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Nickel in PDB 9gp1: Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E

Enzymatic activity of Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E

All present enzymatic activity of Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E:
1.14.11.66; 1.14.11.69;

Protein crystallography data

The structure of Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E, PDB code: 9gp1 was solved by M.Fairhead, C.Strain-Damerell, M.Ye, S.R.Mackinnon, D.Pinkas, E.M.Maclean, L.Koekemoer, D.Damerell, T.Krojer, C.H.Arrowsmith, A.Edwards, C.Bountra, W.Yue, N.Burgess-Brown, B.Marsden, F.Von Delft, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.14 / 2.21
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.03, 101.6, 141.43, 90, 99.38, 90
R / Rfree (%) 21.5 / 25.9

Other elements in 9gp1:

The structure of Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E (pdb code 9gp1). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E, PDB code: 9gp1:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 9gp1

Go back to Nickel Binding Sites List in 9gp1
Nickel binding site 1 out of 4 in the Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni401

b:48.8
occ:1.00
 NE2 A:HIS189 2.1 40.9 1.0
O A:HOH546 2.1 27.3 1.0
O A:HOH538 2.2 26.2 1.0
OE1 A:GLU191 2.2 29.6 1.0
NE2 A:HIS277 2.4 39.2 1.0
CE1 A:HIS189 2.9 40.1 1.0
CD2 A:HIS189 3.2 35.6 1.0
CD A:GLU191 3.2 28.5 1.0
CD2 A:HIS277 3.3 35.4 1.0
CE1 A:HIS277 3.3 29.9 1.0
OE2 A:GLU191 3.4 33.6 1.0
ND1 A:HIS189 4.1 40.5 1.0
CG A:HIS189 4.2 36.0 1.0
ND1 A:HIS277 4.4 34.7 1.0
CG A:HIS277 4.4 36.9 1.0
OG A:SER197 4.5 37.5 1.0
CG A:GLU191 4.6 24.5 1.0

Nickel binding site 2 out of 4 in 9gp1

Go back to Nickel Binding Sites List in 9gp1
Nickel binding site 2 out of 4 in the Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni401

b:41.0
occ:1.00
 O B:HOH607 2.1 33.2 1.0
OE1 B:GLU191 2.2 33.0 1.0
O B:HOH513 2.3 31.4 1.0
NE2 B:HIS189 2.3 29.2 1.0
NE2 B:HIS277 2.3 21.2 1.0
O B:HOH635 2.4 27.4 1.0
CE1 B:HIS189 3.1 30.0 1.0
CD B:GLU191 3.2 29.2 1.0
CD2 B:HIS277 3.3 20.2 1.0
CD2 B:HIS189 3.3 29.1 1.0
CE1 B:HIS277 3.3 19.6 1.0
OE2 B:GLU191 3.4 26.7 1.0
O B:HOH648 4.2 43.0 1.0
ND1 B:HIS189 4.2 28.2 1.0
O B:HOH600 4.3 43.6 1.0
OG B:SER197 4.4 33.3 1.0
CG B:HIS189 4.4 28.0 1.0
CG B:HIS277 4.4 20.4 1.0
ND1 B:HIS277 4.5 19.2 1.0
CG B:GLU191 4.5 28.1 1.0
CB B:SER197 5.0 27.2 1.0

Nickel binding site 3 out of 4 in 9gp1

Go back to Nickel Binding Sites List in 9gp1
Nickel binding site 3 out of 4 in the Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni401

b:50.0
occ:1.00
 OE1 C:GLU191 2.2 49.4 1.0
NE2 C:HIS277 2.2 34.3 1.0
NE2 C:HIS189 2.3 36.8 1.0
O C:HOH571 2.3 32.4 1.0
O C:HOH600 2.3 42.5 1.0
O C:HOH588 2.6 33.8 1.0
CE1 C:HIS189 3.1 37.5 1.0
CD C:GLU191 3.2 42.8 1.0
CD2 C:HIS277 3.2 30.0 1.0
CE1 C:HIS277 3.3 33.3 1.0
CD2 C:HIS189 3.3 42.0 1.0
OE2 C:GLU191 3.5 41.9 1.0
ND1 C:HIS189 4.2 35.7 1.0
OG C:SER197 4.3 45.4 1.0
CG C:HIS277 4.4 32.6 1.0
ND1 C:HIS277 4.4 33.5 1.0
CG C:HIS189 4.4 37.9 1.0
CG C:GLU191 4.6 39.6 1.0
O C:HOH517 4.7 35.2 1.0
CB C:SER197 5.0 36.7 1.0
CG2 C:THR271 5.0 33.0 1.0

Nickel binding site 4 out of 4 in 9gp1

Go back to Nickel Binding Sites List in 9gp1
Nickel binding site 4 out of 4 in the Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Jumonji Domain-Containing Protein 2A with Crystallization Epitope Mutatios K330R:A334E within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni401

b:34.8
occ:1.00
 OE1 D:GLU191 2.2 28.1 1.0
NE2 D:HIS277 2.3 22.7 1.0
NE2 D:HIS189 2.3 23.9 1.0
O D:HOH666 2.3 26.8 1.0
O D:HOH675 2.6 32.0 1.0
CE1 D:HIS189 3.0 20.6 1.0
CD D:GLU191 3.1 22.6 1.0
CD2 D:HIS277 3.2 19.8 1.0
CE1 D:HIS277 3.2 21.1 1.0
CD2 D:HIS189 3.3 25.7 1.0
OE2 D:GLU191 3.3 26.3 1.0
ND1 D:HIS189 4.2 25.0 1.0
O D:HOH516 4.2 43.9 1.0
OG D:SER197 4.3 33.7 1.0
CG D:HIS189 4.3 23.7 1.0
CG D:HIS277 4.4 19.2 1.0
ND1 D:HIS277 4.4 19.5 1.0
CG D:GLU191 4.5 23.1 1.0
CB D:SER197 4.9 28.1 1.0
CG2 D:THR271 5.0 22.2 1.0

Reference:

M.Fairhead, C.Strain-Damerell, M.Ye, S.R.Mackinnon, D.Pinkas, E.M.Maclean, L.Koekemoer, D.Damerell, T.Krojer, W.Yue, N.Burgess-Brown, B.Marsden, F.Von Delft. A Fast, Parallel Method For Efficiently Exploring Crystallization Behaviour of Large Numbers of Protein Variants To Be Published.
Page generated: Thu Oct 31 23:12:05 2024

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