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Potassium in PDB 4rfl: Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii

Enzymatic activity of Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii

All present enzymatic activity of Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii:
1.1.1.261;

Protein crystallography data

The structure of Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii, PDB code: 4rfl was solved by V.Carbone, R.S.Ronimus, L.R.Schofield, A.J.Sutherland-Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.68 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.391, 72.115, 101.714, 77.62, 79.58, 75.63
R / Rfree (%) 18.5 / 22.5

Other elements in 4rfl:

The structure of Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Sodium (Na) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii (pdb code 4rfl). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii, PDB code: 4rfl:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 4rfl

Go back to Potassium Binding Sites List in 4rfl
Potassium binding site 1 out of 4 in the Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:33.2
occ:1.00
 O A:ASP148 2.5 37.3 1.0
OD1 A:ASN152 2.6 22.6 1.0
O A:ALA221 2.9 23.8 1.0
OD2 A:ASP105 2.9 31.5 1.0
OG A:SER151 3.1 30.2 1.0
OD1 A:ASP148 3.4 38.1 1.0
C A:ASP148 3.5 29.6 1.0
C A:ALA221 3.8 23.7 1.0
CB A:ALA221 3.8 21.8 1.0
CG A:ASN152 3.8 22.6 1.0
O A:HOH538 3.9 36.4 1.0
CG A:ASP105 3.9 27.6 1.0
CA A:ALA221 4.0 22.8 1.0
CG A:ASP148 4.0 34.9 1.0
CE1 A:HIS226 4.1 33.6 1.0
N A:ASN152 4.2 23.1 1.0
CA A:ASP148 4.2 28.7 1.0
CB A:SER151 4.3 26.2 1.0
N A:ILE149 4.4 28.5 1.0
CB A:ASP148 4.5 30.3 1.0
NE2 A:HIS226 4.6 35.3 1.0
C A:SER151 4.6 22.8 1.0
CB A:ASP105 4.6 25.7 1.0
ND2 A:ASN152 4.6 22.5 1.0
CA A:ILE149 4.6 24.0 1.0
ZN A:ZN403 4.6 30.7 0.5
OD2 A:ASP148 4.7 33.9 1.0
CA A:ASN152 4.7 22.5 1.0
OD1 A:ASP105 4.7 28.3 1.0
O A:ILE149 4.8 23.1 1.0
CB A:ASN152 4.9 21.5 1.0
CA A:SER151 4.9 23.9 1.0
C A:ILE149 4.9 23.3 1.0

Potassium binding site 2 out of 4 in 4rfl

Go back to Potassium Binding Sites List in 4rfl
Potassium binding site 2 out of 4 in the Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:34.2
occ:1.00
 O B:ASP148 2.3 35.3 1.0
OD1 B:ASN152 2.7 22.6 1.0
O B:ALA221 2.8 24.0 1.0
OD2 B:ASP105 2.9 32.7 1.0
OG B:SER151 3.0 24.5 1.0
C B:ASP148 3.5 25.1 1.0
OD1 B:ASP148 3.5 43.0 1.0
C B:ALA221 3.8 23.4 1.0
CB B:ALA221 3.8 25.2 1.0
CG B:ASN152 3.9 20.1 1.0
CA B:ALA221 4.0 23.6 1.0
CE1 B:HIS226 4.0 31.0 1.0
CG B:ASP105 4.0 30.3 1.0
CG B:ASP148 4.0 37.2 1.0
N B:ASN152 4.1 19.1 1.0
OG B:SER208 4.2 22.2 0.5
CA B:ASP148 4.2 26.3 1.0
CB B:SER151 4.3 21.6 1.0
N B:ILE149 4.5 23.2 1.0
C B:SER151 4.6 19.1 1.0
CB B:ASP148 4.6 28.7 1.0
NE2 B:HIS226 4.6 33.0 1.0
ND2 B:ASN152 4.6 21.4 1.0
OD2 B:ASP148 4.6 38.6 1.0
O B:HOH501 4.7 42.1 1.0
CA B:ASN152 4.7 20.1 1.0
CA B:ILE149 4.7 21.1 1.0
CB B:ASP105 4.7 28.5 1.0
OD1 B:ASP105 4.7 28.7 1.0
ZN B:ZN403 4.8 33.7 0.5
O B:ILE149 4.8 20.8 1.0
CA B:SER151 4.9 20.1 1.0
CB B:ASN152 4.9 18.3 1.0
ND1 B:HIS226 4.9 30.5 1.0
C B:ILE149 5.0 22.0 1.0

Potassium binding site 3 out of 4 in 4rfl

Go back to Potassium Binding Sites List in 4rfl
Potassium binding site 3 out of 4 in the Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K402

b:45.1
occ:1.00
 O C:ALA221 2.6 31.4 1.0
O C:ASP148 2.7 29.6 1.0
OD1 C:ASN152 2.8 22.9 1.0
OD2 C:ASP105 3.0 40.6 1.0
OG C:SER151 3.1 35.7 1.0
C C:ALA221 3.5 25.0 1.0
CB C:ALA221 3.6 26.5 1.0
OD1 C:ASP148 3.7 42.7 1.0
C C:ASP148 3.7 26.4 1.0
O C:HOH567 3.7 35.2 1.0
CA C:ALA221 3.8 25.8 1.0
CE1 C:HIS226 4.0 35.9 1.0
CG C:ASN152 4.0 25.7 1.0
CG C:ASP148 4.0 34.8 1.0
CG C:ASP105 4.1 34.4 1.0
N C:ASN152 4.2 24.6 1.0
OG C:SER208 4.3 24.1 0.5
CA C:ASP148 4.3 27.8 1.0
CB C:SER151 4.3 30.6 1.0
OD2 C:ASP148 4.4 44.7 1.0
ZN C:ZN403 4.5 36.6 0.5
NE2 C:HIS226 4.5 40.2 1.0
C C:SER151 4.6 23.9 1.0
CB C:ASP148 4.6 33.0 1.0
N C:ILE149 4.7 25.3 1.0
OD1 C:ASP105 4.7 33.3 1.0
CA C:ASN152 4.7 24.4 1.0
N C:SER222 4.8 27.5 1.0
ND2 C:ASN152 4.8 29.7 1.0
CA C:ILE149 4.9 24.3 1.0
CA C:SER151 4.9 25.4 1.0
CB C:ASP105 4.9 32.1 1.0
ND1 C:HIS226 5.0 36.6 1.0
CB C:ASN152 5.0 23.8 1.0

Potassium binding site 4 out of 4 in 4rfl

Go back to Potassium Binding Sites List in 4rfl
Potassium binding site 4 out of 4 in the Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of G1PDH with Nadph From Methanocaldococcus Jannaschii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K402

b:35.5
occ:1.00
 O D:ASP148 2.4 43.9 1.0
OD1 D:ASN152 2.6 24.2 1.0
O D:ALA221 2.8 26.9 1.0
OG D:SER151 3.0 33.2 1.0
OD2 D:ASP105 3.1 27.6 1.0
C D:ASP148 3.5 34.9 1.0
C D:ALA221 3.7 26.5 1.0
CB D:ALA221 3.7 25.4 1.0
CG D:ASN152 3.8 21.6 1.0
CA D:ALA221 3.8 24.4 1.0
CE1 D:HIS226 3.9 33.8 1.0
OD1 D:ASP148 3.9 47.0 1.0
O D:HOH529 4.0 36.8 1.0
N D:ASN152 4.1 22.8 1.0
CG D:ASP105 4.1 29.0 1.0
CG D:ASP148 4.1 36.9 1.0
CB D:SER151 4.2 28.1 1.0
OG D:SER208 4.2 24.1 0.5
CA D:ASP148 4.2 36.0 1.0
C D:SER151 4.5 23.9 1.0
OD2 D:ASP148 4.5 38.6 1.0
N D:ILE149 4.5 29.9 1.0
CA D:ASN152 4.6 23.1 1.0
NE2 D:HIS226 4.6 37.4 1.0
CB D:ASP148 4.6 37.4 1.0
ZN D:ZN403 4.6 39.8 0.5
ND2 D:ASN152 4.6 23.2 1.0
CA D:ILE149 4.7 25.4 1.0
CA D:SER151 4.8 24.8 1.0
O D:ILE149 4.8 23.4 1.0
CB D:ASN152 4.8 21.3 1.0
CB D:ASP105 4.8 29.0 1.0
ND1 D:HIS226 4.9 31.8 1.0
OD1 D:ASP105 4.9 31.5 1.0
N D:SER222 4.9 25.7 1.0
C D:ILE149 5.0 25.0 1.0

Reference:

V.Carbone, L.R.Schofield, Y.Zhang, C.Sang, D.Dey, I.M.Hannus, W.F.Martin, A.J.Sutherland-Smith, R.S.Ronimus. Structure and Evolution of the Archaeal Lipid Synthesis Enzyme Sn-Glycerol-1-Phosphate Dehydrogenase. J.Biol.Chem. V. 290 21690 2015.
ISSN: ISSN 0021-9258
PubMed: 26175150
DOI: 10.1074/JBC.M115.647461
Page generated: Mon Aug 12 11:58:47 2024

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