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Sodium in PDB 4ip7: Structure of the S12D Variant of Human Liver Pyruvate Kinase in Complex with Citrate and Fbp.

Enzymatic activity of Structure of the S12D Variant of Human Liver Pyruvate Kinase in Complex with Citrate and Fbp.

All present enzymatic activity of Structure of the S12D Variant of Human Liver Pyruvate Kinase in Complex with Citrate and Fbp.:
2.7.1.40;

Protein crystallography data

The structure of Structure of the S12D Variant of Human Liver Pyruvate Kinase in Complex with Citrate and Fbp., PDB code: 4ip7 was solved by T.Holyoak, A.W.Fenton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.53 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.140, 205.078, 83.910, 90.00, 92.15, 90.00
R / Rfree (%) 18.7 / 22.6

Other elements in 4ip7:

The structure of Structure of the S12D Variant of Human Liver Pyruvate Kinase in Complex with Citrate and Fbp. also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the S12D Variant of Human Liver Pyruvate Kinase in Complex with Citrate and Fbp. (pdb code 4ip7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of the S12D Variant of Human Liver Pyruvate Kinase in Complex with Citrate and Fbp., PDB code: 4ip7:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4ip7

Go back to Sodium Binding Sites List in 4ip7
Sodium binding site 1 out of 4 in the Structure of the S12D Variant of Human Liver Pyruvate Kinase in Complex with Citrate and Fbp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the S12D Variant of Human Liver Pyruvate Kinase in Complex with Citrate and Fbp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:40.5
occ:1.00
 O A:HOH781 2.4 34.0 1.0
OD1 A:ASN87 2.8 28.4 1.0
O A:THR126 3.0 28.2 1.0
OD1 A:ASP125 3.1 27.6 1.0
CG A:ASP125 3.3 24.9 1.0
OG A:SER89 3.4 37.9 1.0
O A:HOH1057 3.4 41.3 1.0
O A:ASP125 3.5 24.6 1.0
NH2 A:ARG85 3.5 30.1 1.0
OG1 A:FLC602 3.5 36.9 1.0
NZ A:LYS282 3.8 24.6 1.0
OD2 A:ASP125 3.8 26.4 1.0
C A:THR126 3.8 28.1 1.0
CG A:ASN87 3.8 29.1 1.0
CB A:ASP125 3.9 21.9 1.0
C A:ASP125 3.9 23.1 1.0
N A:SER89 4.2 29.2 1.0
O A:HOH1005 4.3 31.2 1.0
CB A:SER89 4.3 33.6 1.0
N A:THR126 4.3 24.5 1.0
N A:PHE88 4.4 26.8 1.0
CA A:ASP125 4.5 21.6 1.0
N A:LYS127 4.5 30.4 1.0
CA A:ASN87 4.6 25.6 1.0
ND2 A:ASN87 4.6 30.3 1.0
CA A:LYS127 4.6 33.1 1.0
OG A:SER255 4.6 28.5 1.0
OA2 A:FLC602 4.7 27.6 1.0
CA A:THR126 4.7 27.0 1.0
CZ A:ARG85 4.7 29.9 1.0
CGC A:FLC602 4.7 39.7 1.0
C A:ASN87 4.7 26.3 1.0
CB A:ASN87 4.8 26.6 1.0
CA A:SER89 4.8 33.1 1.0
OHB A:FLC602 5.0 24.1 1.0

Sodium binding site 2 out of 4 in 4ip7

Go back to Sodium Binding Sites List in 4ip7
Sodium binding site 2 out of 4 in the Structure of the S12D Variant of Human Liver Pyruvate Kinase in Complex with Citrate and Fbp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the S12D Variant of Human Liver Pyruvate Kinase in Complex with Citrate and Fbp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na607

b:37.2
occ:1.00
 O B:HOH1024 2.5 40.4 1.0
OD1 B:ASN87 2.9 32.5 1.0
O B:THR126 3.0 32.4 1.0
OD1 B:ASP125 3.1 30.4 1.0
CG B:ASP125 3.4 28.4 1.0
OG B:SER89 3.4 38.1 1.0
OG2 B:FLC602 3.4 44.6 1.0
NH2 B:ARG85 3.5 29.9 1.0
O B:ASP125 3.6 26.7 1.0
NZ B:LYS282 3.7 27.4 1.0
C B:THR126 3.8 30.2 1.0
OD2 B:ASP125 3.9 28.5 1.0
C B:ASP125 3.9 27.1 1.0
CB B:ASP125 3.9 25.5 1.0
CG B:ASN87 3.9 29.7 1.0
N B:THR126 4.3 25.8 1.0
OG B:SER255 4.3 29.8 1.0
N B:SER89 4.4 31.2 1.0
OA1 B:FLC602 4.5 34.5 1.0
CA B:ASP125 4.5 25.3 1.0
N B:PHE88 4.5 28.1 1.0
N B:LYS127 4.5 33.9 1.0
CB B:SER89 4.6 35.5 1.0
CZ B:ARG85 4.6 29.9 1.0
CGC B:FLC602 4.6 42.3 1.0
CA B:LYS127 4.6 34.8 1.0
ND2 B:ASN87 4.7 32.6 1.0
CA B:THR126 4.7 30.1 1.0
CA B:ASN87 4.7 27.3 1.0
CB B:ASN87 4.8 29.8 1.0
O B:HOH877 4.8 44.8 1.0
O B:LYS127 4.8 37.4 1.0
NE B:ARG85 4.9 33.8 1.0
C B:ASN87 4.9 28.0 1.0
OHB B:FLC602 4.9 28.8 1.0
O B:HOH736 4.9 28.0 1.0

Sodium binding site 3 out of 4 in 4ip7

Go back to Sodium Binding Sites List in 4ip7
Sodium binding site 3 out of 4 in the Structure of the S12D Variant of Human Liver Pyruvate Kinase in Complex with Citrate and Fbp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the S12D Variant of Human Liver Pyruvate Kinase in Complex with Citrate and Fbp. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na608

b:41.7
occ:1.00
 O C:HOH1033 2.6 44.3 1.0
O C:THR126 2.8 33.1 1.0
OD1 C:ASN87 2.9 32.4 1.0
OD1 C:ASP125 3.0 35.6 1.0
CG C:ASP125 3.4 30.7 1.0
OG C:SER89 3.4 43.2 1.0
O C:ASP125 3.5 29.1 1.0
OG2 C:FLC603 3.5 41.5 1.0
NH2 C:ARG85 3.7 35.0 1.0
NZ C:LYS282 3.7 30.0 1.0
C C:THR126 3.7 33.1 1.0
C C:ASP125 3.8 29.6 1.0
OD2 C:ASP125 3.9 30.9 1.0
CG C:ASN87 3.9 30.0 1.0
CB C:ASP125 3.9 27.3 1.0
N C:THR126 4.3 29.3 1.0
N C:SER89 4.3 31.0 1.0
O C:HOH837 4.3 36.2 1.0
OG C:SER255 4.3 32.7 1.0
N C:PHE88 4.4 29.8 1.0
CA C:ASP125 4.4 28.2 1.0
N C:LYS127 4.5 36.0 1.0
CB C:SER89 4.5 37.5 1.0
CA C:LYS127 4.6 38.2 1.0
OA1 C:FLC603 4.6 31.9 1.0
CA C:THR126 4.6 32.8 1.0
ND2 C:ASN87 4.7 30.4 1.0
CA C:ASN87 4.7 27.3 1.0
CGC C:FLC603 4.7 47.2 1.0
CZ C:ARG85 4.8 31.9 1.0
C C:ASN87 4.8 28.9 1.0
CB C:ASN87 4.8 28.8 1.0
O C:LYS127 4.9 40.6 1.0
CA C:SER89 4.9 35.6 1.0

Sodium binding site 4 out of 4 in 4ip7

Go back to Sodium Binding Sites List in 4ip7
Sodium binding site 4 out of 4 in the Structure of the S12D Variant of Human Liver Pyruvate Kinase in Complex with Citrate and Fbp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the S12D Variant of Human Liver Pyruvate Kinase in Complex with Citrate and Fbp. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na608

b:38.3
occ:1.00
 O D:HOH738 2.5 39.1 1.0
OD1 D:ASN87 2.7 35.2 1.0
O D:HOH1005 2.9 40.8 1.0
OD1 D:ASP125 3.0 30.7 1.0
O D:THR126 3.1 46.1 1.0
CG D:ASP125 3.1 27.4 1.0
NH2 D:ARG85 3.3 34.0 1.0
OG2 D:FLC602 3.4 40.0 1.0
O D:ASP125 3.5 26.5 1.0
OG D:SER89 3.5 40.5 1.0
OD2 D:ASP125 3.5 29.3 1.0
CB D:ASP125 3.7 25.3 1.0
NZ D:LYS282 3.8 29.1 1.0
C D:ASP125 3.8 27.0 1.0
CG D:ASN87 3.8 33.5 1.0
C D:THR126 4.0 47.3 1.0
O D:HOH1006 4.2 40.9 1.0
N D:THR126 4.3 49.7 1.0
CA D:ASP125 4.3 24.4 1.0
CZ D:ARG85 4.4 32.6 1.0
N D:SER89 4.4 34.5 1.0
N D:PHE88 4.5 31.4 1.0
OA2 D:FLC602 4.5 27.5 1.0
CA D:ASN87 4.5 29.4 1.0
CGC D:FLC602 4.5 42.9 1.0
CB D:SER89 4.6 38.8 1.0
ND2 D:ASN87 4.6 33.5 1.0
N D:LYS127 4.7 48.6 1.0
NE D:ARG85 4.7 32.4 1.0
CB D:ASN87 4.7 29.5 1.0
OG D:SER255 4.7 28.2 1.0
C D:ASN87 4.7 31.1 1.0
CA D:THR126 4.8 50.0 1.0
CA D:LYS127 4.8 47.9 1.0
OG1 D:FLC602 4.9 42.7 1.0
OHB D:FLC602 4.9 35.0 1.0
CAC D:FLC602 5.0 33.0 1.0

Reference:

T.Holyoak, B.Zhang, J.Deng, Q.Tang, C.B.Prasannan, A.W.Fenton. Energetic Coupling Between An Oxidizable Cysteine and the Phosphorylatable N-Terminus of Human Liver Pyruvate Kinase. Biochemistry V. 52 466 2013.
ISSN: ISSN 0006-2960
PubMed: 23270483
DOI: 10.1021/BI301341R
Page generated: Tue Dec 15 06:45:06 2020

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