Atomistry » Manganese » PDB 4fo7-4gv9 » 4gmw
Atomistry »
  Manganese »
    PDB 4fo7-4gv9 »
      4gmw »

Manganese in PDB 4gmw: Structure of Rat Cytosolic Pepck LD_1G in Complex with Pep and Gdp

Enzymatic activity of Structure of Rat Cytosolic Pepck LD_1G in Complex with Pep and Gdp

All present enzymatic activity of Structure of Rat Cytosolic Pepck LD_1G in Complex with Pep and Gdp:
4.1.1.32;

Protein crystallography data

The structure of Structure of Rat Cytosolic Pepck LD_1G in Complex with Pep and Gdp, PDB code: 4gmw 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) 31.03 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.091, 84.940, 119.322, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.9

Other elements in 4gmw:

The structure of Structure of Rat Cytosolic Pepck LD_1G in Complex with Pep and Gdp 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_1G in Complex with Pep and Gdp (pdb code 4gmw). 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 LD_1G in Complex with Pep and Gdp, PDB code: 4gmw:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4gmw

Go back to Manganese Binding Sites List in 4gmw
Manganese binding site 1 out of 4 in the Structure of Rat Cytosolic Pepck LD_1G in Complex with Pep and Gdp


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_1G in Complex with Pep and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn702

b:17.5
occ:1.00
 OD1 A:ASP311 2.1 15.0 1.0
O A:HOH804 2.2 12.4 1.0
NE2 A:HIS264 2.2 19.3 1.0
O A:HOH805 2.3 25.6 1.0
O A:HOH807 2.3 19.7 1.0
NZ A:LYS244 2.3 16.8 1.0
CG A:ASP311 3.0 17.4 1.0
CE1 A:HIS264 3.1 16.7 1.0
CD2 A:HIS264 3.2 16.2 1.0
OD2 A:ASP311 3.3 18.3 1.0
CE A:LYS244 3.3 17.6 1.0
NZ A:LYS290 4.0 25.9 0.5
O A:HOH1131 4.1 27.4 0.5
O1P A:PEP704 4.1 19.4 1.0
O A:HOH806 4.2 28.4 1.0
O3P A:PEP704 4.2 18.5 1.0
ND1 A:HIS264 4.2 18.5 1.0
CG A:HIS264 4.3 17.6 1.0
O A:HOH899 4.3 25.5 1.0
NZ A:LYS290 4.4 22.2 0.5
CB A:ASP311 4.4 17.2 1.0
CE A:LYS290 4.5 24.6 0.5
O A:HOH1033 4.6 29.0 1.0
CE A:LYS290 4.6 24.9 0.5
CD A:LYS244 4.6 16.6 1.0
P A:PEP704 4.8 21.1 1.0
O A:HOH1183 4.8 27.0 0.5
CE2 A:PHE485 4.8 16.8 1.0
CZ A:PHE485 4.8 16.7 1.0

Manganese binding site 2 out of 4 in 4gmw

Go back to Manganese Binding Sites List in 4gmw
Manganese binding site 2 out of 4 in the Structure of Rat Cytosolic Pepck LD_1G in Complex with Pep and Gdp


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_1G in Complex with Pep and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn705

b:42.9
occ:0.50
 O A:HOH1167 1.9 47.1 1.0
O A:HOH1186 2.1 65.7 1.0
NE2 A:HIS502 2.4 40.6 1.0
OE2 A:GLU607 2.6 28.8 0.5
O A:HOH900 2.6 32.4 1.0
CD A:GLU607 2.9 29.1 0.5
OE1 A:GLU607 3.0 30.0 0.5
CE1 A:HIS502 3.3 41.3 1.0
CD2 A:HIS502 3.5 41.1 1.0
OE2 A:GLU607 3.5 25.3 0.5
CG A:GLU607 4.0 23.7 0.5
CG A:GLU607 4.1 26.9 0.5
O A:HOH1094 4.2 46.3 1.0
CD A:GLU607 4.2 23.2 0.5
ND1 A:HIS502 4.5 38.8 1.0
CG A:HIS502 4.6 39.5 1.0
NE2 A:GLN451 4.7 30.8 1.0
O A:LEU498 4.8 25.7 1.0
CG A:GLN451 5.0 25.6 1.0

Manganese binding site 3 out of 4 in 4gmw

Go back to Manganese Binding Sites List in 4gmw
Manganese binding site 3 out of 4 in the Structure of Rat Cytosolic Pepck LD_1G in Complex with Pep and Gdp


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 LD_1G in Complex with Pep and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn706

b:29.9
occ:0.25
 O A:HOH1131 1.7 27.4 0.5
MN A:MN707 2.2 50.0 0.2
O A:HOH1132 2.2 30.2 1.0
O1B A:GDP701 2.5 26.6 0.5
O A:HOH1133 3.1 30.1 1.0
OG1 A:THR291 3.3 21.6 0.5
O A:ASP310 3.5 17.4 1.0
O A:HOH1037 3.5 34.7 1.0
O A:HOH805 3.5 25.6 1.0
OD2 A:ASP310 3.7 37.7 1.0
PB A:GDP701 3.7 28.0 0.5
CE A:LYS290 3.7 24.9 0.5
CE A:LYS290 3.9 24.6 0.5
NZ A:LYS290 4.1 25.9 0.5
O A:HOH899 4.1 25.5 1.0
CG A:ASP310 4.1 28.9 1.0
O2B A:GDP701 4.1 28.3 0.5
CB A:LYS290 4.2 21.1 0.5
CG A:LYS290 4.2 25.8 0.5
OD1 A:ASP311 4.2 15.0 1.0
N A:THR291 4.2 22.4 0.5
O3B A:GDP701 4.3 26.9 0.5
O A:HOH1183 4.3 27.0 0.5
OD1 A:ASP310 4.5 28.1 1.0
O A:HOH806 4.6 28.4 1.0
CB A:THR291 4.6 23.5 0.5
C A:ASP310 4.6 18.4 1.0
CD A:LYS290 4.6 26.5 0.5
O1B A:GDP701 4.7 27.1 0.5
CB A:LYS290 4.7 25.6 0.5
CB A:ASP311 4.8 17.2 1.0
CA A:THR291 4.8 23.8 0.5
N A:THR291 4.8 28.8 0.5
CG A:ASP311 4.9 17.4 1.0
OG1 A:THR291 4.9 38.6 0.5
NZ A:LYS290 4.9 22.2 0.5
CB A:ASP310 4.9 24.7 1.0
O3A A:GDP701 5.0 29.8 0.5
CA A:THR291 5.0 31.5 0.5
C A:LYS290 5.0 22.4 0.5

Manganese binding site 4 out of 4 in 4gmw

Go back to Manganese Binding Sites List in 4gmw
Manganese binding site 4 out of 4 in the Structure of Rat Cytosolic Pepck LD_1G in Complex with Pep and Gdp


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 LD_1G in Complex with Pep and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn707

b:50.0
occ:0.25
 O A:HOH1133 2.0 30.1 1.0
O A:HOH1132 2.0 30.2 1.0
MN A:MN706 2.2 29.9 0.2
O A:HOH1037 2.4 34.7 1.0
OG1 A:THR291 2.7 21.6 0.5
O1B A:GDP701 3.2 26.6 0.5
O A:HOH880 3.3 27.5 1.0
OD2 A:ASP310 3.5 37.7 1.0
CA A:GLY334 3.6 21.4 1.0
O A:HOH1131 3.8 27.4 0.5
CB A:THR291 4.0 23.5 0.5
O A:HOH899 4.1 25.5 1.0
N A:VAL335 4.2 22.1 1.0
CG A:ASP310 4.4 28.9 1.0
PB A:GDP701 4.5 28.0 0.5
C A:GLY334 4.5 24.4 1.0
OG1 A:THR291 4.5 38.6 0.5
O A:PHE333 4.6 21.6 1.0
N A:GLY334 4.6 21.7 1.0
CG2 A:THR291 4.7 35.1 0.5
O1A A:GDP701 4.7 28.3 0.5
O3B A:GDP701 4.8 26.9 0.5
CG2 A:THR291 4.8 24.3 0.5
O A:HOH806 4.8 28.4 1.0
OD1 A:ASP310 4.9 28.1 1.0
N A:THR291 4.9 22.4 0.5
C A:PHE333 4.9 20.7 1.0
CA A:THR291 5.0 23.8 0.5

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: Sat Oct 5 19:34:13 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy