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Nickel in PDB 4gui: 1.78 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Quinate

Enzymatic activity of 1.78 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Quinate

All present enzymatic activity of 1.78 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Quinate:
4.2.1.10;

Protein crystallography data

The structure of 1.78 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Quinate, PDB code: 4gui was solved by S.H.Light, G.Minasov, M.-E.Duban, L.Shuvalova, K.Kwon, A.Lavie, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.66 / 1.78
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.669, 74.427, 63.135, 90.00, 100.57, 90.00
R / Rfree (%) 15.9 / 18.8

Nickel Binding Sites:

The binding sites of Nickel atom in the 1.78 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Quinate (pdb code 4gui). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the 1.78 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Quinate, PDB code: 4gui:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 4gui

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Nickel binding site 1 out of 6 in the 1.78 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Quinate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of 1.78 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Quinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni302

b:62.1
occ:1.00
 O A:HOH484 2.1 44.2 1.0
O A:HOH483 2.2 51.3 1.0
O A:HOH487 2.3 63.5 1.0
NE2 A:HIS250 2.4 42.2 1.0
O A:HOH485 2.5 59.5 1.0
O A:HOH486 2.6 53.5 1.0
CD2 A:HIS250 3.2 39.9 1.0
CE1 A:HIS250 3.4 41.9 1.0
O A:HOH492 4.3 50.6 1.0
CG A:HIS250 4.4 37.6 1.0
ND1 A:HIS250 4.5 40.1 1.0

Nickel binding site 2 out of 6 in 4gui

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Nickel binding site 2 out of 6 in the 1.78 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Quinate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of 1.78 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Quinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni303

b:45.7
occ:0.70
 O A:HOH490 1.8 48.1 1.0
NE2 A:HIS134 2.2 41.5 1.0
O A:HOH489 2.3 53.5 1.0
O A:HOH491 2.7 60.5 1.0
CD2 A:HIS134 3.0 40.3 1.0
CE1 A:HIS134 3.3 40.8 1.0
OD1 A:ASP106 3.3 58.1 1.0
CG A:HIS134 4.2 38.8 1.0
OH A:TYR130 4.3 40.9 1.0
ND1 A:HIS134 4.3 40.1 1.0
CG A:ASP106 4.5 51.7 1.0
CZ A:TYR130 4.9 38.7 1.0

Nickel binding site 3 out of 6 in 4gui

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Nickel binding site 3 out of 6 in the 1.78 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Quinate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of 1.78 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Quinate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni302

b:51.8
occ:1.00
 O B:HOH506 1.9 45.0 1.0
O B:HOH507 2.1 36.8 1.0
O B:HOH505 2.2 47.6 1.0
NE2 B:HIS250 2.3 36.9 1.0
O B:HOH508 2.3 44.4 1.0
O B:HOH504 2.7 54.1 1.0
CD2 B:HIS250 3.1 36.0 1.0
CE1 B:HIS250 3.4 37.2 1.0
O B:HOH453 4.1 47.6 1.0
CG B:HIS250 4.3 34.1 1.0
ND1 B:HIS250 4.4 35.0 1.0

Nickel binding site 4 out of 6 in 4gui

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Nickel binding site 4 out of 6 in the 1.78 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Quinate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of 1.78 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Quinate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni303

b:36.4
occ:1.00
 O B:HOH510 1.8 34.4 1.0
O B:HOH512 2.1 36.9 1.0
NE2 B:HIS134 2.1 31.4 1.0
O B:HOH511 2.2 41.1 1.0
O B:HOH533 2.2 37.6 1.0
O B:HOH509 2.3 38.3 1.0
CD2 B:HIS134 3.0 32.4 1.0
CE1 B:HIS134 3.2 30.3 1.0
O B:HOH534 3.5 53.6 1.0
OD1 B:ASP106 4.1 35.2 1.0
O B:HOH444 4.1 51.0 1.0
CG B:HIS134 4.2 30.9 1.0
ND1 B:HIS134 4.2 29.5 1.0
O B:HOH535 4.4 55.8 1.0
O B:HOH530 4.5 45.7 1.0
OH B:TYR130 4.7 31.3 1.0

Nickel binding site 5 out of 6 in 4gui

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Nickel binding site 5 out of 6 in the 1.78 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Quinate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of 1.78 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Quinate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni304

b:31.1
occ:0.70
 O B:HOH519 1.8 43.9 1.0
O B:HOH514 1.9 35.7 1.0
ND1 B:HIS132 2.2 28.3 1.0
O B:HOH513 2.2 40.0 1.0
CG B:HIS132 3.1 28.6 1.0
CE1 B:HIS132 3.1 29.7 1.0
CB B:HIS132 3.4 27.5 1.0
NE2 B:HIS132 4.3 26.5 1.0
CD2 B:HIS132 4.3 26.1 1.0
O B:HOH520 4.7 55.7 1.0
CA B:HIS132 4.9 27.8 1.0

Nickel binding site 6 out of 6 in 4gui

Go back to Nickel Binding Sites List in 4gui
Nickel binding site 6 out of 6 in the 1.78 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Quinate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of 1.78 Angstrom Crystal Structure of the Salmonella Enterica 3- Dehydroquinate Dehydratase (Arod) in Complex with Quinate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni305

b:52.4
occ:0.70
 O B:HOH516 1.9 51.7 1.0
O B:HOH515 2.1 26.3 1.0
O B:HOH517 2.3 41.1 1.0
ND1 B:HIS146 2.9 47.7 1.0
CG B:HIS146 3.8 42.4 1.0
CB B:HIS146 3.8 36.9 1.0
CE1 B:HIS146 3.9 48.9 1.0
NZ B:LYS147 4.0 37.5 1.0
O B:HOH518 4.6 58.5 1.0
OD1 B:ASP144 4.6 27.5 1.0
O B:HOH432 4.8 33.8 1.0
CD2 B:HIS146 5.0 45.6 1.0

Reference:

S.H.Light, A.Antanasijevic, S.N.Krishna, M.Caffrey, W.F.Anderson, A.Lavie. Crystal Structures of Type I Dehydroquinate Dehydratase in Complex with Quinate and Shikimate Suggest A Novel Mechanism of Schiff Base Formation. Biochemistry V. 53 872 2014.
ISSN: ISSN 0006-2960
PubMed: 24437575
DOI: 10.1021/BI4015506
Page generated: Wed Oct 9 18:11:24 2024

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