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Manganese in PDB 9ej2: Rat Cytosolic Pepck in Complex with Gtp and Oxalate (313K)

Enzymatic activity of Rat Cytosolic Pepck in Complex with Gtp and Oxalate (313K)

All present enzymatic activity of Rat Cytosolic Pepck in Complex with Gtp and Oxalate (313K):
4.1.1.32;

Protein crystallography data

The structure of Rat Cytosolic Pepck in Complex with Gtp and Oxalate (313K), PDB code: 9ej2 was solved by M.J.Mcleod, S.A.E.Barwell, T.Holyoak, R.E.Thorne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.88 / 2.12
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.296, 120.16, 61.118, 90, 111.47, 90
R / Rfree (%) 18.9 / 23.2

Manganese Binding Sites:

The binding sites of Manganese atom in the Rat Cytosolic Pepck in Complex with Gtp and Oxalate (313K) (pdb code 9ej2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Rat Cytosolic Pepck in Complex with Gtp and Oxalate (313K), PDB code: 9ej2:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 9ej2

Go back to Manganese Binding Sites List in 9ej2
Manganese binding site 1 out of 3 in the Rat Cytosolic Pepck in Complex with Gtp and Oxalate (313K)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Rat Cytosolic Pepck in Complex with Gtp and Oxalate (313K) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:53.2
occ:1.00
O A:HOH815 2.0 38.4 1.0
O1G A:GTP705 2.1 40.9 1.0
OG1 A:THR291 2.2 46.3 1.0
O A:HOH811 2.3 42.5 1.0
O1B A:GTP705 2.3 42.6 1.0
O A:HOH802 2.7 34.7 1.0
PG A:GTP705 3.4 43.5 1.0
CB A:THR291 3.5 42.1 1.0
PB A:GTP705 3.6 45.0 1.0
OD2 A:ASP310 3.7 35.8 1.0
O3G A:GTP705 3.8 35.2 1.0
O3B A:GTP705 3.9 48.9 1.0
O A:HOH804 3.9 31.9 1.0
N A:THR291 4.2 42.4 1.0
O1A A:GTP705 4.2 58.2 1.0
O A:ASP310 4.3 30.2 1.0
CA A:GLY334 4.3 39.7 1.0
CA A:THR291 4.4 36.0 1.0
O3A A:GTP705 4.4 52.6 1.0
CG A:ASP310 4.4 43.9 1.0
CG2 A:THR291 4.5 40.2 1.0
O2G A:GTP705 4.5 45.1 1.0
O A:PHE333 4.5 40.5 1.0
NH1 A:ARG405 4.6 40.6 1.0
PA A:GTP705 4.7 50.3 1.0
OD1 A:ASP311 4.7 34.0 1.0
O2B A:GTP705 4.7 43.6 1.0
O2A A:GTP705 4.8 49.0 1.0
N A:VAL335 5.0 37.2 1.0
O1 A:OXL704 5.0 37.3 1.0

Manganese binding site 2 out of 3 in 9ej2

Go back to Manganese Binding Sites List in 9ej2
Manganese binding site 2 out of 3 in the Rat Cytosolic Pepck in Complex with Gtp and Oxalate (313K)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Rat Cytosolic Pepck in Complex with Gtp and Oxalate (313K) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn702

b:39.3
occ:1.00
OD1 A:ASP311 2.1 34.0 1.0
O2 A:OXL704 2.1 41.4 1.0
O3G A:GTP705 2.3 35.2 1.0
NE2 A:HIS264 2.4 36.6 1.0
O1 A:OXL704 2.4 37.3 1.0
NZ A:LYS244 2.4 46.0 1.0
C2 A:OXL704 2.9 49.1 1.0
CG A:ASP311 3.1 41.6 1.0
C1 A:OXL704 3.1 46.9 1.0
CE1 A:HIS264 3.2 29.5 1.0
CD2 A:HIS264 3.4 31.7 1.0
CE A:LYS244 3.4 38.8 1.0
OD2 A:ASP311 3.4 40.1 1.0
PG A:GTP705 3.5 43.5 1.0
O2G A:GTP705 3.7 45.1 1.0
NZ A:LYS290 4.0 32.6 1.0
O A:HOH804 4.1 31.9 1.0
O4 A:OXL704 4.1 45.6 1.0
O1G A:GTP705 4.2 40.9 1.0
O A:HOH815 4.2 38.4 1.0
O3 A:OXL704 4.3 42.3 1.0
ND1 A:HIS264 4.3 33.3 1.0
CE A:LYS290 4.4 40.3 1.0
CB A:ASP311 4.4 33.4 1.0
OG A:SER286 4.4 46.9 1.0
CG A:HIS264 4.4 29.3 1.0
CD A:LYS244 4.8 46.2 1.0
O3B A:GTP705 4.8 48.9 1.0

Manganese binding site 3 out of 3 in 9ej2

Go back to Manganese Binding Sites List in 9ej2
Manganese binding site 3 out of 3 in the Rat Cytosolic Pepck in Complex with Gtp and Oxalate (313K)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Rat Cytosolic Pepck in Complex with Gtp and Oxalate (313K) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn703

b:109.5
occ:1.00
OE2 A:GLU607 2.5 76.8 1.0
NE2 A:HIS502 2.8 78.5 1.0
O A:HOH878 2.9 68.5 1.0
OE1 A:GLU607 3.0 70.2 1.0
CD A:GLU607 3.1 71.7 1.0
CE1 A:HIS502 3.7 78.0 1.0
CD2 A:HIS502 3.9 76.9 1.0
CG A:GLU607 4.5 62.3 1.0
NE2 A:GLN451 4.6 64.5 1.0
ND1 A:HIS502 4.8 73.1 1.0
O A:LEU498 4.9 56.9 1.0
CG A:HIS502 5.0 75.0 1.0

Reference:

M.J.Mcleod, S.A.E.Barwell, T.Holyoak, R.E.Thorne. A Structural Perspective on the Temperature Dependent Activity of Enzymes. Structure 2025.
ISSN: ISSN 0969-2126
PubMed: 40120576
DOI: 10.1016/J.STR.2025.02.013
Page generated: Sun Aug 17 02:28:41 2025

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