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Nickel in PDB 7oi1: Crystal Structure of Synechocystis Sp PCC6803 Guanidinium Hydrolase

Enzymatic activity of Crystal Structure of Synechocystis Sp PCC6803 Guanidinium Hydrolase

All present enzymatic activity of Crystal Structure of Synechocystis Sp PCC6803 Guanidinium Hydrolase:
3.5.3.11;

Protein crystallography data

The structure of Crystal Structure of Synechocystis Sp PCC6803 Guanidinium Hydrolase, PDB code: 7oi1 was solved by J.R.Fleming, O.M.Mayans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.15 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.36, 140.21, 86.85, 90, 119.75, 90
R / Rfree (%) 17.3 / 20.8

Other elements in 7oi1:

The structure of Crystal Structure of Synechocystis Sp PCC6803 Guanidinium Hydrolase also contains other interesting chemical elements:

Arsenic (As) 3 atoms
Chlorine (Cl) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Synechocystis Sp PCC6803 Guanidinium Hydrolase (pdb code 7oi1). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Crystal Structure of Synechocystis Sp PCC6803 Guanidinium Hydrolase, PDB code: 7oi1:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 7oi1

Go back to Nickel Binding Sites List in 7oi1
Nickel binding site 1 out of 6 in the Crystal Structure of Synechocystis Sp PCC6803 Guanidinium Hydrolase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Synechocystis Sp PCC6803 Guanidinium Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni402

b:43.2
occ:0.86
 O2 A:CAC404 1.9 51.5 0.8
ND1 A:HIS201 2.2 41.1 1.0
OD1 A:ASP199 2.2 37.4 1.0
OD2 A:ASP291 2.2 40.0 1.0
OD2 A:ASP293 2.3 42.5 1.0
OD1 A:ASP293 2.4 43.7 1.0
CG A:ASP293 2.7 42.1 1.0
AS A:CAC404 3.0 49.4 0.8
CE1 A:HIS201 3.0 44.2 1.0
CG A:ASP291 3.1 45.0 1.0
O1 A:CAC404 3.1 43.0 0.8
NI A:NI403 3.2 45.3 0.9
CG A:ASP199 3.2 40.6 1.0
CG A:HIS201 3.4 43.5 1.0
OD2 A:ASP199 3.5 49.2 1.0
OD1 A:ASP291 3.7 45.0 1.0
CB A:HIS201 3.8 41.8 1.0
CB A:ASP291 4.0 42.0 1.0
N A:HIS201 4.2 36.8 1.0
CB A:ASP293 4.2 38.6 1.0
NE2 A:HIS201 4.2 39.9 1.0
C2 A:CAC404 4.3 41.9 0.8
N A:ARG200 4.4 38.0 1.0
CD2 A:HIS201 4.4 42.5 1.0
CB A:ASP199 4.5 38.7 1.0
C1 A:CAC404 4.6 41.9 0.8
CA A:HIS201 4.6 35.4 1.0
O A:HOH543 4.7 39.4 1.0
OD2 A:ASP203 4.8 42.5 1.0
CA A:ASP199 4.8 39.7 1.0
CE3 A:TRP305 4.9 46.3 1.0
CB A:TRP305 4.9 41.4 1.0

Nickel binding site 2 out of 6 in 7oi1

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Nickel binding site 2 out of 6 in the Crystal Structure of Synechocystis Sp PCC6803 Guanidinium Hydrolase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Synechocystis Sp PCC6803 Guanidinium Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni403

b:45.3
occ:0.91
 OD2 A:ASP199 2.1 49.2 1.0
ND1 A:HIS174 2.2 41.1 1.0
O2 A:CAC404 2.2 51.5 0.8
OD2 A:ASP203 2.2 42.5 1.0
OD2 A:ASP291 2.3 40.0 1.0
C2 A:CAC404 2.7 41.9 0.8
AS A:CAC404 2.9 49.4 0.8
CG A:ASP199 3.0 40.6 1.0
CE1 A:HIS174 3.1 44.7 1.0
NI A:NI402 3.2 43.2 0.9
CG A:HIS174 3.2 45.3 1.0
CG A:ASP203 3.2 44.1 1.0
OD1 A:ASP199 3.2 37.4 1.0
CG A:ASP291 3.2 45.0 1.0
OD1 A:ASP203 3.5 45.5 1.0
CB A:HIS174 3.5 41.1 1.0
CB A:ASP291 3.6 42.0 1.0
O1 A:CAC404 4.1 43.0 0.8
NE2 A:HIS197 4.1 41.6 1.0
NE2 A:HIS174 4.2 42.1 1.0
CD2 A:HIS174 4.3 39.0 1.0
CB A:ASP199 4.4 38.7 1.0
OD1 A:ASP291 4.4 45.0 1.0
C1 A:CAC404 4.5 41.9 0.8
O A:HIS214 4.5 42.5 1.0
CB A:ASP203 4.6 38.1 1.0
O A:HIS201 4.6 41.8 1.0
CE1 A:HIS197 4.8 43.2 1.0
ND1 A:HIS201 4.9 41.1 1.0
OE2 A:GLU336 4.9 39.5 1.0
OD2 A:ASP293 4.9 42.5 1.0
CB A:HIS201 4.9 41.8 1.0
CA A:ASP291 4.9 38.8 1.0
OD1 A:ASP293 5.0 43.7 1.0
CG A:GLU336 5.0 38.1 1.0

Nickel binding site 3 out of 6 in 7oi1

Go back to Nickel Binding Sites List in 7oi1
Nickel binding site 3 out of 6 in the Crystal Structure of Synechocystis Sp PCC6803 Guanidinium Hydrolase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Synechocystis Sp PCC6803 Guanidinium Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni401

b:47.7
occ:0.90
 OD2 B:ASP203 2.2 45.2 1.0
O2 B:CAC403 2.2 51.4 0.8
OD2 B:ASP291 2.2 41.6 1.0
OD2 B:ASP199 2.2 44.3 1.0
ND1 B:HIS174 2.3 41.4 1.0
C2 B:CAC403 2.6 44.5 0.8
AS B:CAC403 2.9 53.9 0.8
CG B:ASP199 3.1 46.0 1.0
CG B:ASP203 3.2 42.4 1.0
CG B:HIS174 3.2 42.6 1.0
CG B:ASP291 3.3 41.7 1.0
NI B:NI402 3.3 47.8 0.8
OD1 B:ASP199 3.3 41.8 1.0
CE1 B:HIS174 3.3 46.3 1.0
CB B:HIS174 3.5 42.8 1.0
OD1 B:ASP203 3.5 44.3 1.0
CB B:ASP291 3.7 42.4 1.0
O1 B:CAC403 4.0 48.3 0.8
NE2 B:HIS197 4.1 44.3 1.0
OD1 B:ASP291 4.3 40.0 1.0
CD2 B:HIS174 4.4 41.8 1.0
NE2 B:HIS174 4.4 41.8 1.0
CB B:ASP199 4.5 42.3 1.0
C1 B:CAC403 4.5 41.5 0.8
CB B:ASP203 4.5 43.3 1.0
O B:HIS214 4.5 43.5 1.0
O B:HIS201 4.6 44.5 1.0
CB B:HIS201 4.9 45.6 1.0
ND1 B:HIS201 4.9 45.3 1.0
CG B:GLU336 4.9 36.4 1.0
CE1 B:HIS197 4.9 48.4 1.0
CA B:HIS174 5.0 37.1 1.0
OE2 B:GLU336 5.0 41.0 1.0
OD2 B:ASP293 5.0 41.0 1.0

Nickel binding site 4 out of 6 in 7oi1

Go back to Nickel Binding Sites List in 7oi1
Nickel binding site 4 out of 6 in the Crystal Structure of Synechocystis Sp PCC6803 Guanidinium Hydrolase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Synechocystis Sp PCC6803 Guanidinium Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni402

b:47.8
occ:0.85
 O2 B:CAC403 2.0 51.4 0.8
OD1 B:ASP199 2.2 41.8 1.0
ND1 B:HIS201 2.3 45.3 1.0
OD1 B:ASP293 2.3 42.1 1.0
OD2 B:ASP293 2.4 41.0 1.0
OD2 B:ASP291 2.4 41.6 1.0
CG B:ASP293 2.7 43.5 1.0
CE1 B:HIS201 3.1 45.5 1.0
CG B:ASP291 3.1 41.7 1.0
AS B:CAC403 3.2 53.9 0.8
CG B:ASP199 3.2 46.0 1.0
O1 B:CAC403 3.2 48.3 0.8
NI B:NI401 3.3 47.7 0.9
CG B:HIS201 3.4 45.3 1.0
OD2 B:ASP199 3.6 44.3 1.0
OD1 B:ASP291 3.6 40.0 1.0
CB B:HIS201 3.8 45.6 1.0
CB B:ASP291 4.0 42.4 1.0
N B:HIS201 4.1 39.8 1.0
CB B:ASP293 4.2 43.7 1.0
NE2 B:HIS201 4.3 47.6 1.0
N B:ARG200 4.3 41.1 1.0
CD2 B:HIS201 4.4 52.1 1.0
C2 B:CAC403 4.5 44.5 0.8
CB B:ASP199 4.5 42.3 1.0
CA B:HIS201 4.6 42.6 1.0
C1 B:CAC403 4.7 41.5 0.8
O B:HOH532 4.7 40.9 1.0
CA B:ASP199 4.8 42.1 1.0
OD2 B:ASP203 4.8 45.2 1.0
CB B:TRP305 4.9 44.4 1.0
C B:ARG200 4.9 43.4 1.0
CE3 B:TRP305 5.0 48.1 1.0
CA B:ARG200 5.0 42.7 1.0

Nickel binding site 5 out of 6 in 7oi1

Go back to Nickel Binding Sites List in 7oi1
Nickel binding site 5 out of 6 in the Crystal Structure of Synechocystis Sp PCC6803 Guanidinium Hydrolase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Synechocystis Sp PCC6803 Guanidinium Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni402

b:49.6
occ:0.89
 O2 C:CAC404 2.1 48.8 0.8
OD1 C:ASP199 2.2 39.1 1.0
OD2 C:ASP293 2.2 42.2 1.0
OD2 C:ASP291 2.3 42.2 1.0
ND1 C:HIS201 2.3 43.6 1.0
OD1 C:ASP293 2.4 42.5 1.0
CG C:ASP293 2.6 43.1 1.0
CG C:ASP291 3.0 42.9 1.0
CE1 C:HIS201 3.1 38.7 1.0
NI C:NI403 3.2 49.3 0.9
CG C:ASP199 3.2 44.5 1.0
AS C:CAC404 3.2 54.5 0.8
O1 C:CAC404 3.3 45.0 0.8
CG C:HIS201 3.4 44.7 1.0
OD1 C:ASP291 3.5 43.7 1.0
OD2 C:ASP199 3.5 43.6 1.0
CB C:HIS201 3.8 44.1 1.0
CB C:ASP291 3.9 41.6 1.0
CB C:ASP293 4.2 41.8 1.0
N C:HIS201 4.2 41.8 1.0
NE2 C:HIS201 4.3 39.9 1.0
N C:ARG200 4.4 42.5 1.0
C2 C:CAC404 4.4 40.2 0.8
CD2 C:HIS201 4.5 42.1 1.0
CB C:ASP199 4.5 38.0 1.0
CA C:HIS201 4.6 38.6 1.0
C1 C:CAC404 4.8 40.9 0.8
CA C:ASP199 4.8 40.8 1.0
O C:HOH513 4.8 46.3 1.0
OD2 C:ASP203 4.9 49.8 1.0
CE3 C:TRP305 4.9 50.6 1.0
CB C:TRP305 4.9 41.2 1.0

Nickel binding site 6 out of 6 in 7oi1

Go back to Nickel Binding Sites List in 7oi1
Nickel binding site 6 out of 6 in the Crystal Structure of Synechocystis Sp PCC6803 Guanidinium Hydrolase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of Synechocystis Sp PCC6803 Guanidinium Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni403

b:49.3
occ:0.90
 OD2 C:ASP291 2.1 42.2 1.0
OD2 C:ASP199 2.2 43.6 1.0
OD2 C:ASP203 2.2 49.8 1.0
O2 C:CAC404 2.3 48.8 0.8
ND1 C:HIS174 2.3 43.5 1.0
C2 C:CAC404 2.5 40.2 0.8
AS C:CAC404 2.9 54.5 0.8
CG C:ASP199 3.1 44.5 1.0
CG C:ASP291 3.1 42.9 1.0
NI C:NI402 3.2 49.6 0.9
CG C:ASP203 3.2 44.6 1.0
CE1 C:HIS174 3.2 43.1 1.0
OD1 C:ASP199 3.3 39.1 1.0
CG C:HIS174 3.3 42.2 1.0
OD1 C:ASP203 3.5 42.1 1.0
CB C:ASP291 3.5 41.6 1.0
CB C:HIS174 3.6 41.5 1.0
O1 C:CAC404 3.9 45.0 0.8
NE2 C:HIS197 4.1 46.8 1.0
OD1 C:ASP291 4.3 43.7 1.0
NE2 C:HIS174 4.3 43.6 1.0
CD2 C:HIS174 4.4 41.8 1.0
CB C:ASP199 4.4 38.0 1.0
C1 C:CAC404 4.6 40.9 0.8
CB C:ASP203 4.6 44.9 1.0
O C:HIS201 4.6 43.1 1.0
O C:HIS214 4.7 44.3 1.0
OD2 C:ASP293 4.9 42.2 1.0
CA C:ASP291 4.9 41.4 1.0
CE1 C:HIS197 4.9 43.5 1.0
ND1 C:HIS201 4.9 43.6 1.0
CB C:HIS201 4.9 44.1 1.0
CG C:GLU336 5.0 38.9 1.0
OE2 C:GLU336 5.0 43.4 1.0

Reference:

D.Funck, M.Sinn, J.R.Fleming, M.Stanoppi, J.Dietrich, R.Lopez-Igual, O.Mayans, J.S.Hartig. Guanidine Hydrolase Is A Novel NI2+-Dependent Enzyme From the Arginase Family Nature 2021.
ISSN: ESSN 1476-4687
Page generated: Thu Oct 10 09:21:41 2024

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