Phosphorus in PDB 1a3w: Pyruvate Kinase From Saccharomyces Cerevisiae Complexed with Fbp, Pg, MN2+ and K+

Enzymatic activity of Pyruvate Kinase From Saccharomyces Cerevisiae Complexed with Fbp, Pg, MN2+ and K+

All present enzymatic activity of Pyruvate Kinase From Saccharomyces Cerevisiae Complexed with Fbp, Pg, MN2+ and K+:
2.7.1.40;

Protein crystallography data

The structure of Pyruvate Kinase From Saccharomyces Cerevisiae Complexed with Fbp, Pg, MN2+ and K+, PDB code: 1a3w was solved by M.S.Jurica, A.Mesecar, P.J.Heath, W.Shi, T.Nowak, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 3.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.400, 102.700, 110.900, 90.00, 112.30, 90.00
R / Rfree (%) 21.8 / 32.3

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Pyruvate Kinase From Saccharomyces Cerevisiae Complexed with Fbp, Pg, MN2+ and K+ (pdb code 1a3w). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 6 binding sites of Phosphorus where determined in the Pyruvate Kinase From Saccharomyces Cerevisiae Complexed with Fbp, Pg, MN2+ and K+, PDB code: 1a3w:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6;

Phosphorus binding site 1 out of 6 in 1a3w

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Phosphorus binding site 1 out of 6 in the Pyruvate Kinase From Saccharomyces Cerevisiae Complexed with Fbp, Pg, MN2+ and K+


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Pyruvate Kinase From Saccharomyces Cerevisiae Complexed with Fbp, Pg, MN2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P1005

b:20.0
occ:1.00
 P A:PGA1005 0.0 20.0 1.0
O4P A:PGA1005 1.5 20.0 1.0
O1P A:PGA1005 1.6 20.0 1.0
O2P A:PGA1005 1.6 20.0 1.0
O3P A:PGA1005 1.7 20.0 1.0
C2 A:PGA1005 2.7 20.0 1.0
MN A:MN1001 3.3 16.0 1.0
C1 A:PGA1005 4.0 20.0 1.0
OD2 A:ASP266 4.1 36.8 1.0
K A:K1002 4.2 16.0 1.0
NH1 A:ARG49 4.5 28.3 1.0
O1 A:PGA1005 4.5 20.0 1.0
OE2 A:GLU242 4.5 76.7 1.0
CE A:LYS240 4.9 41.9 1.0

Phosphorus binding site 2 out of 6 in 1a3w

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Phosphorus binding site 2 out of 6 in the Pyruvate Kinase From Saccharomyces Cerevisiae Complexed with Fbp, Pg, MN2+ and K+


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Pyruvate Kinase From Saccharomyces Cerevisiae Complexed with Fbp, Pg, MN2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P1007

b:20.0
occ:1.00
 P1 A:FBP1007 0.0 20.0 1.0
O1P A:FBP1007 1.5 20.0 1.0
O3P A:FBP1007 1.5 20.0 1.0
O2P A:FBP1007 1.5 20.0 1.0
O1 A:FBP1007 1.6 20.0 1.0
C1 A:FBP1007 2.6 20.0 1.0
NE1 A:TRP452 3.3 83.0 1.0
NH2 A:ARG459 3.6 6.7 1.0
NH1 A:ARG459 3.7 6.7 1.0
C2 A:FBP1007 3.9 20.0 1.0
O5 A:FBP1007 4.1 20.0 1.0
CD1 A:TRP452 4.1 83.0 1.0
CZ A:ARG459 4.1 6.7 1.0
CE2 A:TRP452 4.2 83.0 1.0
C3 A:FBP1007 4.4 20.0 1.0
CZ2 A:TRP452 4.5 83.0 1.0
CG2 A:THR403 4.6 27.1 1.0

Phosphorus binding site 3 out of 6 in 1a3w

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Phosphorus binding site 3 out of 6 in the Pyruvate Kinase From Saccharomyces Cerevisiae Complexed with Fbp, Pg, MN2+ and K+


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Pyruvate Kinase From Saccharomyces Cerevisiae Complexed with Fbp, Pg, MN2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P1007

b:20.0
occ:1.00
 P2 A:FBP1007 0.0 20.0 1.0
O5P A:FBP1007 1.5 20.0 1.0
O4P A:FBP1007 1.5 20.0 1.0
O6P A:FBP1007 1.5 20.0 1.0
O6 A:FBP1007 1.6 20.0 1.0
C6 A:FBP1007 2.6 20.0 1.0
OG A:SER402 3.4 10.1 1.0
CB A:SER402 3.6 10.1 1.0
C5 A:FBP1007 3.8 20.0 1.0
OG1 A:THR407 3.9 32.4 1.0
N A:SER404 3.9 20.4 1.0
N A:THR403 4.0 19.0 1.0
CB A:SER404 4.1 84.3 1.0
N A:THR407 4.1 4.3 1.0
CB A:THR406 4.1 24.2 1.0
CA A:SER402 4.2 2.0 1.0
CD2 A:HIS491 4.3 96.4 1.0
OG A:SER404 4.4 84.3 1.0
N A:THR406 4.4 31.1 1.0
CB A:THR407 4.4 32.4 1.0
CA A:SER404 4.5 20.4 1.0
N A:GLY405 4.5 16.7 1.0
C A:SER402 4.5 2.0 1.0
NE2 A:HIS491 4.6 96.4 1.0
CA A:THR406 4.7 31.1 1.0
O5 A:FBP1007 4.7 20.0 1.0
OG1 A:THR406 4.7 24.2 1.0
C A:SER404 4.8 20.4 1.0
C4 A:FBP1007 4.8 20.0 1.0
OG A:SER492 4.9 10.7 1.0
CA A:THR407 4.9 4.3 1.0
C A:THR403 4.9 19.0 1.0
C A:THR406 4.9 31.1 1.0
CA A:THR403 4.9 19.0 1.0

Phosphorus binding site 4 out of 6 in 1a3w

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Phosphorus binding site 4 out of 6 in the Pyruvate Kinase From Saccharomyces Cerevisiae Complexed with Fbp, Pg, MN2+ and K+


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Pyruvate Kinase From Saccharomyces Cerevisiae Complexed with Fbp, Pg, MN2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P1006

b:20.0
occ:1.00
 P B:PGA1006 0.0 20.0 1.0
O4P B:PGA1006 1.5 20.0 1.0
O1P B:PGA1006 1.6 20.0 1.0
O2P B:PGA1006 1.6 20.0 1.0
O3P B:PGA1006 1.7 20.0 1.0
C2 B:PGA1006 2.7 20.0 1.0
MN B:MN1003 3.4 16.0 1.0
C1 B:PGA1006 4.1 20.0 1.0
K B:K1004 4.2 16.0 1.0
OD2 B:ASP266 4.3 41.5 1.0
NH1 B:ARG49 4.3 2.0 1.0
O1 B:PGA1006 4.6 20.0 1.0
OE2 B:GLU242 4.6 21.0 1.0
CE B:LYS240 4.8 46.0 1.0
NH2 B:ARG49 4.9 2.0 1.0

Phosphorus binding site 5 out of 6 in 1a3w

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Phosphorus binding site 5 out of 6 in the Pyruvate Kinase From Saccharomyces Cerevisiae Complexed with Fbp, Pg, MN2+ and K+


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Pyruvate Kinase From Saccharomyces Cerevisiae Complexed with Fbp, Pg, MN2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P1008

b:20.0
occ:1.00
 P1 B:FBP1008 0.0 20.0 1.0
O1P B:FBP1008 1.5 20.0 1.0
O2P B:FBP1008 1.5 20.0 1.0
O3P B:FBP1008 1.5 20.0 1.0
O1 B:FBP1008 1.6 20.0 1.0
C1 B:FBP1008 2.7 20.0 1.0
NH1 B:ARG459 3.3 9.0 1.0
NH2 B:ARG459 3.6 9.0 1.0
C2 B:FBP1008 3.8 20.0 1.0
NE1 B:TRP452 3.8 0.0 1.0
O5 B:FBP1008 3.9 20.0 1.0
CZ B:ARG459 3.9 9.0 1.0
CG2 B:THR403 4.3 42.3 1.0
C3 B:FBP1008 4.4 20.0 1.0
CD1 B:TRP452 4.6 0.0 1.0
CE2 B:TRP452 4.7 0.0 1.0
C5 B:FBP1008 4.9 20.0 1.0
O2 B:FBP1008 5.0 20.0 1.0

Phosphorus binding site 6 out of 6 in 1a3w

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Phosphorus binding site 6 out of 6 in the Pyruvate Kinase From Saccharomyces Cerevisiae Complexed with Fbp, Pg, MN2+ and K+


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Pyruvate Kinase From Saccharomyces Cerevisiae Complexed with Fbp, Pg, MN2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P1008

b:20.0
occ:1.00
 P2 B:FBP1008 0.0 20.0 1.0
O6P B:FBP1008 1.5 20.0 1.0
O5P B:FBP1008 1.5 20.0 1.0
O4P B:FBP1008 1.5 20.0 1.0
O6 B:FBP1008 1.6 20.0 1.0
C6 B:FBP1008 2.7 20.0 1.0
OG B:SER402 3.2 2.0 1.0
CB B:SER402 3.3 2.0 1.0
N B:THR403 3.7 87.3 1.0
C5 B:FBP1008 3.8 20.0 1.0
CA B:SER402 3.8 66.8 1.0
N B:SER404 3.9 5.7 1.0
OG1 B:THR407 4.0 46.5 1.0
C B:SER402 4.3 66.8 1.0
CB B:SER404 4.3 17.6 1.0
N B:THR407 4.3 29.2 1.0
CD2 B:HIS491 4.4 0.0 1.0
CB B:THR406 4.5 14.0 1.0
CB B:THR407 4.5 46.5 1.0
CA B:SER404 4.6 5.7 1.0
N B:GLY405 4.6 34.2 1.0
N B:THR406 4.6 8.8 1.0
O5 B:FBP1008 4.6 20.0 1.0
OG B:SER404 4.7 17.6 1.0
NE2 B:HIS491 4.7 0.0 1.0
CA B:THR403 4.7 87.3 1.0
C B:THR403 4.8 87.3 1.0
OG B:SER492 4.9 30.0 1.0
C4 B:FBP1008 4.9 20.0 1.0
C B:SER404 4.9 5.7 1.0
CA B:THR406 5.0 8.8 1.0

Reference:

M.S.Jurica, A.Mesecar, P.J.Heath, W.Shi, T.Nowak, B.L.Stoddard. The Allosteric Regulation of Pyruvate Kinase By Fructose-1,6-Bisphosphate. Structure V. 6 195 1998.
ISSN: ISSN 0969-2126
PubMed: 9519410
DOI: 10.1016/S0969-2126(98)00021-5
Page generated: Fri Sep 25 12:11:12 2020

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