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Zinc in PDB 4rgq: Crystal Structure of the Methanocaldococcus Jannaschii G1PDH with Nadph and Dhap

Enzymatic activity of Crystal Structure of the Methanocaldococcus Jannaschii G1PDH with Nadph and Dhap

All present enzymatic activity of Crystal Structure of the Methanocaldococcus Jannaschii G1PDH with Nadph and Dhap:
1.1.1.261;

Protein crystallography data

The structure of Crystal Structure of the Methanocaldococcus Jannaschii G1PDH with Nadph and Dhap, PDB code: 4rgq 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) 46.66 / 2.23
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.382, 71.898, 101.697, 77.52, 79.54, 75.60
R / Rfree (%) 18.2 / 22.9

Other elements in 4rgq:

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

Potassium (K) 4 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 4rgq

Go back to Zinc Binding Sites List in 4rgq
Zinc binding site 1 out of 4 in the Crystal Structure of the Methanocaldococcus Jannaschii G1PDH with Nadph and Dhap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Methanocaldococcus Jannaschii G1PDH with Nadph and Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:44.0
occ:1.00
 NE2 A:HIS226 2.0 32.3 1.0
O2 A:13P404 2.1 51.1 1.0
OD1 A:ASP148 2.2 40.8 1.0
NE2 A:HIS247 2.3 30.2 1.0
O3 A:13P404 2.7 40.0 1.0
CE1 A:HIS226 3.0 28.9 1.0
CD2 A:HIS226 3.1 27.8 1.0
C2 A:13P404 3.1 51.9 1.0
CG A:ASP148 3.1 33.4 1.0
CE1 A:HIS247 3.2 29.5 1.0
CD2 A:HIS247 3.3 30.4 1.0
OD2 A:ASP148 3.3 37.9 1.0
C3 A:13P404 3.5 47.1 1.0
OD1 A:ASP105 3.6 26.6 1.0
C4N A:NDP401 4.1 78.5 0.7
ND1 A:HIS226 4.1 29.5 1.0
O A:HOH637 4.1 35.9 1.0
C5N A:NDP401 4.1 76.9 0.7
CG A:HIS226 4.2 29.0 1.0
K A:K402 4.3 40.7 1.0
ND1 A:HIS247 4.3 32.3 1.0
CG A:ASP105 4.4 26.1 1.0
CG A:HIS247 4.4 26.6 1.0
SG A:CYS251 4.4 23.9 1.0
C1 A:13P404 4.5 54.9 1.0
CB A:ASP148 4.5 29.8 1.0
OD2 A:ASP105 4.5 26.8 1.0

Zinc binding site 2 out of 4 in 4rgq

Go back to Zinc Binding Sites List in 4rgq
Zinc binding site 2 out of 4 in the Crystal Structure of the Methanocaldococcus Jannaschii G1PDH with Nadph and Dhap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Methanocaldococcus Jannaschii G1PDH with Nadph and Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:52.0
occ:1.00
 O2 B:1GP404 2.1 24.0 0.3
NE2 B:HIS226 2.1 30.8 1.0
OD1 B:ASP148 2.2 50.8 1.0
NE2 B:HIS247 2.3 36.3 1.0
O3 B:1GP404 2.7 26.7 0.7
O2 B:1GP404 2.8 23.5 0.3
CE1 B:HIS226 3.0 25.9 1.0
CE1 B:HIS247 3.1 30.1 1.0
CD2 B:HIS226 3.2 27.4 1.0
C3 B:1GP404 3.2 26.6 1.0
CG B:ASP148 3.2 38.5 1.0
CD2 B:HIS247 3.3 32.2 1.0
OD2 B:ASP148 3.5 42.9 1.0
C2 B:1GP404 3.6 24.6 0.7
OD1 B:ASP105 3.7 26.2 1.0
C4N B:NDP401 3.7 80.9 0.7
C5N B:NDP401 4.0 78.9 0.7
ND1 B:HIS226 4.2 25.7 1.0
CG B:HIS226 4.3 24.4 1.0
CG B:ASP105 4.3 26.7 1.0
OD2 B:ASP105 4.3 27.5 1.0
ND1 B:HIS247 4.3 29.4 1.0
K B:K402 4.3 40.5 1.0
CG B:HIS247 4.4 32.0 1.0
SG B:CYS251 4.5 24.0 1.0
CB B:ASP148 4.6 30.6 1.0
O1P B:1GP404 4.6 26.1 0.7
C1 B:1GP404 4.7 24.3 0.7

Zinc binding site 3 out of 4 in 4rgq

Go back to Zinc Binding Sites List in 4rgq
Zinc binding site 3 out of 4 in the Crystal Structure of the Methanocaldococcus Jannaschii G1PDH with Nadph and Dhap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Methanocaldococcus Jannaschii G1PDH with Nadph and Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:44.6
occ:1.00
 O C:HOH501 2.0 30.9 0.5
NE2 C:HIS226 2.0 28.7 1.0
O2 C:13P404 2.1 46.7 1.0
OD1 C:ASP148 2.2 39.5 1.0
NE2 C:HIS247 2.3 31.5 1.0
O3 C:13P404 2.5 45.7 1.0
CE1 C:HIS226 2.9 24.8 1.0
C2 C:13P404 3.0 46.1 1.0
CD2 C:HIS226 3.1 27.2 1.0
CG C:ASP148 3.2 34.2 1.0
CE1 C:HIS247 3.2 29.4 1.0
CD2 C:HIS247 3.2 30.3 1.0
C3 C:13P404 3.3 49.1 1.0
OD2 C:ASP148 3.5 40.5 1.0
OD1 C:ASP105 3.8 28.6 1.0
ND1 C:HIS226 4.1 23.7 1.0
CG C:HIS226 4.2 24.0 1.0
C4N C:NDP401 4.2 87.0 0.7
ND1 C:HIS247 4.3 31.7 1.0
K C:K402 4.3 43.7 1.0
C1 C:13P404 4.4 47.8 1.0
CG C:HIS247 4.4 30.0 1.0
SG C:CYS251 4.5 33.4 1.0
CB C:ASP148 4.5 32.0 1.0
CG C:ASP105 4.6 30.3 1.0
OD2 C:ASP105 4.7 35.9 1.0
C5N C:NDP401 4.7 84.7 0.7
O1 C:13P404 4.7 44.0 1.0
CB C:ASN104 4.9 34.6 1.0

Zinc binding site 4 out of 4 in 4rgq

Go back to Zinc Binding Sites List in 4rgq
Zinc binding site 4 out of 4 in the Crystal Structure of the Methanocaldococcus Jannaschii G1PDH with Nadph and Dhap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Methanocaldococcus Jannaschii G1PDH with Nadph and Dhap within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn403

b:58.3
occ:1.00
 O2 D:13P404 2.0 54.2 0.8
O D:HOH501 2.0 36.3 0.5
NE2 D:HIS226 2.1 36.9 1.0
OD1 D:ASP148 2.1 47.2 1.0
NE2 D:HIS247 2.2 38.5 1.0
CE1 D:HIS226 2.9 35.5 1.0
O3 D:13P404 3.1 45.6 0.8
C2 D:13P404 3.1 50.1 0.8
CG D:ASP148 3.1 36.8 1.0
CE1 D:HIS247 3.1 41.1 1.0
CD2 D:HIS226 3.2 33.5 1.0
CD2 D:HIS247 3.2 38.0 1.0
OD2 D:ASP148 3.4 40.2 1.0
C3 D:13P404 3.6 48.0 0.8
OD1 D:ASP105 3.7 29.5 1.0
C4N D:NDP401 3.9 72.5 0.7
ND1 D:HIS226 4.0 34.4 1.0
C5N D:NDP401 4.2 74.6 0.7
CG D:HIS226 4.2 32.7 1.0
ND1 D:HIS247 4.3 39.1 1.0
CG D:ASP105 4.3 29.7 1.0
K D:K402 4.3 43.9 1.0
CG D:HIS247 4.3 37.6 1.0
C1 D:13P404 4.4 50.4 0.8
SG D:CYS251 4.4 27.4 1.0
OD2 D:ASP105 4.4 27.9 1.0
CB D:ASP148 4.5 34.5 1.0
CB D:ASN104 4.9 38.5 1.0
O1 D:13P404 5.0 49.0 0.8
CA D:ASP148 5.0 31.0 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: Sun Oct 27 07:06:55 2024

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