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Nickel in PDB 4xca: Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound

Protein crystallography data

The structure of Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound, PDB code: 4xca was solved by K.M.Mcculloch, E.K.Mccranie, M.Sarwar, J.L.Mathieu, B.L.Gitschlag, Y.Du, B.O.Bachmann, T.M.Iverson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.71 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.399, 112.044, 177.803, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 23.6

Other elements in 4xca:

The structure of Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound also contains other interesting chemical elements:

Caesium (Cs) 3 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound (pdb code 4xca). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound, PDB code: 4xca:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 4xca

Go back to Nickel Binding Sites List in 4xca
Nickel binding site 1 out of 4 in the Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound


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 Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:30.1
occ:1.00
O A:HOH458 1.9 20.4 1.0
O A:HOH459 2.1 31.8 1.0
NE2 A:HIS206 2.1 24.9 1.0
NE2 A:HIS102 2.2 21.4 1.0
O5 A:AKG302 2.2 27.1 1.0
O1 A:AKG302 2.3 32.4 1.0
C2 A:AKG302 2.9 31.6 1.0
C1 A:AKG302 3.0 30.0 1.0
CD2 A:HIS206 3.0 20.6 1.0
CE1 A:HIS102 3.1 25.4 1.0
CE1 A:HIS206 3.2 18.8 1.0
CD2 A:HIS102 3.2 25.7 1.0
O A:HOH530 4.0 43.6 1.0
OE1 A:GLU202 4.1 33.6 1.0
OE2 A:GLU202 4.1 27.0 1.0
CG A:HIS206 4.2 26.2 1.0
O2 A:AKG302 4.2 31.2 1.0
ND1 A:HIS206 4.2 19.3 1.0
ND1 A:HIS102 4.3 27.7 1.0
CG A:HIS102 4.3 25.0 1.0
C3 A:AKG302 4.4 25.9 1.0
NZ A:LYS137 4.5 23.6 1.0
CD A:GLU202 4.6 24.9 1.0
CD2 A:LEU200 4.8 24.5 1.0
C4 A:AKG302 4.9 25.4 1.0
CD2 A:LEU99 5.0 23.5 1.0

Nickel binding site 2 out of 4 in 4xca

Go back to Nickel Binding Sites List in 4xca
Nickel binding site 2 out of 4 in the Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound


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 Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni301

b:32.3
occ:1.00
O B:HOH462 1.9 29.8 1.0
O5 B:AKG302 2.1 35.0 1.0
O B:HOH463 2.1 33.6 1.0
NE2 B:HIS102 2.2 32.4 1.0
NE2 B:HIS206 2.2 33.0 1.0
O1 B:AKG302 2.2 40.7 1.0
C2 B:AKG302 2.8 37.6 1.0
C1 B:AKG302 2.8 37.4 1.0
CE1 B:HIS102 3.0 31.3 1.0
CD2 B:HIS206 3.0 27.5 1.0
CD2 B:HIS102 3.1 31.4 1.0
CE1 B:HIS206 3.2 25.3 1.0
O2 B:AKG302 4.1 40.6 1.0
OE1 B:GLU202 4.1 36.9 1.0
ND1 B:HIS102 4.1 31.0 1.0
CG B:HIS206 4.2 26.8 1.0
CG B:HIS102 4.2 27.6 1.0
OE2 B:GLU202 4.2 32.2 1.0
C3 B:AKG302 4.2 31.3 1.0
ND1 B:HIS206 4.2 28.3 1.0
NZ B:LYS137 4.3 36.1 1.0
CD B:GLU202 4.6 37.0 1.0
CD2 B:LEU200 4.7 25.9 1.0
C4 B:AKG302 4.9 34.5 1.0
CD2 B:LEU99 4.9 35.1 1.0

Nickel binding site 3 out of 4 in 4xca

Go back to Nickel Binding Sites List in 4xca
Nickel binding site 3 out of 4 in the Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound


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 Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni301

b:35.6
occ:1.00
O C:HOH492 1.9 26.1 1.0
O C:HOH493 2.1 30.9 1.0
NE2 C:HIS206 2.1 23.6 1.0
NE2 C:HIS102 2.2 34.7 1.0
O5 C:AKG302 2.3 27.6 1.0
O2 C:AKG302 2.4 46.5 1.0
CD2 C:HIS206 3.0 21.9 1.0
C2 C:AKG302 3.0 38.0 1.0
C1 C:AKG302 3.1 38.0 1.0
CE1 C:HIS102 3.1 23.7 1.0
CE1 C:HIS206 3.1 24.6 1.0
CD2 C:HIS102 3.3 27.0 1.0
OE1 C:GLU202 4.0 27.5 1.0
ND1 C:HIS206 4.2 23.8 1.0
CG C:HIS206 4.2 24.6 1.0
ND1 C:HIS102 4.3 28.3 1.0
O1 C:AKG302 4.3 39.8 1.0
CG C:HIS102 4.4 25.5 1.0
OE2 C:GLU202 4.4 39.3 1.0
C3 C:AKG302 4.5 28.4 1.0
NZ C:LYS137 4.6 28.6 1.0
CD C:GLU202 4.7 33.5 1.0
CD2 C:LEU99 4.9 26.7 1.0

Nickel binding site 4 out of 4 in 4xca

Go back to Nickel Binding Sites List in 4xca
Nickel binding site 4 out of 4 in the Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound


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 Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni301

b:27.4
occ:1.00
O D:HOH495 2.1 22.1 1.0
O1 D:AKG302 2.1 36.5 1.0
NE2 D:HIS206 2.2 22.2 1.0
NE2 D:HIS102 2.2 32.0 1.0
O5 D:AKG302 2.2 27.9 1.0
O D:HOH496 2.2 33.1 1.0
C1 D:AKG302 2.8 32.9 1.0
C2 D:AKG302 2.9 29.5 1.0
CD2 D:HIS206 3.1 22.1 1.0
CE1 D:HIS102 3.1 26.8 1.0
CE1 D:HIS206 3.2 19.1 1.0
CD2 D:HIS102 3.2 33.6 1.0
O2 D:AKG302 4.0 31.6 1.0
OE1 D:GLU202 4.2 32.2 1.0
ND1 D:HIS102 4.2 26.5 1.0
NZ D:LYS137 4.2 27.7 1.0
CG D:HIS206 4.2 22.5 1.0
ND1 D:HIS206 4.2 25.2 1.0
OE2 D:GLU202 4.3 27.3 1.0
CG D:HIS102 4.3 26.2 1.0
O D:HOH523 4.4 39.5 1.0
C3 D:AKG302 4.4 24.3 1.0
CD D:GLU202 4.7 28.0 1.0
CD2 D:LEU200 4.7 24.9 1.0
CD2 D:LEU99 4.8 18.7 1.0
C4 D:AKG302 5.0 25.1 1.0

Reference:

K.M.Mcculloch, E.K.Mccranie, J.A.Smith, M.Sarwar, J.L.Mathieu, B.L.Gitschlag, Y.Du, B.O.Bachmann, T.M.Iverson. Oxidative Cyclizations in Orthosomycin Biosynthesis Expand the Known Chemistry of An Oxygenase Superfamily. Proc.Natl.Acad.Sci.Usa V. 112 11547 2015.
ISSN: ESSN 1091-6490
PubMed: 26240321
DOI: 10.1073/PNAS.1500964112
Page generated: Wed Dec 16 01:38:12 2020

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