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Manganese in PDB 2qf2: Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp.

Enzymatic activity of Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp.

All present enzymatic activity of Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp.:
4.1.1.32;

Protein crystallography data

The structure of Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp., PDB code: 2qf2 was solved by S.M.Sullivan, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.33 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.506, 119.112, 86.710, 90.00, 107.35, 90.00
R / Rfree (%) 20.4 / 23.8

Other elements in 2qf2:

The structure of Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp. also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp. (pdb code 2qf2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp., PDB code: 2qf2:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 2qf2

Go back to Manganese Binding Sites List in 2qf2
Manganese binding site 1 out of 7 in the Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp.


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 Oxaloacetic Acid and Gdp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn623

b:19.6
occ:1.00
 O1 A:PYR4083 1.9 14.4 0.6
O A:HOH4110 2.1 22.8 1.0
OD1 A:ASP311 2.2 13.3 1.0
O3 A:PYR4083 2.2 17.6 0.6
NE2 A:HIS264 2.2 13.3 1.0
O5 A:OAA701 2.3 23.7 0.4
NZ A:LYS244 2.3 14.1 1.0
O3 A:OAA701 2.5 23.0 0.4
C1 A:PYR4083 2.7 17.9 0.6
C2 A:PYR4083 2.7 17.9 0.6
CG A:ASP311 3.1 12.7 1.0
C4 A:OAA701 3.1 24.4 0.4
CE1 A:HIS264 3.2 13.1 1.0
CD2 A:HIS264 3.2 14.8 1.0
C3 A:OAA701 3.2 24.1 0.4
OD2 A:ASP311 3.3 14.0 1.0
CE A:LYS244 3.3 14.3 1.0
O2 A:PYR4083 3.9 18.9 0.6
NZ A:LYS290 4.0 14.5 1.0
O A:HOH4148 4.0 26.6 1.0
OG A:SER286 4.2 15.2 0.7
C3 A:PYR4083 4.2 16.6 0.6
CE A:LYS290 4.2 15.5 1.0
O A:HOH4247 4.2 25.0 1.0
ND1 A:HIS264 4.3 13.0 1.0
CG A:HIS264 4.4 13.1 1.0
O A:HOH4215 4.4 22.9 1.0
O4 A:OAA701 4.4 23.9 0.4
CB A:ASP311 4.5 12.6 1.0
OG A:SER286 4.5 15.6 0.3
CD A:LYS244 4.7 14.0 1.0
C2 A:OAA701 4.7 24.5 0.4
CA A:SER286 4.7 14.4 0.7
CB A:SER286 4.8 14.4 0.7
O A:ASP311 4.9 13.5 1.0
CZ A:PHE485 5.0 13.8 1.0

Manganese binding site 2 out of 7 in 2qf2

Go back to Manganese Binding Sites List in 2qf2
Manganese binding site 2 out of 7 in the Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp.


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 Oxaloacetic Acid and Gdp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn624

b:20.4
occ:0.30
 O A:HOH4142 1.4 30.3 1.0
MN A:MN625 1.5 19.1 0.7
O2B A:GDP702 1.8 18.9 0.7
O2B A:GDP703 2.1 17.6 0.3
O1B A:GDP702 2.3 19.8 0.7
PB A:GDP702 2.5 17.9 0.7
O2A A:GDP702 2.7 17.0 0.7
OG1 A:THR291 2.7 16.7 1.0
O A:HOH4312 3.1 26.7 1.0
O A:HOH4215 3.3 22.9 1.0
O3A A:GDP702 3.3 16.9 0.7
PB A:GDP703 3.4 18.0 0.3
PA A:GDP702 3.5 17.3 0.7
CB A:THR291 3.5 16.3 1.0
O3B A:GDP702 3.8 18.9 0.7
O1B A:GDP703 3.8 16.2 0.3
O3B A:GDP703 4.1 16.4 0.3
N A:VAL335 4.1 17.1 1.0
O A:HOH4148 4.1 26.6 1.0
N A:THR291 4.2 15.7 1.0
O2A A:GDP703 4.2 18.5 0.3
O1A A:GDP702 4.2 17.3 0.7
O A:HOH4144 4.3 21.7 1.0
CA A:GLY334 4.3 16.3 1.0
O A:HOH4110 4.4 22.8 1.0
CA A:THR291 4.5 15.8 1.0
CG2 A:VAL335 4.5 18.6 1.0
NH1 A:ARG405 4.6 22.8 1.0
O3A A:GDP703 4.6 17.8 0.3
OD2 A:ASP310 4.6 18.6 1.0
CG2 A:THR291 4.7 15.9 1.0
CB A:VAL335 4.8 17.6 1.0
C A:GLY334 4.8 16.7 1.0
PA A:GDP703 4.8 18.1 0.3
O A:HOH4247 4.9 25.0 1.0
O5' A:GDP702 4.9 17.9 0.7
O A:PHE333 4.9 15.8 1.0
O1A A:GDP703 4.9 18.7 0.3

Manganese binding site 3 out of 7 in 2qf2

Go back to Manganese Binding Sites List in 2qf2
Manganese binding site 3 out of 7 in the Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp.


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 Oxaloacetic Acid and Gdp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn625

b:19.1
occ:0.70
 MN A:MN624 1.5 20.4 0.3
O A:HOH4215 2.0 22.9 1.0
O2B A:GDP702 2.0 18.9 0.7
O A:HOH4312 2.1 26.7 1.0
OG1 A:THR291 2.2 16.7 1.0
O A:HOH4142 2.5 30.3 1.0
PB A:GDP702 3.2 17.9 0.7
O2B A:GDP703 3.2 17.6 0.3
O1B A:GDP702 3.3 19.8 0.7
CB A:THR291 3.4 16.3 1.0
OD2 A:ASP310 3.4 18.6 1.0
N A:THR291 3.9 15.7 1.0
O A:ASP310 3.9 15.2 1.0
O2A A:GDP702 4.0 17.0 0.7
O A:HOH4247 4.0 25.0 1.0
CG A:ASP310 4.1 15.6 1.0
O3B A:GDP702 4.1 18.9 0.7
CA A:THR291 4.2 15.8 1.0
O A:HOH4110 4.3 22.8 1.0
O3A A:GDP702 4.4 16.9 0.7
OD1 A:ASP311 4.4 13.3 1.0
PB A:GDP703 4.5 18.0 0.3
CG2 A:THR291 4.5 15.9 1.0
CA A:GLY334 4.5 16.3 1.0
PA A:GDP702 4.6 17.3 0.7
OD1 A:ASP310 4.7 16.2 1.0
O A:PHE333 4.7 15.8 1.0
CB A:LYS290 4.7 15.5 1.0
O A:HOH4148 4.7 26.6 1.0
CB A:ASP310 4.8 15.2 1.0
O3B A:GDP703 4.8 16.4 0.3
C A:ASP310 4.8 14.5 1.0
O3 A:PYR4083 4.8 17.6 0.6
CB A:ASP311 4.9 12.6 1.0
O1A A:GDP702 5.0 17.3 0.7
C A:LYS290 5.0 15.3 1.0
CG A:ASP311 5.0 12.7 1.0
CE A:LYS290 5.0 15.5 1.0

Manganese binding site 4 out of 7 in 2qf2

Go back to Manganese Binding Sites List in 2qf2
Manganese binding site 4 out of 7 in the Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn626

b:32.8
occ:1.00
 OE2 A:GLU607 2.0 22.2 1.0
O A:HOH4482 2.1 36.1 1.0
O A:HOH4384 2.2 32.4 1.0
NE2 A:HIS502 2.2 19.4 1.0
CD A:GLU607 3.0 21.9 1.0
CE1 A:HIS502 3.0 19.6 1.0
O A:HOH4139 3.1 31.2 1.0
CD2 A:HIS502 3.3 19.1 1.0
OE1 A:GLU607 3.3 23.3 1.0
ND1 A:HIS502 4.2 20.4 1.0
O A:HOH4452 4.2 34.7 1.0
CG A:GLU607 4.3 19.0 1.0
CG A:HIS502 4.3 19.8 1.0
O A:HOH4292 4.3 34.7 1.0
O A:HOH4598 4.4 31.4 1.0
O A:HOH4593 4.5 34.5 1.0
NE2 A:GLN451 4.9 15.2 1.0
O A:LEU498 5.0 14.7 1.0

Manganese binding site 5 out of 7 in 2qf2

Go back to Manganese Binding Sites List in 2qf2
Manganese binding site 5 out of 7 in the Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn623

b:18.3
occ:1.00
 OD1 B:ASP311 2.1 15.7 1.0
O1 B:PYR4083 2.1 24.8 0.6
O5 B:OAA801 2.3 25.4 0.4
NE2 B:HIS264 2.3 9.7 1.0
O3 B:PYR4083 2.3 26.2 0.6
O B:HOH4676 2.3 21.9 1.0
NZ B:LYS244 2.3 13.5 1.0
O3 B:OAA801 2.4 24.0 0.4
C1 B:PYR4083 2.9 27.6 0.6
C2 B:PYR4083 2.9 27.5 0.6
CG B:ASP311 3.0 16.8 1.0
C4 B:OAA801 3.0 25.1 0.4
C3 B:OAA801 3.0 25.1 0.4
CD2 B:HIS264 3.2 10.3 1.0
CE1 B:HIS264 3.2 11.2 1.0
OD2 B:ASP311 3.3 16.9 1.0
CE B:LYS244 3.3 11.3 1.0
NZ B:LYS290 3.8 20.0 0.3
CE B:LYS290 4.1 19.7 0.7
O2 B:PYR4083 4.1 28.5 0.6
O B:HOH4227 4.2 26.7 1.0
C3 B:PYR4083 4.3 27.8 0.6
O4 B:OAA801 4.3 24.0 0.4
ND1 B:HIS264 4.3 10.7 1.0
CG B:HIS264 4.4 9.5 1.0
O B:HOH4226 4.4 25.8 1.0
CB B:ASP311 4.4 16.2 1.0
OG B:SER286 4.4 23.2 1.0
O B:HOH4421 4.4 32.4 1.0
NZ B:LYS290 4.4 17.2 0.7
C2 B:OAA801 4.5 25.3 0.4
CE B:LYS290 4.7 20.1 0.3
CD B:LYS244 4.7 9.9 1.0
O2 B:OAA801 4.8 27.2 0.4
CE2 B:PHE485 5.0 10.8 1.0
CZ B:PHE485 5.0 10.8 1.0

Manganese binding site 6 out of 7 in 2qf2

Go back to Manganese Binding Sites List in 2qf2
Manganese binding site 6 out of 7 in the Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn624

b:27.2
occ:0.80
 O2B B:GDP802 2.2 26.2 1.0
O B:HOH4226 2.2 25.8 1.0
OG1 B:THR291 2.2 21.5 1.0
O B:HOH4407 2.3 30.6 1.0
O B:HOH4240 2.3 34.3 1.0
O B:HOH4421 2.5 32.4 1.0
PB B:GDP802 3.4 27.2 1.0
CB B:THR291 3.4 21.5 1.0
O1B B:GDP802 3.5 27.5 1.0
OD2 B:ASP310 3.9 22.0 1.0
N B:THR291 4.1 21.0 1.0
O B:HOH4227 4.1 26.7 1.0
O2A B:GDP802 4.1 28.4 1.0
CA B:THR291 4.3 21.7 1.0
O3B B:GDP802 4.3 27.4 1.0
O B:HOH4332 4.4 40.0 1.0
O B:HOH4676 4.4 21.9 1.0
O B:ASP310 4.4 17.4 1.0
CG2 B:THR291 4.5 22.1 1.0
O3A B:GDP802 4.5 27.1 1.0
CG B:ASP310 4.6 18.4 1.0
CA B:GLY334 4.7 20.3 1.0
PA B:GDP802 4.7 27.6 1.0
NZ B:LYS290 4.7 20.0 0.3
O1A B:GDP802 4.8 28.1 1.0
N B:VAL335 4.9 21.0 1.0
CB B:LYS290 4.9 20.7 0.7
CB B:LYS290 4.9 20.6 0.3

Manganese binding site 7 out of 7 in 2qf2

Go back to Manganese Binding Sites List in 2qf2
Manganese binding site 7 out of 7 in the Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn626

b:23.9
occ:1.00
 OE2 B:GLU607 2.1 14.9 1.0
NE2 B:HIS502 2.1 12.8 1.0
O B:HOH4325 2.2 27.8 1.0
O B:HOH4180 2.9 26.2 1.0
CE1 B:HIS502 3.0 16.4 1.0
CD B:GLU607 3.0 15.9 1.0
CD2 B:HIS502 3.1 15.3 1.0
OE1 B:GLU607 3.4 18.9 1.0
O B:HOH4412 3.8 40.5 1.0
ND1 B:HIS502 4.2 14.2 1.0
CG B:HIS502 4.3 15.2 1.0
CG B:GLU607 4.4 12.8 1.0
O B:HOH4399 4.4 31.1 1.0
O B:HOH4301 4.5 31.9 1.0
NE2 B:GLN451 4.7 10.1 1.0
O B:LEU498 4.9 10.4 1.0

Reference:

S.M.Sullivan, T.Holyoak. Structures of Rat Cytosolic Pepck: Insight Into the Mechanism of Phosphorylation and Decarboxylation of Oxaloacetic Acid. Biochemistry V. 46 10078 2007.
ISSN: ISSN 0006-2960
PubMed: 17685635
DOI: 10.1021/BI701038X
Page generated: Sat Aug 16 10:50:52 2025

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