Atomistry » Nickel » PDB 9ant-9gp1 » 9gp1
Atomistry »
  Nickel »
    PDB 9ant-9gp1 »
      9gp1 »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy