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Manganese in PDB 4gnq: Structure of Rat Cytosolic Pepck LD_3G in Complex with Oxalate and Gtp

Enzymatic activity of Structure of Rat Cytosolic Pepck LD_3G in Complex with Oxalate and Gtp

All present enzymatic activity of Structure of Rat Cytosolic Pepck LD_3G in Complex with Oxalate and Gtp:
4.1.1.32;

Protein crystallography data

The structure of Structure of Rat Cytosolic Pepck LD_3G in Complex with Oxalate and Gtp, PDB code: 4gnq was solved by T.A.Johnson, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.36 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.487, 84.329, 118.971, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 19.7

Other elements in 4gnq:

The structure of Structure of Rat Cytosolic Pepck LD_3G in Complex with Oxalate and Gtp also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Rat Cytosolic Pepck LD_3G in Complex with Oxalate and Gtp (pdb code 4gnq). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of Rat Cytosolic Pepck LD_3G in Complex with Oxalate and Gtp, PDB code: 4gnq:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 4gnq

Go back to Manganese Binding Sites List in 4gnq
Manganese binding site 1 out of 2 in the Structure of Rat Cytosolic Pepck LD_3G in Complex with Oxalate and Gtp


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 LD_3G in Complex with Oxalate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn702

b:9.7
occ:1.00
OD1 A:ASP311 2.1 9.2 1.0
O2 A:OXL705 2.2 12.0 1.0
O1 A:OXL705 2.2 11.9 1.0
O1G A:GTP701 2.2 9.6 1.0
NZ A:LYS244 2.2 9.5 0.7
NE2 A:HIS264 2.3 9.8 1.0
O A:HOH1477 2.6 9.1 0.3
C1 A:OXL705 2.9 13.0 1.0
C2 A:OXL705 2.9 14.2 1.0
CG A:ASP311 3.1 8.9 1.0
CD2 A:HIS264 3.2 9.5 1.0
CE1 A:HIS264 3.3 9.0 1.0
PG A:GTP701 3.3 10.4 1.0
OD2 A:ASP311 3.3 9.0 1.0
CE A:LYS244 3.4 9.9 0.7
O3G A:GTP701 3.8 11.8 1.0
O2G A:GTP701 3.9 10.5 1.0
NZ A:LYS290 4.0 10.3 1.0
O3 A:OXL705 4.1 14.0 1.0
CE A:LYS290 4.1 9.8 1.0
O4 A:OXL705 4.2 15.8 1.0
O A:HOH855 4.2 10.0 1.0
O A:HOH866 4.3 11.4 1.0
OG A:SER286 4.3 12.7 0.3
CG A:HIS264 4.4 9.4 1.0
ND1 A:HIS264 4.4 9.0 1.0
CB A:ASP311 4.5 8.7 1.0
O3B A:GTP701 4.6 11.1 1.0
CD A:LYS244 4.8 9.7 0.7
O A:ASP311 5.0 9.5 1.0
CZ A:PHE485 5.0 11.3 1.0

Manganese binding site 2 out of 2 in 4gnq

Go back to Manganese Binding Sites List in 4gnq
Manganese binding site 2 out of 2 in the Structure of Rat Cytosolic Pepck LD_3G in Complex with Oxalate and Gtp


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 LD_3G in Complex with Oxalate and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn703

b:9.3
occ:0.90
O2G A:GTP701 2.1 10.5 1.0
O2B A:GTP701 2.2 10.9 1.0
OG1 A:THR291 2.2 6.9 0.7
O A:HOH821 2.2 10.8 1.0
O A:HOH855 2.2 10.0 1.0
O A:HOH850 2.3 10.3 1.0
PG A:GTP701 3.3 10.4 1.0
CB A:THR291 3.3 8.7 0.7
PB A:GTP701 3.3 10.8 1.0
O3B A:GTP701 3.5 11.1 1.0
CB A:THR291 3.5 11.7 0.3
OD2 A:ASP310 3.7 11.5 1.0
CG2 A:THR291 3.8 12.9 0.3
O1G A:GTP701 3.9 9.6 1.0
O2A A:GTP701 4.0 12.3 1.0
N A:THR291 4.1 10.0 1.0
O A:HOH866 4.2 11.4 1.0
CA A:THR291 4.3 9.6 0.7
CA A:THR291 4.3 11.1 0.3
NH1 A:ARG405 4.4 11.5 1.0
CG2 A:THR291 4.4 9.5 0.7
O3A A:GTP701 4.4 10.9 1.0
O A:ASP310 4.4 9.6 1.0
O1B A:GTP701 4.4 10.4 1.0
CG A:ASP310 4.4 10.0 1.0
CA A:GLY334 4.5 10.7 1.0
O3G A:GTP701 4.5 11.8 1.0
OG1 A:THR291 4.5 12.6 0.3
OD1 A:ASP311 4.5 9.2 1.0
O A:HOH804 4.6 10.8 1.0
O A:PHE333 4.7 10.6 1.0
N A:VAL335 4.7 10.9 1.0
PA A:GTP701 4.8 11.9 1.0
CB A:LYS290 4.9 9.3 1.0
O1 A:OXL705 5.0 11.9 1.0

Reference:

T.A.Johnson, T.Holyoak. The {Omega}-Loop Lid Domain of Phosphoenolpyruvate Carboxykinase Is Essential For Catalytic Function. Biochemistry V. 51 9547 2012.
ISSN: ISSN 0006-2960
PubMed: 23127136
DOI: 10.1021/BI301278T
Page generated: Tue Dec 15 04:21:32 2020

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