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Manganese in PDB 5v9h: Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp.

Enzymatic activity of Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp.

All present enzymatic activity of Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp.:
4.1.1.32;

Protein crystallography data

The structure of Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp., PDB code: 5v9h was solved by T.Holyoak, D.S.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 85.04 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.480, 119.433, 88.166, 90.00, 105.30, 90.00
R / Rfree (%) 24.1 / 28.5

Other elements in 5v9h:

The structure of Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp. also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp. (pdb code 5v9h). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp., PDB code: 5v9h:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 5v9h

Go back to Manganese Binding Sites List in 5v9h
Manganese binding site 1 out of 6 in the Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate 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 the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn702

b:43.5
occ:1.00
 O3B A:GDP706 2.1 43.1 1.0
O3P A:PGA707 2.2 39.7 1.0
O A:HOH813 2.3 33.4 1.0
O A:HOH808 2.3 36.3 1.0
O A:HOH802 2.4 41.3 1.0
OG1 A:THR291 2.4 38.4 1.0
O1B A:GDP706 2.8 41.5 1.0
PB A:GDP706 2.9 40.9 1.0
P A:PGA707 3.4 40.1 1.0
CB A:THR291 3.5 38.2 1.0
OD2 A:ASP310 3.9 34.2 1.0
O4P A:PGA707 3.9 39.0 1.0
O2B A:GDP706 4.0 41.1 1.0
N A:THR291 4.1 37.1 1.0
O1A A:GDP706 4.1 45.1 1.0
O3A A:GDP706 4.2 42.4 1.0
O2P A:PGA707 4.2 39.6 1.0
O A:HOH835 4.3 28.9 1.0
O A:ASP310 4.3 33.1 1.0
CA A:THR291 4.3 38.2 1.0
CA A:GLY334 4.3 34.7 1.0
O1P A:PGA707 4.5 36.7 1.0
PA A:GDP706 4.6 44.1 1.0
O A:PHE333 4.6 33.1 1.0
CG2 A:THR291 4.6 38.1 1.0
CG A:ASP310 4.6 33.7 1.0
NH1 A:ARG405 4.6 33.7 1.0
OD1 A:ASP311 4.7 27.2 1.0
CB A:LYS290 4.8 35.1 1.0
N A:VAL335 4.8 35.0 1.0
O2A A:GDP706 4.9 45.1 1.0
CE A:LYS290 5.0 33.9 1.0

Manganese binding site 2 out of 6 in 5v9h

Go back to Manganese Binding Sites List in 5v9h
Manganese binding site 2 out of 6 in the Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate 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 the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn703

b:60.1
occ:1.00
 OE2 A:GLU607 2.1 42.3 1.0
O A:HOH872 2.2 32.8 1.0
NE2 A:HIS502 2.7 53.7 1.0
CE1 A:HIS502 2.8 53.8 1.0
CD A:GLU607 2.9 39.9 1.0
OE1 A:GLU607 3.0 40.2 1.0
CD2 A:HIS502 4.0 52.7 1.0
ND1 A:HIS502 4.0 52.6 1.0
NE2 A:GLN451 4.0 32.5 1.0
CG A:GLU607 4.3 39.1 1.0
O A:HOH947 4.4 37.2 1.0
CG A:HIS502 4.6 51.5 1.0
O A:LEU498 4.7 29.1 1.0
CD A:GLN451 4.8 31.9 1.0
CG A:GLN451 4.9 31.7 1.0

Manganese binding site 3 out of 6 in 5v9h

Go back to Manganese Binding Sites List in 5v9h
Manganese binding site 3 out of 6 in the Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate 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 the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn704

b:31.6
occ:1.00
 OD1 A:ASP311 2.1 27.2 1.0
O4P A:PGA707 2.2 39.0 1.0
O2 A:PGA707 2.2 37.0 1.0
NE2 A:HIS264 2.4 26.8 1.0
O1P A:PGA707 2.4 36.7 1.0
NZ A:LYS244 2.5 30.1 1.0
P A:PGA707 2.8 40.1 1.0
C1 A:PGA707 3.0 37.4 1.0
CG A:ASP311 3.1 29.5 1.0
C2 A:PGA707 3.1 36.9 1.0
CD2 A:HIS264 3.2 27.0 1.0
OD2 A:ASP311 3.3 31.1 1.0
CE1 A:HIS264 3.3 26.7 1.0
CE A:LYS244 3.3 30.3 1.0
O3P A:PGA707 3.8 39.7 1.0
O2P A:PGA707 3.9 39.6 1.0
NZ A:LYS290 4.1 35.3 1.0
CE A:LYS290 4.1 33.9 1.0
OG A:SER286 4.1 35.7 1.0
O1 A:PGA707 4.2 37.7 1.0
O A:HOH813 4.2 33.4 1.0
CG A:HIS264 4.3 27.1 1.0
ND1 A:HIS264 4.4 27.2 1.0
O A:HOH835 4.5 28.9 1.0
CB A:ASP311 4.5 30.3 1.0
CB A:SER286 4.7 35.8 1.0
CA A:SER286 4.7 35.4 1.0
CD A:LYS244 4.7 30.0 1.0
CZ A:PHE485 4.9 25.7 1.0
CE2 A:PHE485 5.0 25.7 1.0

Manganese binding site 4 out of 6 in 5v9h

Go back to Manganese Binding Sites List in 5v9h
Manganese binding site 4 out of 6 in the Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate 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 the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:56.8
occ:1.00
 OE2 B:GLU63 2.4 62.5 1.0
CD B:GLU63 3.1 60.2 1.0
OE1 B:GLU63 3.2 61.1 1.0
CG B:GLU63 4.6 59.9 1.0

Manganese binding site 5 out of 6 in 5v9h

Go back to Manganese Binding Sites List in 5v9h
Manganese binding site 5 out of 6 in the Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn702

b:44.9
occ:1.00
 O B:HOH812 1.9 29.3 1.0
O B:HOH846 2.1 60.3 1.0
O3B B:GDP705 2.1 51.6 1.0
O B:HOH803 2.4 38.9 1.0
OG1 B:THR291 2.4 43.2 1.0
O3P B:PGA706 2.4 51.2 1.0
PB B:GDP705 3.1 52.6 1.0
O1B B:GDP705 3.1 51.4 1.0
CB B:THR291 3.6 43.3 1.0
P B:PGA706 3.6 50.5 1.0
OD2 B:ASP310 3.8 38.4 1.0
O1A B:GDP705 3.9 49.6 1.0
O4P B:PGA706 4.0 47.9 1.0
N B:THR291 4.0 43.8 1.0
O2B B:GDP705 4.1 51.6 1.0
O B:ASP310 4.1 39.5 1.0
O B:HOH869 4.1 35.0 1.0
O3A B:GDP705 4.2 50.5 1.0
CA B:THR291 4.3 44.4 1.0
O2P B:PGA706 4.4 51.3 1.0
CG B:ASP310 4.4 39.1 1.0
OD1 B:ASP311 4.5 33.9 1.0
PA B:GDP705 4.5 50.6 1.0
CA B:GLY334 4.6 37.4 1.0
CB B:LYS290 4.6 41.5 1.0
NH1 B:ARG405 4.6 43.6 1.0
CG2 B:THR291 4.7 43.4 1.0
O1P B:PGA706 4.8 47.5 1.0
O B:PHE333 4.8 33.9 1.0
O2A B:GDP705 4.8 49.5 1.0
CE B:LYS290 4.9 40.7 1.0
NZ B:LYS290 4.9 42.0 1.0
C B:ASP310 5.0 39.2 1.0
C B:LYS290 5.0 42.8 1.0
CB B:ASP310 5.0 39.3 1.0

Manganese binding site 6 out of 6 in 5v9h

Go back to Manganese Binding Sites List in 5v9h
Manganese binding site 6 out of 6 in the Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn703

b:38.5
occ:1.00
 O4P B:PGA706 2.0 47.9 1.0
OD1 B:ASP311 2.1 33.9 1.0
O1P B:PGA706 2.2 47.5 1.0
O2 B:PGA706 2.3 47.9 1.0
NE2 B:HIS264 2.4 31.6 1.0
NZ B:LYS244 2.5 39.1 1.0
P B:PGA706 2.6 50.5 1.0
CG B:ASP311 3.0 36.4 1.0
C1 B:PGA706 3.1 48.0 1.0
C2 B:PGA706 3.1 48.1 1.0
OD2 B:ASP311 3.2 36.9 1.0
CD2 B:HIS264 3.2 32.2 1.0
CE B:LYS244 3.4 38.1 1.0
CE1 B:HIS264 3.5 31.9 1.0
O3P B:PGA706 3.6 51.2 1.0
O2P B:PGA706 3.8 51.3 1.0
NZ B:LYS290 4.0 42.0 1.0
CE B:LYS290 4.1 40.7 1.0
O B:HOH846 4.2 60.3 1.0
OG B:SER286 4.3 44.8 1.0
O B:HOH869 4.3 35.0 1.0
O1 B:PGA706 4.3 49.5 1.0
CG B:HIS264 4.4 32.8 1.0
CB B:ASP311 4.4 36.5 1.0
ND1 B:HIS264 4.5 33.3 1.0
CB B:SER286 4.7 45.2 1.0
CD B:LYS244 4.7 37.6 1.0
CA B:SER286 4.8 44.8 1.0
CZ B:PHE485 4.9 27.8 1.0
CA B:ASP311 5.0 37.0 1.0
CE2 B:PHE485 5.0 28.3 1.0
O B:ASP311 5.0 36.5 1.0

Reference:

D.S.Cui, A.Broom, M.J.Mcleod, E.M.Meiering, T.Holyoak. Asymmetric Anchoring Is Required For Efficient Omega-Loop Opening and Closing in Cytosolic Phosphoenolpyruvate Carboxykinase. Biochemistry V. 56 2106 2017.
ISSN: ISSN 1520-4995
PubMed: 28345895
DOI: 10.1021/ACS.BIOCHEM.7B00178
Page generated: Sun Oct 6 03:09:55 2024

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