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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

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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

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