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Zinc in PDB 2gp5: Crystal Structure of Catalytic Core Domain of JMJD2A Complexed with Alpha-Ketoglutarate

Protein crystallography data

The structure of Crystal Structure of Catalytic Core Domain of JMJD2A Complexed with Alpha-Ketoglutarate, PDB code: 2gp5 was solved by Z.Chen, J.Zang, J.Whetstine, X.Hong, F.Davrazou, T.G.Kutateladze, M.Simpson, S.Dai, J.Hagman, Y.Shi, G.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.67 / 2.28
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.107, 149.524, 57.028, 90.00, 90.00, 90.00
R / Rfree (%) 23.6 / 28.5

Other elements in 2gp5:

The structure of Crystal Structure of Catalytic Core Domain of JMJD2A Complexed with Alpha-Ketoglutarate also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Catalytic Core Domain of JMJD2A Complexed with Alpha-Ketoglutarate (pdb code 2gp5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Catalytic Core Domain of JMJD2A Complexed with Alpha-Ketoglutarate, PDB code: 2gp5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2gp5

Go back to Zinc Binding Sites List in 2gp5
Zinc binding site 1 out of 2 in the Crystal Structure of Catalytic Core Domain of JMJD2A Complexed with Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Catalytic Core Domain of JMJD2A Complexed with Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:40.7
occ:0.60
NE2 A:HIS240 2.3 45.6 1.0
SG A:CYS234 2.3 42.6 1.0
SG A:CYS306 2.4 59.4 1.0
SG A:CYS308 2.6 68.6 1.0
CB A:CYS306 3.0 56.3 1.0
CD2 A:HIS240 3.1 45.9 1.0
CB A:CYS234 3.2 44.9 1.0
CE1 A:HIS240 3.4 45.7 1.0
CA A:CYS306 3.8 47.9 1.0
N A:ARG309 3.9 82.0 1.0
N A:CYS308 4.0 81.0 1.0
CB A:CYS308 4.0 72.1 1.0
N A:SER307 4.0 61.1 1.0
CG A:ARG309 4.0 81.2 1.0
C A:CYS306 4.1 51.8 1.0
CG A:HIS240 4.3 45.7 1.0
CA A:CYS308 4.4 78.9 1.0
ND1 A:HIS240 4.4 46.0 1.0
CB A:ARG309 4.4 81.1 1.0
CD A:ARG309 4.5 81.4 1.0
CA A:CYS234 4.5 52.7 1.0
C A:SER307 4.7 74.7 1.0
C A:CYS308 4.7 80.2 1.0
O A:ALA236 4.7 49.0 1.0
CA A:ARG309 4.8 88.3 1.0
O A:CYS306 4.9 44.0 1.0
NE A:ARG309 4.9 81.1 1.0
CA A:SER307 4.9 72.1 1.0

Zinc binding site 2 out of 2 in 2gp5

Go back to Zinc Binding Sites List in 2gp5
Zinc binding site 2 out of 2 in the Crystal Structure of Catalytic Core Domain of JMJD2A Complexed with Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Catalytic Core Domain of JMJD2A Complexed with Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:39.4
occ:0.60
SG B:CYS306 2.3 62.8 1.0
SG B:CYS234 2.3 45.9 1.0
NE2 B:HIS240 2.4 42.6 1.0
SG B:CYS308 2.7 70.7 1.0
CB B:CYS306 2.8 61.9 1.0
CD2 B:HIS240 3.1 42.6 1.0
CB B:CYS234 3.3 53.9 1.0
CE1 B:HIS240 3.5 42.1 1.0
CA B:CYS306 3.6 63.1 1.0
N B:SER307 3.9 79.9 1.0
C B:CYS306 3.9 67.4 1.0
N B:ARG309 3.9 80.4 1.0
N B:CYS308 4.0 0.6 1.0
CG B:ARG309 4.1 78.7 1.0
CB B:CYS308 4.2 76.2 1.0
CG B:HIS240 4.4 42.1 1.0
CB B:ARG309 4.4 80.1 1.0
CA B:CYS308 4.5 0.6 1.0
CD B:ARG309 4.5 77.9 1.0
ND1 B:HIS240 4.5 42.4 1.0
O B:ALA236 4.5 50.6 1.0
CA B:CYS234 4.7 60.1 1.0
C B:SER307 4.7 87.7 1.0
O B:CYS306 4.7 65.3 1.0
C B:CYS308 4.7 0.9 1.0
CA B:ARG309 4.8 79.7 1.0
CA B:SER307 4.9 83.9 1.0
NE B:ARG309 5.0 77.5 1.0
N B:CYS306 5.0 53.8 1.0

Reference:

Z.Chen, J.Zang, J.Whetstine, X.Hong, F.Davrazou, T.G.Kutateladze, M.Simpson, Q.Mao, C.H.Pan, S.Dai, J.Hagman, K.Hansen, Y.Shi, G.Zhang. Structural Insights Into Histone Demethylation By JMJD2 Family Members Cell(Cambridge,Mass.) V. 125 691 2006.
ISSN: ISSN 0092-8674
PubMed: 16677698
DOI: 10.1016/J.CELL.2006.04.024
Page generated: Wed Dec 16 03:29:34 2020

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