31.6 1.0
OG1 A:THR291 2.3 29.6 1.0
PG A:GTP703 3.2 27.1 1.0
PB A:GTP703 3.3 30.9 1.0
CB A:THR291 3.4 27.6 1.0
O3B A:GTP703 3.5 28.8 1.0
OD2 A:ASP310 3.7 28.8 1.0
O3G A:GTP703 3.9 24.8 1.0
O A:HOH1002 4.0 34.8 1.0
N A:THR291 4.2 25.9 1.0
O3A A:GTP703 4.3 31.6 1.0
O2A A:GTP703 4.4 35.8 1.0
NH1 A:ARG405 4.4 24.0 1.0
CA A:THR291 4.4 28.2 1.0
O2G A:GTP703 4.4 26.2 1.0
CA A:GLY334 4.4 25.7 1.0
O A:ASP310 4.4 27.0 1.0
CG A:ASP310 4.4 27.6 1.0
O2B A:GTP703 4.4 28.0 1.0
CG2 A:THR291 4.5 29.5 1.0
O A:PHE333 4.5 24.7 1.0
O1A A:GTP703 4.5 33.7 1.0
PA A:GTP703 4.6 42.4 1.0
OD1 A:ASP311 4.6 19.2 1.0
N A:VAL335 4.7 28.9 1.0
O A:HOH943 4.8 34.4 1.0
OD1 A:ASP310 5.0 29.3 1.0
CB A:LYS290 5.0 24.6 1.0

Manganese binding site 3 out of 6 in 4ox2

Go back to Manganese Binding Sites List in 4ox2
Manganese binding site 3 out of 6 in the I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn705

b:41.5
occ:0.50
 O A:HOH822 2.1 62.7 1.0
OE2 A:GLU63 2.1 48.3 1.0
CD A:GLU63 3.0 45.8 1.0
OE1 A:GLU63 3.3 49.3 1.0
CG A:GLU63 4.4 45.0 1.0

Manganese binding site 4 out of 6 in 4ox2

Go back to Manganese Binding Sites List in 4ox2
Manganese binding site 4 out of 6 in the I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:28.0
occ:1.00
 O B:HOH863 1.9 23.0 1.0
O B:HOH872 2.0 27.8 1.0
O1B B:GTP703 2.1 28.0 1.0
O1G B:GTP703 2.1 30.8 1.0
O B:HOH1010 2.2 32.9 1.0
OG1 B:THR291 2.3 25.6 1.0
PB B:GTP703 3.2 30.4 1.0
PG B:GTP703 3.2 27.6 1.0
CB B:THR291 3.3 26.4 1.0
O3B B:GTP703 3.4 30.4 1.0
OD2 B:ASP310 3.6 26.6 1.0
O2G B:GTP703 3.8 26.8 1.0
N B:THR291 4.1 26.9 1.0
O B:HOH850 4.1 28.7 1.0
O2A B:GTP703 4.2 28.7 1.0
O3A B:GTP703 4.2 27.5 1.0
CA B:THR291 4.2 27.8 1.0
O B:ASP310 4.2 23.3 1.0
OD1 B:ASP311 4.3 18.1 1.0
CG B:ASP310 4.3 25.0 1.0
CG2 B:THR291 4.4 26.5 1.0
O2B B:GTP703 4.4 27.4 1.0
O B:PHE333 4.4 22.8 1.0
NH1 B:ARG405 4.4 25.2 1.0
PA B:GTP703 4.5 29.0 1.0
CA B:GLY334 4.5 23.7 1.0
O3G B:GTP703 4.5 27.3 1.0
O1A B:GTP703 4.8 27.5 1.0
OD1 B:ASP310 5.0 26.8 1.0
O2 B:SPV704 5.0 26.1 1.0
CB B:LYS290 5.0 23.7 1.0
CB B:ASP310 5.0 24.0 1.0

Manganese binding site 5 out of 6 in 4ox2

Go back to Manganese Binding Sites List in 4ox2
Manganese binding site 5 out of 6 in the I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn702

b:23.0
occ:1.00
 O2 B:SPV704 2.2 26.1 1.0
O1 B:SPV704 2.2 19.1 1.0
O2G B:GTP703 2.2 26.8 1.0
NE2 B:HIS264 2.2 22.7 1.0
OD1 B:ASP311 2.2 18.1 1.0
NZ B:LYS244 2.4 26.1 1.0
C1 B:SPV704 2.9 26.0 1.0
C2 B:SPV704 2.9 25.7 1.0
CG B:ASP311 3.1 21.0 1.0
CE1 B:HIS264 3.1 23.0 1.0
CD2 B:HIS264 3.2 23.3 1.0
OD2 B:ASP311 3.3 21.5 1.0
PG B:GTP703 3.3 27.6 1.0
CE B:LYS244 3.5 26.6 1.0
O3G B:GTP703 3.9 27.3 1.0
O1G B:GTP703 3.9 30.8 1.0
NZ B:LYS290 4.0 22.9 1.0
O B:HOH863 4.0 23.0 1.0
CE B:LYS290 4.1 24.5 1.0
O2' B:SPV704 4.1 27.5 1.0
ND1 B:HIS264 4.3 23.5 1.0
O B:HOH850 4.3 28.7 1.0
CG B:HIS264 4.3 23.9 1.0
C3 B:SPV704 4.4 28.1 1.0
OG B:SER286 4.5 27.3 1.0
CB B:ASP311 4.6 21.1 1.0
O3B B:GTP703 4.7 30.4 1.0
CB B:SER286 4.8 26.7 1.0
CA B:SER286 4.8 26.9 1.0
CD B:LYS244 4.8 25.4 1.0
O B:ASP311 5.0 22.6 1.0
CZ B:PHE485 5.0 23.8 1.0

Manganese binding site 6 out of 6 in 4ox2

Go back to Manganese Binding Sites List in 4ox2
Manganese binding site 6 out of 6 in the I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn705

b:40.4
occ:0.50
 NE2 B:HIS502 2.4 51.6 1.0
OE2 B:GLU607 2.5 41.0 1.0
O B:HOH816 2.5 36.0 1.0
OE1 B:GLU607 2.7 44.1 1.0
CD B:GLU607 2.8 35.8 1.0
CE1 B:HIS502 2.9 51.6 1.0
CD2 B:HIS502 3.6 50.3 1.0
ND1 B:HIS502 4.1 53.0 1.0
CG B:GLU607 4.2 33.5 1.0
CG B:HIS502 4.5 48.5 1.0
O B:LEU498 4.6 24.8 1.0
NE2 B:GLN451 4.9 34.0 1.0

Reference:

D.R.Adams, H.Yuan, T.Holyoak, K.H.Arajs, P.Hakimi, T.C.Markello, L.A.Wolfe, T.Vilboux, B.K.Burton, K.F.Fajardo, G.Grahame, C.Holloman, M.Sincan, A.C.Smith, G.A.Wells, Y.Huang, H.Vega, J.P.Snyder, G.A.Golas, C.J.Tifft, C.F.Boerkoel, R.W.Hanson, S.F.Traynelis, D.S.Kerr, W.A.Gahl. Three Rare Diseases in One Sib Pair: RAI1, PCK1, GRIN2B Mutations Associated with Smith-Magenis Syndrome, Cytosolic Pepck Deficiency and Nmda Receptor Glutamate Insensitivity. Mol.Genet.Metab. 2014.
ISSN: ESSN 1096-7206
PubMed: 24863970
DOI: 10.1016/J.YMGME.2014.04.001
Page generated: Sat Oct 5 20:43:08 2024

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