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Zinc in PDB 5fb3: Structure of Glycerophosphate Dehydrogenase in Complex with Nadph

Enzymatic activity of Structure of Glycerophosphate Dehydrogenase in Complex with Nadph

All present enzymatic activity of Structure of Glycerophosphate Dehydrogenase in Complex with Nadph:
1.1.1.261;

Protein crystallography data

The structure of Structure of Glycerophosphate Dehydrogenase in Complex with Nadph, PDB code: 5fb3 was solved by H.Sakuraba, J.Hayashi, K.Yamamoto, K.Yoneda, T.Ohshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 102.182, 123.335, 166.724, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 26

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Glycerophosphate Dehydrogenase in Complex with Nadph (pdb code 5fb3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of Glycerophosphate Dehydrogenase in Complex with Nadph, PDB code: 5fb3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5fb3

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Zinc binding site 1 out of 6 in the Structure of Glycerophosphate Dehydrogenase in Complex with Nadph


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Glycerophosphate Dehydrogenase in Complex with Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:82.2
occ:1.00
 OD2 A:ASP157 2.4 76.0 1.0
NE2 A:HIS256 2.5 60.4 1.0
NE2 A:HIS238 2.6 60.1 1.0
CD2 A:HIS238 3.0 57.2 1.0
CG A:ASP157 3.0 66.0 1.0
OD1 A:ASP157 3.1 63.4 1.0
CD2 A:HIS256 3.2 57.9 1.0
CE1 A:HIS256 3.6 61.3 1.0
CE1 A:HIS238 3.8 63.2 1.0
OD2 A:ASP108 4.0 78.4 1.0
OD1 A:ASP108 4.1 76.5 1.0
CG2 A:VAL260 4.2 54.6 1.0
CG A:ASP108 4.2 72.0 1.0
CG A:HIS238 4.3 56.3 1.0
CB A:ASP157 4.4 62.2 1.0
CG A:HIS256 4.5 56.8 1.0
ND1 A:HIS256 4.6 58.8 1.0
ND1 A:HIS238 4.7 62.2 1.0
NZ A:LYS161 4.8 61.5 1.0
N A:ASP108 4.9 69.2 1.0
CA A:ASP157 4.9 58.7 1.0

Zinc binding site 2 out of 6 in 5fb3

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Zinc binding site 2 out of 6 in the Structure of Glycerophosphate Dehydrogenase in Complex with Nadph


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Glycerophosphate Dehydrogenase in Complex with Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:77.0
occ:1.00
 OD1 B:ASP157 1.9 64.6 1.0
NE2 B:HIS238 2.4 58.4 1.0
NE2 B:HIS256 2.5 91.3 1.0
CG B:ASP157 2.9 66.2 1.0
CE1 B:HIS238 3.0 54.6 1.0
CD2 B:HIS256 3.1 86.7 1.0
OD2 B:ASP157 3.3 75.6 1.0
CD2 B:HIS238 3.5 51.8 1.0
CE1 B:HIS256 3.6 91.1 1.0
OD2 B:ASP108 3.7 83.3 1.0
CB B:ASP108 3.7 80.2 1.0
CB B:ASP157 4.2 63.4 1.0
CG B:ASP108 4.2 79.5 1.0
ND1 B:HIS238 4.2 54.4 1.0
CG2 B:VAL260 4.2 56.4 1.0
N B:ASP108 4.3 77.4 1.0
CG B:HIS256 4.4 86.2 1.0
CG B:HIS238 4.5 51.8 1.0
ND1 B:HIS256 4.6 85.4 1.0
CA B:ASP108 4.7 76.7 1.0
NZ B:LYS161 4.9 59.3 1.0
CA B:ASP157 5.0 62.6 1.0

Zinc binding site 3 out of 6 in 5fb3

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Zinc binding site 3 out of 6 in the Structure of Glycerophosphate Dehydrogenase in Complex with Nadph


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Glycerophosphate Dehydrogenase in Complex with Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2001

b:96.2
occ:1.00
 OD2 C:ASP157 1.9 68.7 1.0
NE2 C:HIS256 2.4 68.6 1.0
NE2 C:HIS238 2.4 59.7 1.0
CD2 C:HIS238 3.1 56.4 1.0
CG C:ASP157 3.1 65.2 1.0
CD2 C:HIS256 3.2 67.7 1.0
CE1 C:HIS256 3.4 69.2 1.0
OD2 C:ASP108 3.5 76.4 1.0
CE1 C:HIS238 3.6 59.7 1.0
OD1 C:ASP157 3.6 71.0 1.0
OD1 C:ASP108 3.8 70.3 1.0
CG C:ASP108 3.9 67.0 1.0
CB C:ASP157 4.3 61.7 1.0
CG C:HIS238 4.3 53.4 1.0
CG C:HIS256 4.4 68.8 1.0
ND1 C:HIS256 4.4 69.0 1.0
ND1 C:HIS238 4.6 56.4 1.0
CG2 C:VAL260 4.6 57.2 1.0
N C:ASP108 4.6 68.4 1.0
CA C:HIS107 4.8 81.3 1.0

Zinc binding site 4 out of 6 in 5fb3

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Zinc binding site 4 out of 6 in the Structure of Glycerophosphate Dehydrogenase in Complex with Nadph


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Glycerophosphate Dehydrogenase in Complex with Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1002

b:47.2
occ:1.00
 OD1 D:ASP157 2.1 34.6 1.0
NE2 D:HIS256 2.2 38.7 1.0
NE2 D:HIS238 2.2 34.9 1.0
CD2 D:HIS256 2.9 35.8 1.0
CG D:ASP157 3.1 35.9 1.0
CD2 D:HIS238 3.1 36.5 1.0
CE1 D:HIS238 3.2 36.2 1.0
OD2 D:ASP157 3.3 38.5 1.0
CE1 D:HIS256 3.4 37.4 1.0
OD1 D:ASP108 3.6 56.5 1.0
CG D:HIS256 4.1 37.4 1.0
CG2 D:VAL260 4.2 36.9 1.0
ND1 D:HIS238 4.2 38.3 1.0
CG D:HIS238 4.2 36.2 1.0
CG D:ASP108 4.3 49.2 1.0
ND1 D:HIS256 4.3 37.3 1.0
NZ D:LYS161 4.4 46.3 1.0
OD2 D:ASP108 4.4 48.7 1.0
CB D:ASP157 4.4 35.4 1.0
C4N D:NDP1001 4.6 47.8 1.0
CB D:HIS107 4.6 46.3 1.0
O7N D:NDP1001 4.6 56.8 1.0
O D:CYS233 4.9 57.5 1.0

Zinc binding site 5 out of 6 in 5fb3

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Zinc binding site 5 out of 6 in the Structure of Glycerophosphate Dehydrogenase in Complex with Nadph


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Glycerophosphate Dehydrogenase in Complex with Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1002

b:57.0
occ:1.00
 OD1 E:ASP157 2.0 51.0 1.0
NE2 E:HIS238 2.2 37.1 1.0
NE2 E:HIS256 2.2 48.9 1.0
CG E:ASP157 2.9 49.3 1.0
CD2 E:HIS238 2.9 37.8 1.0
CD2 E:HIS256 3.1 49.2 1.0
OD2 E:ASP157 3.1 48.9 1.0
CE1 E:HIS256 3.2 50.7 1.0
CE1 E:HIS238 3.3 39.2 1.0
OD2 E:ASP108 4.0 54.9 1.0
O7N E:NDP1001 4.1 58.9 1.0
CG E:HIS238 4.2 38.8 1.0
ND1 E:HIS256 4.3 50.0 1.0
CG E:HIS256 4.3 49.8 1.0
OD1 E:ASP108 4.3 53.9 1.0
CB E:ASP157 4.3 48.1 1.0
ND1 E:HIS238 4.3 37.9 1.0
CG2 E:VAL260 4.3 55.4 1.0
CG E:ASP108 4.4 52.8 1.0
CB E:HIS107 4.4 49.9 1.0
NZ E:LYS161 4.6 52.2 1.0
C4N E:NDP1001 4.6 54.7 1.0
N E:ASP108 4.9 48.5 1.0
CA E:ASP157 5.0 49.1 1.0

Zinc binding site 6 out of 6 in 5fb3

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Zinc binding site 6 out of 6 in the Structure of Glycerophosphate Dehydrogenase in Complex with Nadph


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Glycerophosphate Dehydrogenase in Complex with Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn403

b:40.9
occ:1.00
 OD1 F:ASP157 2.0 36.1 1.0
NE2 F:HIS238 2.1 33.8 1.0
NE2 F:HIS256 2.2 28.0 1.0
O F:HOH527 3.0 45.8 1.0
CG F:ASP157 3.0 35.1 1.0
CE1 F:HIS238 3.0 35.6 1.0
CD2 F:HIS256 3.0 29.3 1.0
CD2 F:HIS238 3.1 35.4 1.0
OD2 F:ASP157 3.3 37.0 1.0
CE1 F:HIS256 3.3 28.6 1.0
OD1 F:ASP108 4.1 35.1 1.0
OD2 F:ASP108 4.1 41.8 1.0
CG2 F:VAL260 4.1 37.0 1.0
ND1 F:HIS238 4.1 36.9 1.0
CG F:HIS238 4.2 34.7 1.0
CG F:HIS256 4.3 30.7 1.0
CB F:ASP157 4.3 35.6 1.0
ND1 F:HIS256 4.4 29.8 1.0
CG F:ASP108 4.4 36.9 1.0
CB F:HIS107 4.4 35.4 1.0
NZ F:LYS161 4.6 43.3 1.0
C4N F:NDP402 4.8 36.5 1.0
O7N F:NDP402 4.8 37.8 1.0
CA F:ASP157 5.0 37.3 1.0

Reference:

J.Hayashi, K.Yamamoto, K.Yoneda, T.Ohshima, H.Sakuraba. Unique Coenzyme Binding Mode of Hyperthermophilic Archaeal Sn-Glycerol-1-Phosphate Dehydrogenase From Pyrobaculum Calidifontis Proteins V. 84 1786 2016.
ISSN: ESSN 1097-0134
PubMed: 27616573
DOI: 10.1002/PROT.25161
Page generated: Sun Oct 27 15:54:57 2024

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