Atomistry » Magnesium » PDB 8cgj-8csu » 8cjy
Atomistry »
  Magnesium »
    PDB 8cgj-8csu »
      8cjy »

Magnesium in PDB 8cjy: [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T

Enzymatic activity of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T

All present enzymatic activity of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T:
1.12.7.2;

Protein crystallography data

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T, PDB code: 8cjy was solved by C.Brocks, J.Duan, E.Hofmann, T.Happe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.33 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.73, 72.29, 103.04, 90, 96.95, 90
R / Rfree (%) 16.4 / 18.7

Other elements in 8cjy:

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Iron (Fe) 40 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T (pdb code 8cjy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T, PDB code: 8cjy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8cjy

Go back to Magnesium Binding Sites List in 8cjy
Magnesium binding site 1 out of 4 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg607

b:32.9
occ:1.00
 O A:HOH900 2.0 35.8 1.0
O A:HOH784 2.1 26.4 1.0
O A:HOH811 2.1 27.7 1.0
O A:HOH897 2.1 29.7 1.0
O A:HOH835 2.1 30.7 1.0
O A:LEU218 2.1 29.1 1.0
C A:LEU218 3.2 29.8 1.0
HA A:LEU218 3.3 31.6 1.0
CA A:LEU218 3.7 26.3 1.0
OD2 A:ASP263 4.0 29.4 1.0
HG23 A:VAL225 4.1 27.6 1.0
O A:ALA220 4.1 29.1 1.0
O A:HOH862 4.2 28.8 1.0
HB3 A:LEU218 4.2 28.8 1.0
O A:LYS223 4.2 28.1 1.0
OD1 A:ASP263 4.2 29.7 1.0
O A:ALA217 4.2 26.0 1.0
HA A:ASN219 4.3 39.2 1.0
N A:ASN219 4.3 30.1 1.0
HD23 A:LEU218 4.4 38.8 1.0
CG A:ASP263 4.6 30.4 1.0
CB A:LEU218 4.6 23.9 1.0
O A:GLY261 4.6 30.0 1.0
CA A:ASN219 4.7 32.7 1.0
HD22 A:LEU218 4.8 38.8 1.0
H A:ALA220 4.9 33.8 1.0
N A:LEU218 4.9 26.9 1.0
C A:ASN219 4.9 32.5 1.0
N A:ALA220 4.9 28.2 1.0
CG2 A:VAL225 5.0 23.0 1.0
CD2 A:LEU218 5.0 32.3 1.0

Magnesium binding site 2 out of 4 in 8cjy

Go back to Magnesium Binding Sites List in 8cjy
Magnesium binding site 2 out of 4 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg609

b:28.8
occ:1.00
 OD1 A:ASP42 2.0 34.0 1.0
OD1 A:ASN40 2.0 27.9 1.0
O A:HOH814 2.1 29.4 1.0
O A:HOH932 2.1 33.9 1.0
O A:HOH852 2.1 29.7 1.0
O A:HOH843 2.1 31.7 1.0
CG A:ASP42 3.2 37.2 1.0
CG A:ASN40 3.2 29.9 1.0
H A:ASN40 3.2 29.3 1.0
HD21 A:ASN40 3.6 34.8 1.0
OD2 A:ASP42 3.7 45.0 1.0
ND2 A:ASN40 3.8 28.9 1.0
HB3 A:ASP63 3.9 31.3 1.0
HB2 A:ASP63 4.0 31.3 1.0
HA A:ASP42 4.0 37.0 1.0
O A:HOH968 4.1 44.6 1.0
N A:ASN40 4.1 24.4 1.0
O A:HOH743 4.1 37.8 1.0
O B:HOH788 4.2 40.3 1.0
OD1 B:ASN452 4.2 36.9 1.0
HB3 B:ASN452 4.3 29.4 1.0
O A:ASN40 4.3 27.1 1.0
OD2 A:ASP63 4.3 30.0 1.0
CB A:ASP63 4.4 26.1 1.0
CB A:ASP42 4.4 28.9 1.0
O A:HOH888 4.4 43.5 1.0
CB A:ASN40 4.4 25.1 1.0
C A:ASN40 4.5 27.1 1.0
HA A:CYS39 4.5 30.3 1.0
CA A:ASN40 4.5 26.1 1.0
CG B:ASN452 4.6 31.2 1.0
CA A:ASP42 4.6 30.8 1.0
HD22 A:ASN40 4.7 34.8 1.0
HB3 A:ASP42 4.7 34.6 1.0
O B:HOH895 4.7 28.4 1.0
HB2 A:CYS39 4.7 51.8 1.0
HB3 A:ASN40 4.8 30.2 1.0
HE2 A:LYS45 4.9 42.8 0.5
CG A:ASP63 4.9 32.0 1.0
N A:ASP42 4.9 29.6 1.0
HE2 A:LYS45 4.9 42.8 0.5
CB B:ASN452 4.9 24.5 1.0
H B:GLY453 4.9 27.9 1.0
H A:ASP42 5.0 35.6 1.0

Magnesium binding site 3 out of 4 in 8cjy

Go back to Magnesium Binding Sites List in 8cjy
Magnesium binding site 3 out of 4 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg607

b:32.5
occ:1.00
 O B:HOH793 2.0 24.4 1.0
O B:HOH879 2.1 32.3 1.0
O B:HOH897 2.1 34.5 1.0
O B:HOH744 2.1 29.2 1.0
O B:HOH813 2.1 29.4 1.0
O B:LEU218 2.2 32.5 1.0
C B:LEU218 3.3 26.9 1.0
HA B:LEU218 3.3 29.2 1.0
CA B:LEU218 3.8 24.4 1.0
OD2 B:ASP263 3.9 26.7 1.0
O B:HOH740 4.0 28.9 1.0
O B:ALA220 4.0 29.1 1.0
HG23 B:VAL225 4.1 29.7 1.0
O B:LYS223 4.2 26.6 1.0
OD1 B:ASP263 4.2 28.0 1.0
O B:ALA217 4.3 25.2 1.0
HB3 B:LEU218 4.3 30.1 1.0
N B:ASN219 4.4 27.7 1.0
HA B:ASN219 4.4 36.7 1.0
HD23 B:LEU218 4.5 33.9 1.0
CG B:ASP263 4.5 31.9 1.0
O B:GLY261 4.6 27.3 1.0
CB B:LEU218 4.7 25.1 1.0
HD22 B:LEU218 4.8 33.9 1.0
HA B:PRO221 4.8 37.0 1.0
CA B:ASN219 4.8 30.6 1.0
H B:ALA220 4.9 34.0 1.0
C B:ASN219 4.9 34.1 1.0
C B:ALA220 4.9 32.2 1.0
HG21 B:VAL225 4.9 29.7 1.0
N B:ALA220 5.0 28.3 1.0
N B:LEU218 5.0 23.5 1.0
CG2 B:VAL225 5.0 24.8 1.0

Magnesium binding site 4 out of 4 in 8cjy

Go back to Magnesium Binding Sites List in 8cjy
Magnesium binding site 4 out of 4 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S357T within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg609

b:37.6
occ:1.00
 O B:HOH960 2.0 45.2 1.0
O B:HOH859 2.1 35.8 1.0
O B:HOH907 2.1 36.4 1.0
O B:HOH734 2.1 42.1 1.0
OD1 B:ASP42 2.1 43.7 1.0
OD1 B:ASN40 2.1 30.4 1.0
CG B:ASN40 3.2 31.8 1.0
H B:ASN40 3.3 34.4 1.0
CG B:ASP42 3.3 42.1 1.0
HD21 B:ASN40 3.4 46.0 1.0
ND2 B:ASN40 3.7 38.4 1.0
OD2 B:ASP42 3.9 47.0 1.0
HA B:ASP42 4.0 44.1 1.0
N B:ASN40 4.1 28.7 1.0
O A:HOH741 4.1 41.0 1.0
HB3 B:ASP63 4.2 39.8 1.0
OD2 B:ASP63 4.3 34.4 1.0
O B:ASN40 4.3 27.2 1.0
HB3 A:ASN452 4.4 36.2 1.0
CB B:ASN40 4.4 26.7 1.0
HB3 B:CYS39 4.4 51.5 1.0
CB B:ASP42 4.5 38.2 1.0
HA B:CYS39 4.5 37.6 1.0
HB2 B:ASP63 4.5 39.8 1.0
HD22 B:ASN40 4.6 46.0 1.0
CG A:ASN452 4.6 35.2 1.0
C B:ASN40 4.6 25.1 1.0
CA B:ASN40 4.6 28.1 1.0
ND2 A:ASN452 4.6 41.1 1.0
CA B:ASP42 4.6 36.8 1.0
OD1 A:ASN452 4.7 38.8 1.0
HD21 A:ASN452 4.7 49.3 1.0
CB B:ASP63 4.8 33.1 1.0
HB3 B:ASP42 4.8 45.8 1.0
HB3 B:ASN40 4.8 32.1 1.0
HD22 A:ASN452 4.8 49.3 1.0
H A:GLY453 4.9 29.9 1.0
N B:ASP42 4.9 32.9 1.0
H B:ASP42 4.9 39.5 1.0
HD2 B:LYS45 4.9 54.9 1.0
O A:HOH945 5.0 40.6 1.0
CB A:ASN452 5.0 30.1 1.0

Reference:

C.Brocks, C.K.Das, J.Duan, S.Yadav, U.P.Apfel, S.Ghosh, E.Hofmann, M.Winkler, V.Engelbrecht, L.V.Schafer, T.Happe. A Dynamic Water Channel Affects O2 Stability in [Fefe] Hydrogenases. Chemsuschem 01365 2023.
ISSN: ESSN 1864-564X
PubMed: 37830175
DOI: 10.1002/CSSC.202301365
Page generated: Thu Dec 28 08:45:21 2023

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