Atomistry » Zinc » PDB 5f8h-5fi3 » 5fb3
Atomistry »
  Zinc »
    PDB 5f8h-5fi3 »
      5fb3 »

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

Go back to Zinc Binding Sites List in 5fb3
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

Go back to Zinc Binding Sites List in 5fb3
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

Go back to Zinc Binding Sites List in 5fb3
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

Go back to Zinc Binding Sites List in 5fb3
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

Go back to Zinc Binding Sites List in 5fb3
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

Go back to Zinc Binding Sites List in 5fb3
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: Wed Dec 16 06:13:30 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy